Beginning Jan 1, 2004: ++++------+------+------+------+------+------+------+------+------+------+ From: Mike Garbett Subject: Cell Membrane Modelling Date: Sun, 04 Jan 2004 18:12:14 +0000 To: rasmol@lists.umass.edu This may be a little 'off topic' so I apologise in advance. I have been using Rasmol, Chime and Protein explorer with my A-level (pre-university) students for some time and have found the teaching resources produced by Eric and others of great value. Recently my current 'star student' came up with the idea of writing a programme which could be used to build 'on-screen' a functional (if rather simplistic) model of the cell membrane. The aim would be to see the effects of dropping intrinsic proteins with specific ion channels into the basic bilayer structure. The idea came out of our studies relating to the generation and propagation of nerve impulses via ion-pumping and facilitated diffusion. The project is probably beyond my rather limited programming skills but I would be interested to know if anyone has come across a similar resource. Mike Garbett Science College Director The Aldridge School Tynings Lane Aldridge WS9 0BG United Kingdom Tel. 01922 743988 extn. 277 e-mail: mike@mikegarbett.demon.co.uk ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed Content-disposition: inline ++++------+------+------+------+------+------+------+------+------+------+ From: Darrell Brooks Subject: Re: Cell Membrane Modelling Date: Mon, 05 Jan 2004 17:47:37 +0000 To: rasmol Hi Mike I was at conference over the summer 2003 (last year!) and there was a group from Middlebury College, VT, USA who had used a program called Lightwave. This is an old program that is used in the media industry to produce 3D virtual objects. This package was demonstrated by a short animation that the group had produced showing the sodium/potassium pump in cell membranes. The real advantage of this program however is that it is possible to import 3D files of molecules (PDB files) without having to build them de novo. The disadvantage is that is does not allow any interactivity. It will only produce sequences for animation. Nevertheless during discussion it became clear that it was possible to export the 'objects' to Shockwave and then QuickTime to produce interactivity that was otherwise missing. Don't know if this help regards Darrell Brooks >>> rasmol@mikegarbett.demon.co.uk 01/04/04 06:12pm >>> This may be a little 'off topic' so I apologise in advance. I have been using Rasmol, Chime and Protein explorer with my A-level (pre-university) students for some time and have found the teaching resources produced by Eric and others of great value. Recently my current 'star student' came up with the idea of writing a programme which could be used to build 'on-screen' a functional (if rather simplistic) model of the cell membrane. The aim would be to see the effects of dropping intrinsic proteins with specific ion channels into the basic bilayer structure. The idea came out of our studies relating to the generation and propagation of nerve impulses via ion-pumping and facilitated diffusion. The project is probably beyond my rather limited programming skills but I would be interested to know if anyone has come across a similar resource. Mike Garbett Science College Director The Aldridge School Tynings Lane Aldridge WS9 0BG United Kingdom Tel. 01922 743988 extn. 277 e-mail: mike@mikegarbett.demon.co.uk ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <9ej+drA+dF+$EwDx@mikegarbett.demon.co.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Dave Hurley Subject: Re: Cell Membrane Modelling Date: Mon, 05 Jan 2004 16:50:02 -0800 To: rasmol@lists.umass.edu How detailed do you want this representation to be? It wouldn't be hard, I think, to create a somewhat schematized interactive animation in Flash (for instance) that would demonstrate the effects of arbitrary numbers of channels and pumps on transmembrane potentials. Dave Hurley Senior Computer Specialist Department of Biology University of Washington On Jan 4, 2004, at 10:12 AM, Mike Garbett wrote: > > This may be a little 'off topic' so I apologise in advance. > > I have been using Rasmol, Chime and Protein explorer with my A-level > (pre-university) students for some time and have found the teaching > resources produced by Eric and others of great value. > Recently my current 'star student' came up with the idea of writing a > programme which could be used to build 'on-screen' a functional (if > rather simplistic) model of the cell membrane. > The aim would be to see the effects of dropping intrinsic proteins with > specific ion channels into the basic bilayer structure. The idea came > out of our studies relating to the generation and propagation of nerve > impulses via ion-pumping and facilitated diffusion. > The project is probably beyond my rather limited programming skills but > I would be interested to know if anyone has come across a similar > resource. > > Mike Garbett > Science College Director > The Aldridge School > Tynings Lane > Aldridge > WS9 0BG > United Kingdom > Tel. 01922 743988 extn. 277 > e-mail: mike@mikegarbett.demon.co.uk > > ---------------------------------------------------------------- > rasmol-+ > > To change your address, unsubscribe, view previous messages/history, > receive messages as weekly digests, or for any other information > about the RasMol EMail List, please go to > http://www.umass.edu/microbio/rasmol/raslist.htm > > ---------------------------------------------------------------- > rasmol-- > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: lpotapov@pceg2.weizmann.ac.il X-Authentication-warning: pceg2.weizmann.ac.il: lpotapov owned process doing -bs ++++------+------+------+------+------+------+------+------+------+------+ From: Vladimir Potapov Subject: Molscript and Molecular Surfaces Date: Wed, 07 Jan 2004 14:11:19 +0200 (IST) To: rasmol@lists.umass.edu Hello, I am preparing illustrations in Molscript. Additionally, I need to visualize molecular surfaces for a whole protein or just a small region. As far as I understand, Molscript cannot generate molecular surfaces and uses for this purpose external files. Could anyone share his/her experience on this subject? What is "the standart program" to generate surfaces? How to plug it into Molscript? Is it worth to deal with Molscript for such task? Regards, Vladimir Potapov ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Win98; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en References: ++++------+------+------+------+------+------+------+------+------+------+ From: Ilan Samish Subject: Re: Molscript and Molecular Surfaces Date: Wed, 07 Jan 2004 14:21:36 +0200 To: rasmol@lists.umass.edu Hi, The best software I know for this is DINO (combined with msms). For example: http://cobra.mih.unibas.ch/dino/gallery.php?cat=2 Best Regards, Ilan Vladimir Potapov wrote: >Hello, > >I am preparing illustrations in Molscript. Additionally, I need to >visualize molecular surfaces for a whole protein or just a small region. >As far as I understand, Molscript cannot generate molecular surfaces and >uses for this purpose external files. > >Could anyone share his/her experience on this subject? What is "the >standart program" to generate surfaces? How to plug it into Molscript? Is >it worth to deal with Molscript for such task? > >Regards, >Vladimir Potapov > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: MODEL...TER Date: Thu, 08 Jan 2004 16:48:53 +0000 (GMT) To: rasmol@lists.umass.edu Hi Multi model pdb files (such as 1htq) give rasmol problems as it tries to draw bonds between all atoms, making these files slow to load / manipulate. How do I select individual models in rasmol? Could rasmol be made to only connect atoms within models and not between? I know I should just read the manual, but how do I select individual nucleotides with rasmol? Cheers, Dan. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: <45889.193.60.81.207.1073580533.squirrel@www.mrc-dunn.cam.ac.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Re: MODEL...TER Date: Thu, 08 Jan 2004 20:28:51 +0100 (CET) To: rasmol@lists.umass.edu I don't have much direct experience as an actual rasmol user, but I'll take a crack at it ... > Multi model pdb files (such as 1htq) give rasmol problems as it tries to > draw bonds between all atoms, making these files slow to load / > manipulate. > > How do I select individual models in rasmol? In RasMol 2.6 you can say select model=2 or select *::2 // select :: The RasMol 2.7 doc says select model=2 or select */2 > Could rasmol be made to only connect atoms within models and not > between? Surely you are not seeing this behavior. If so then I would call it a bug. (If it is *not* a bug, then someone please explain :-) > I know I should just read the manual, but how do I select individual > nucleotides with rasmol? ummm ... not sure exactly what you mean by 'individual nucleotides' try select 1 or select a Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: MODEL...TER Date: Thu, 08 Jan 2004 14:59:41 -0500 To: rasmol@lists.umass.edu Miguel Howard already answered some of Dan's questions. At 1/8/04, you wrote: >Could rasmol be made to only connect atoms within models and not between? In all RasMol discussions it will be helpful to specify 2.6 or 2.7. Although bonds should not be drawn between models, there is a bug in RasMol 2.6 and Chime: SS bonds (only disulfide bonds) ARE drawn between models. If you have a lot of disulfides, this can be somewhat problematic. If you don't need multiple models, use Olderado to choose the most representative model (in Protein Explorer, when an NMR file is loaded, the External Resources / Mol Info menu lists a link to Olderado). http://neon.chem.le.ac.uk/olderado/ >I know I should just read the manual, but how do I select individual >nucleotides >with rasmol? The guide to selection is at http://www.umass.edu/microbio/rasmol/seleccmd.htm The "reference manual" really doesn't give you a good overview of how to select, which is why I wrote the above. Of course you can "and" model selection with other criteria, e.g. select model=1 and G and 32 and :A (Guanosine 32 in chain A in model 1) /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned References: <5.2.0.9.2.20040108145242.02422b10@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: MODEL...TER Date: Fri, 09 Jan 2004 10:15:44 +0000 (GMT) To: rasmol@lists.umass.edu Cc: emartz@microbio.umass.edu ++ Eric Martz-- > Miguel Howard already answered some of Dan's questions. Thanks to him for that! > At 1/8/04, you wrote: >>Could rasmol be made to only connect atoms within models and not between? > > In all RasMol discussions it will be helpful to specify 2.6 or 2.7. I am using Version 2.7.2.1 April 2001 > Although bonds should not be drawn between models, there is a bug in RasMol 2.6 > and Chime: SS bonds (only disulfide bonds) ARE drawn between models. If you have > a lot of disulfides, this can be somewhat problematic. I am seeing bonds everywhere! For example in the structure 1gtv... restrict 39-41a, 39-41b center selected However, I cant find MODEL lines in this structure (only TER). Which is probably why... RasMol> select *::0 3700 atoms selected! RasMol> select *::1 No atoms selected! Hence the whole problem. > If you don't need multiple models, use Olderado to choose the most representative > model (in Protein Explorer, when an NMR file is loaded, the External Resources / > Mol Info menu lists a link to Olderado). > http://neon.chem.le.ac.uk/olderado/ Olderado is very nice, but it is only (currently?) applicable to multi-model NMR structures, and does not keep records for multi-model X-Ray structures. In this class I find (the hard way)... 1gtv - 2 models (no MODEL lines, chain A/B) 1cm4 - 4 models (no MODEL lines, chain A+B/C+D/E+F/G+H) 1cwq - 2 models (no MODEL lines, chain A/B) 1e0p - 2 models (no MODEL lines, chain A/B) 1gu8 - 2 models (MODEL lines! - hey this one works fine!) Again I am too ignorant of the PDB format specification to know if these PDB files are correctly formatted. >>I know I should just read the manual, but how do I select individual nucleotides >>with rasmol? > > > The guide to selection is at > http://www.umass.edu/microbio/rasmol/seleccmd.htm Bookmarked! Cheers, Dan. > > /* - - - - - - - - - - - - - - - - - - - - - - - - - - - > Protein Explorer - 3D Visualization: http://proteinexplorer.org > Workshops: http://www.umass.edu/molvis/workshop > World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - > Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of > Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm > PDB Lite Macromolecule Finder: http://pdblite.org > Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > > Eric Martz, Professor Emeritus, Dept Microbiology > U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz > - - - - - - - - - - - - - - - - - - - - - - - - - - - */ > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: <5.2.0.9.2.20040108145242.02422b10@marlin.bio.umass.edu> <58243.193.60.81.207.1073643344.squirrel@www.mrc-dunn.cam.ac.uk> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Re: MODEL...TER Date: Fri, 09 Jan 2004 12:05:50 +0100 (CET) To: rasmol@lists.umass.edu > However, I cant find MODEL lines in this structure (only TER). > > Which is probably why... > 1gtv - 2 models (no MODEL lines, chain A/B) > 1cm4 - 4 models (no MODEL lines, chain A+B/C+D/E+F/G+H) > 1cwq - 2 models (no MODEL lines, chain A/B) > 1e0p - 2 models (no MODEL lines, chain A/B) > 1gu8 - 2 models (MODEL lines! - hey this one works fine!) > > Again I am too ignorant of the PDB format specification to know if these > PDB files are correctly formatted. Models should be started with MODEL and ended with ENDMDL I have seen evidence that TER records are completely ignored in RasMol 2.6/Chime. Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned References: <5.2.0.9.2.20040108145242.02422b10@marlin.bio.umass.edu> <58243.193.60.81.207.1073643344.squirrel@www.mrc-dunn.cam.ac.uk> <34865.212.128.142.25.1073646350.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Dan Bolser Subject: Re: MODEL...TER Date: Fri, 09 Jan 2004 11:03:02 +0000 (GMT) To: rasmol@lists.umass.edu Cc: mth@mth.com ++ Miguel Howard-- >> However, I cant find MODEL lines in this structure (only TER). >> >> Which is probably why... > > > Models should be started with MODEL and ended with ENDMDL > > I have seen evidence that TER records are completely ignored in RasMol 2.6/Chime. Sorry, now I know better... Overview The TER record indicates the end of a list of ATOM/HETATM records for a chain. Details * Every chain of ATOM/HETATM records presented on SEQRES records is terminated with a TER record. > > > Miguel > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- References: <0HRB000IM783KI@ponzi.oit.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Robert M. Horton, PhD" Subject: Re: Cell Membrane Modelling Date: Sun, 11 Jan 2004 14:31:49 -0800 To: rasmol@lists.umass.edu Cc: rasmol@mikegarbett.demon.co.uk > Recently my current 'star student' came up with the idea of writing a > programme which could be used to build 'on-screen' a functional (if > rather simplistic) model of the cell membrane. > The aim would be to see the effects of dropping intrinsic proteins with > specific ion channels into the basic bilayer structure. The idea came > out of our studies relating to the generation and propagation of nerve > impulses via ion-pumping and facilitated diffusion. You can do this sort of thing in VRML. It is not as nice for molecular viewing as a real molecule viewer, but it lets you put non-molecular things (like planes representing membrane surfaces) into the molecular "world". See: http://gaia.ecs.csus.edu/~cs296n/assignments/w9/1PRHmemb.html (Shout3D version, if you have Java) or http://gaia.ecs.csus.edu/~cs296n/assignments/w9/1PRHmemb.wrl (straight VRML; requires a VRML plugin that can view extrusions). This example uses a simple extrusion to trace the alpha carbons. You can get much nicer VRML models of your favorite protein from PDB, though they take a lot more hardware resources to view and examine. __ Robert M. Horton, Ph.D. 0 [] ~ ~ ~ http://www.cybertory.com ~ ~ ~ ~[] 0 |-/_| rmhorton@attotron.com |_\-| -\_|| He travels swiftest who telecommutes. ||_/- ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-return: allowed boundary="Boundary_(ID_98/07KW2781tE/Mo0tYFwA)" ++++------+------+------+------+------+------+------+------+------+------+ From: "Conrad, Steven" Subject: RE: Cell Membrane Modelling Date: Mon, 12 Jan 2004 10:16:32 -0600 To: "'rasmol@lists.umass.edu'" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. --Boundary_(ID_98/07KW2781tE/Mo0tYFwA) This type of interface (or something very similar) for cellular process modeling has been developed by a group at the University of Texas Health Science Center-Houston and Rice University. Contact Akhil Bidani, MD PhD in the Department of Medicine at UTHSC-H. -----Original Message----- Sent: Sunday, January 11, 2004 4:32 PM From: Robert M. Horton, PhD [mailto:rmhorton@attotron.com] Subject: Re: Cell Membrane Modelling To: rasmol@lists.umass.edu Cc: rasmol@mikegarbett.demon.co.uk > Recently my current 'star student' came up with the idea of writing a > programme which could be used to build 'on-screen' a functional (if > rather simplistic) model of the cell membrane. > The aim would be to see the effects of dropping intrinsic proteins > with specific ion channels into the basic bilayer structure. The idea > came out of our studies relating to the generation and propagation of > nerve impulses via ion-pumping and facilitated diffusion. You can do this sort of thing in VRML. It is not as nice for molecular viewing as a real molecule viewer, but it lets you put non-molecular things (like planes representing membrane surfaces) into the molecular "world". See: http://gaia.ecs.csus.edu/~cs296n/assignments/w9/1PRHmemb.html (Shout3D version, if you have Java) or http://gaia.ecs.csus.edu/~cs296n/assignments/w9/1PRHmemb.wrl (straight VRML; requires a VRML plugin that can view extrusions). This example uses a simple extrusion to trace the alpha carbons. You can get much nicer VRML models of your favorite protein from PDB, though they take a lot more hardware resources to view and examine. __ Robert M. Horton, Ph.D. 0 [] ~ ~ ~ http://www.cybertory.com ~ ~ ~ ~[] 0 |-/_| rmhorton@attotron.com |_\-| -\_|| He travels swiftest who telecommutes. ||_/- --Boundary_(ID_98/07KW2781tE/Mo0tYFwA) * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --Boundary_(ID_98/07KW2781tE/Mo0tYFwA)-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-MSMail-priority: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: "IKEHATA, Akihisa" Subject: I need your help Date: Wed, 14 Jan 2004 19:32:58 +0900 To: rasmol@lists.umass.edu Dear all I need your help. I installed the rasmol ver. 2.7.2.1. I opened the some pdb files, but unfortunately, the structures did not show up and the commandline said the file not found!. I previously installed other viewer and uninstallled it. The kind of file showed pdb. I do not know how to do that. Please help me! Akihisa from Yokohama, Japan. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: timothy driscoll Subject: fink rasmol (panther) Date: Fri, 16 Jan 2004 13:30:54 -0500 To: LIST rasmol hello, still trying to 'install' RasMol via fink. I have installed Apple's X11 and X11 SDK packages, based on XFree86-4.3. however, running fink install rasmol from a bash shell crunches along merrily for about an hour before failing with this message: Unpacking xfree86 (from .../xfree86_4.3.99.16-2_darwin-powerpc.deb) ... WARNING: if you compile X11 applications against this XFree86 release, you will *not* be able to run them if you decide to revert to Apple's X11 provided with Panther. You have an existing X11 installation in /usr/X11R6 and/or /etc/X11. This package refuses to overwrite these. Remove them, then tell Fink to install xfree86 again. (The package won't be recompiled.) If you want to keep your X11 installation, install system-xfree86 resp. system-xtools instead to make this known to Fink's package system. I don't want to remove my existing X11. so can anyone give me a hint - how do I install system-xfree86 resp. system-xtools, and then make it known to fink? thanks for any help, :tim -- timothy driscoll molvisions - molecular graphics & visualization usa:north carolina:wake forest ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: helgew@gollum.grajagan.net ++++------+------+------+------+------+------+------+------+------+------+ From: Helge Weissig Subject: Re: fink rasmol (panther) Date: Fri, 16 Jan 2004 11:21:54 -0800 (PST) To: LIST rasmol Hi Tim, you should be able to install them with 'fink install system-xfree86 system-xtools'. AFAIK, both are just flags to let fink know that X11 is installed already. hth, h. On Fri, 16 Jan 2004 at 13:30 -0500, owner-rasmol@lists.umass.edu wrote: td> hello, td> td> still trying to 'install' RasMol via fink. I have installed Apple's X11 and td> X11 SDK packages, based on XFree86-4.3. however, running td> td> fink install rasmol td> td> from a bash shell crunches along merrily for about an hour before failing td> with this message: td> td> td> Unpacking xfree86 (from .../xfree86_4.3.99.16-2_darwin-powerpc.deb) ... td> WARNING: if you compile X11 applications against this XFree86 release, td> you will *not* be able to run them if you decide to revert to Apple's td> X11 provided with Panther. td> td> You have an existing X11 installation in /usr/X11R6 and/or /etc/X11. td> This package refuses to overwrite these. Remove them, then tell Fink to td> install xfree86 again. (The package won't be recompiled.) If you want td> to keep your X11 installation, install system-xfree86 resp. system-xtools td> instead to make this known to Fink's package system. td> td> td> I don't want to remove my existing X11. so can anyone give me a hint - how td> do I install system-xfree86 resp. system-xtools, and then make it known to td> fink? td> td> td> thanks for any help, td> td> :tim td> td> ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Win98; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en ++++------+------+------+------+------+------+------+------+------+------+ From: Ilan Samish Subject: 3D SIG: 1st Structural Bioinformatics ISMB/ECCB Satellite meeting Date: Mon, 19 Jan 2004 08:08:25 +0200 To: rasmol@lists.umass.edu Dear Friends, We are happy to announce a 2-day Satellite Meeting called "3D SIG" that is dedicated exclusively to STRUCTURAL BIOINFORMATICS. 3D SIG will be held on 29-30 July 2004, at Glasgow, Scotland, UK., immediately preceding ISMB/ECCB 2004. The 3D SIG web site is http://3dsig.weizmann.ac.il/ 3D SIG will go on for 2 full days (don't plan anything for the evenings!) and will include a balanced mix of main talks, short presentations (selected from laptop-session submissions - see below) and panel discussions. TOPICS will include: =============== * 3D data-mining * 3D programming modules * Docking and protein-protein/ligand interaction prediction * Membrane protein assembly prediction * Secondary structure and domain assignment * Structure-based function prediction * Structural databases * Structural genomics * Structure prediction * Structure representation * The role of geometry and energetics in protein structure and function LAPTOP SESSION =============== A novel Laptop Session will take place following lunch each day where authors will be at their numbered stations with their laptops describing their work. The idea is to offer a semi-formal, yet intimate, channel during the meeting to facilitate the discussion of individual research. 3D SIG participants are encouraged to submit an abstract and representative figure/table that will be placed online. 20 short talks will be selected by the Scientific Committee for inclusion in the program based on the submitted abstracts. The number of Laptop Session stations is limited, so reserve a place in advance. For details see http://3dsig.weizmann.ac.il/laptop.html SCIENTIFIC COMMITTEE: ===================== John Moult (chair) - Center for Advanced Research in Biotech., U. Maryland, USA Phil Bourne - University of California San Diego, USA Luis Serrano - European Molecular Biology Laboratory, Heidelberg, Germany Michael Sternberg - Dept. Biological Sciences, Imperial College, London, UK Ron Unger - Faculty of Life Science, Bar-Ilan University, Israel David Gilbert (honorary) - Dept. Computing Science, U. Glasgow, Scotland, UK Janet Thornton (honorary) - European Bioinformatics Institute, Hingston, UK ORGANIZING COMMITTEE: ====================== Ilan Samish and Marvin Edelman - Weizmann Institute of Science, Rehovot, Israel John Moult - Center for Advanced Research in Biotech., U. Maryland, USA Looking forward to seeing you at 3D SIG, --------------------------------- 3D SIG Organizing Committee 3Dsig@weizmann.ac.il http://3dsig.weizmann.ac.il/ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-MSMail-priority: Normal X-Spam-Level: ++++------+------+------+------+------+------+------+------+------+------+ From: Raanan Subject: No compren marca NIKE - DO NOT BUY NIKE ANYMORE Date: Thu, 29 Jan 2004 12:43:36 +0200 To: Raanan Dunowicz This is a multi-part message in MIME format. --Boundary_(ID_4dR7YsRpvaPSrGxeWz5Ehw) > >Subject: Fw: No compren marca NIKE - DO NOT BUY NIKE ANYMORE Dear people I am sending this email to all the people I was once in contact, or I am still (Hope it wont change...). Sorry for the inconvenient. It is my first time I have decided to send an email to every one, since Enough is enough! Please forward it around the entire world! Raanan Dunowicz --Boundary_(ID_4dR7YsRpvaPSrGxeWz5Ehw) * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --Boundary_(ID_4dR7YsRpvaPSrGxeWz5Ehw)-- X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 boundary="Boundary_(ID_BrzDWXSWPp3/Z24C8cTknA)" X-MSMail-priority: High X-Spam-Level: ++++------+------+------+------+------+------+------+------+------+------+ From: Raanan Subject: Date: Thu, 29 Jan 2004 13:10:40 +0200 To: !000 This is a multi-part message in MIME format. --Boundary_(ID_BrzDWXSWPp3/Z24C8cTknA) =E8=F2=E5=FA =E8=E5=F2=E9=ED =E8=F2=E9=F0=E5, =EE=FA=E9=E7=E4 = =EE=E2=F2=E9=EC=E4.... http://info.org.il/irrelevant/item.php/107479305878947129 Soory it was a fake This is an answer from Nike Nike is committed to being a good corporate citizen including = understanding and appreciating the values of all communities. We would like you to know this e-mail is not related to the Nike = Corporation in any way. Nike's trademark Swoosh is among the most widely recognized = in the world and unfortunately is sometimes misappropriated for = unauthorized uses. We do our best to protect our trademark and prevent its = association with inappropriate subject matter, such as in this case, which = trivializes human suffering. To help us stop the spread of this e-mail, we ask that you refrain from forwarding it. We are currently investigating the source of this e-mail. Thank you for bringing this to our attention and we hope you continue to think of Nike as a name that represents quality. Sincerely, Kim Nike Raanan --Boundary_(ID_BrzDWXSWPp3/Z24C8cTknA) * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * ---REMAINDER OF MESSAGE TRUNCATED--- * * This post contains a forbidden message format * * (such as an attached file, a v-card, HTML formatting) * * This mailing list only accepts PLAIN TEXT messages * * If your postings display this message your mail program * * is not set to send PLAIN TEXT ONLY and needs adjusting * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * --Boundary_(ID_BrzDWXSWPp3/Z24C8cTknA)-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Oops, "pbd" registry typo not fixed in SP5 Date: Tue, 10 Feb 2004 18:18:39 -0500 To: bdickey@mdli.com, chime-team@mdli.com, johno@mdli.com Cc: rasmol@lists.umass.edu To: Bob Dickey at MDL & MDL Chime Team Dear Bob and Chime Team: I just noticed that unfortunately the typographical error in the Chime installer that puts "pbd" in the Windows registry instead of "pdb" did not get fixed in SP5. Please put it at the top of the list for SP6. I reported this bug to you in May, 2003. Search for chimeshim "pbd" [including double quotes] at to review the full details. The bug was introduced in SP4. This bug breaks the central Chime troubleshooting tool I have offered for years on my websites, clicking on http://www.umass.edu/microbio/chime/atp.pdb to display the ATP molecule in Internet Explorer! (It does not seem to affect Netscape 4.8.) As with the earlier bug in the installer, the only fix for this that I know is to edit the Windows registry -- not what someone having trouble getting Chime to work should be trying! Thanks, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Robert Dickey , chime-team@mdli.com, John Olson ++++------+------+------+------+------+------+------+------+------+------+ From: Robert Dickey Subject: RE: Oops, "pbd" registry typo not fixed in SP5 Date: Tue, 10 Feb 2004 15:45:57 -0800 To: "'Eric Martz'" , Cc: rasmol@lists.umass.edu Eric, I apologize for this oversight. I will make sure that this problem is corrected in the next Chime service pack. Regards, Bob Dickey -----Original Message----- Sent: Tuesday, February 10, 2004 3:19 PM From: Eric Martz [mailto:emartz@microbio.umass.edu] Subject: Oops, "pbd" registry typo not fixed in SP5 To: bdickey@mdli.com; chime-team@mdli.com; johno@mdli.com Cc: rasmol@lists.umass.edu To: Bob Dickey at MDL & MDL Chime Team Dear Bob and Chime Team: I just noticed that unfortunately the typographical error in the Chime installer that puts "pbd" in the Windows registry instead of "pdb" did not get fixed in SP5. Please put it at the top of the list for SP6. I reported this bug to you in May, 2003. Search for chimeshim "pbd" [including double quotes] at to review the full details. The bug was introduced in SP4. This bug breaks the central Chime troubleshooting tool I have offered for years on my websites, clicking on http://www.umass.edu/microbio/chime/atp.pdb to display the ATP molecule in Internet Explorer! (It does not seem to affect Netscape 4.8.) As with the earlier bug in the installer, the only fix for this that I know is to edit the Windows registry -- not what someone having trouble getting Chime to work should be trying! Thanks, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.5) Gecko/20031007 X-Accept-Language: en-us, en X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned ++++------+------+------+------+------+------+------+------+------+------+ From: Richard Harrington Subject: secondary structure for small pdb segments Date: Fri, 13 Feb 2004 17:34:50 +0000 To: rasmol list Dear all, I'm using Rasmol to select sections of a pdb file (portions of the surface of the pdb structure), and then save them as a smaller, surface pdb file. Most of the files are between 20-80 residues in length, and usually comprise 2 or more sequence fragments. As far as I understand, Rasmol uses some implementation of DSSP to determine the secondary structre of the pdb file it is showing. Thus, when I save the small surface file as a pdb, although it may include every atom that was selected in the original rasmol rendering of the pdb molecule (which is easy to check by eye by viewing in spacefill), it still doesn't allocate all the same secondary structure elements. This is presumably because the secondary structure elements in the original pdb are designated by a combination of the non-highlighted (non-selected) regions of the pdb aswell as the highlighted regions. Does anyone know if there is a way that I could explicitly get the secondary structure calculation from the original pdb file, say by using the rasmol 'structure' command, and then use this saved secondary structure by applying it to the small surface file? Many thanks for any help, Richie _______________________________________________ Richard Harrington, Men's Boat Club Captain, Homerton College. PhD student, ATP Synthase Group, MRC-Dunn Human Nutrition Unit, Cambridge University. e-mail: rah@mrc-dunn.cam.ac.uk telephone: +44 (0) 1223 252861 mobile: 07817 927175 _______________________________________________ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: secondary structure for small pdb segments Date: Fri, 13 Feb 2004 17:00:42 -0500 To: rasmol@lists.umass.edu At 2/13/04, Richard Harrington wrote: >Does anyone know if there is a way that I could explicitly get the >secondary structure calculation from the original pdb file, say by using >the rasmol 'structure' command, and then use this saved secondary >structure by applying it to the small surface file? Well, you can designate any residues you wish as helix, sheet, or turn, with HELIX, SHEET, and TURN records in the PDB file header. By default, RasMol & Chime use this information. Only if such records are missing, or if you enter the command "structure" is the internal algorithm run (superceding the header records, if any). -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: compatible *restrict* behavior Date: Sat, 14 Feb 2004 20:55:31 +0100 (CET) To: jmol-developers@lists.sourceforge.net, rasmol@lists.umass.edu This question refers to the 'restrict' scripting command. I have received several complaints that the Jmol implementation of 'restrict' is not correct. The RasMol doc says: This command is very similar to the RasMol 'select' command, except 'restrict' disables the 'wireframe', 'spacefill' and 'backbone' representations in the non-selected region. Q: Is it the case that 'restrict' applies to *all* graphic shapes ... cartoons, strands, etc? Q: Are there any special cases or anomolies that I should be aware of? Thanks, Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Roger Sayle Subject: Re: compatible *restrict* behavior Date: Sat, 14 Feb 2004 12:43:19 -0700 (MST) To: rasmol@lists.umass.edu Cc: jmol-developers@lists.sourceforge.net Hi Miguel, On Sat, 14 Feb 2004, Miguel Howard wrote: > Q: Is it the case that 'restrict' applies to *all* graphic shapes ... > cartoons, strands, etc? The intention is that RasMol's restrict command applies to all graphics representations. The documentation was written when there were only a handful of representations used by RasMol, and (of course) it was rarely updated as new representations were subsequently added. > Q: Are there any special cases or anomolies that I should be aware of? There may be exceptions in existing RasMol/Chime implementations; perhaps dot surfaces, Chime's solid surfaces, distance monitors, hydrogen bonds, disulphide bridges, atom labels, etc... However these should be considered bugs (perhaps quirks or features) of a particular RasMol script interpreter. Script writers shouldn't rely on "restrict none" leaving anything behind, and future versions may "fix" any anomalies that currently exist. If JMol supports more representations than RasMol and/or Chime, these should ideally also be turned off by the restrict command. In theory, "restrict none" should be a portable way for a RasMol/Chime/JMol script to reset the "display list" independent of any additional functionality that may be added in future. I hope this explains the intend or prescribed behaviour of "restrict" if not any particular implementation. Roger -- ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- ++++------+------+------+------+------+------+------+------+------+------+ From: Eric Martz Subject: Re: compatible *restrict* behavior Date: Sat, 14 Feb 2004 16:29:03 -0500 To: jmol-developers@lists.sourceforge.net, rasmol@lists.umass.edu I would love to see Jmol's "restrict" command turn off all renderings. The fact that neither RasMol nor Chime do this is problematic. Typically, when trying to hide everything ("restrict none"), one ends up with stray disulfide bonds, hydrogen bonds, or surfaces. I vote for "restrict" in Jmol to hide *all* renderings. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 http://www.umass.edu/molvis/martz - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: <40656.80.58.16.235.1076788531.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Re: compatible *restrict* behavior Date: Sun, 15 Feb 2004 00:02:17 +0100 (CET) To: rasmol@lists.umass.edu Cc: roger@eyesopen.com, jmol-developers@lists.sourceforge.net >> Q: Is it the case that 'restrict' applies to *all* graphic shapes ... >> cartoons, strands, etc? > > The intention is that RasMol's restrict command applies to all graphics > representations. The documentation was written when there were only a > handful of representations used by RasMol, and (of course) it was rarely > updated as new representations were subsequently added. Very good. Thanks! Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-pair-Authenticated: 209.197.6.81 References: <5.2.0.9.2.20040214162154.0213f918@marlin.bio.umass.edu> ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: compatible *restrict* behavior Date: Sat, 14 Feb 2004 23:15:49 -0500 To: rasmol@lists.umass.edu, jmol-developers@lists.sourceforge.net I am agreeable to cleaning up this problem to the extent it exists in RasMol 2.7. Please forward sample scripts for which "restrict none" leaves around artifacts and I'll fix as many as possible in the 2.7.3 test release that will be coming up shortly after the 2.7.2.1.1 release is finished. -- HJB At 4:29 PM -0500 2/14/04, Eric Martz wrote: >I would love to see Jmol's "restrict" command turn off all >renderings. The fact that neither RasMol nor Chime do this is >problematic. Typically, when trying to hide everything ("restrict >none"), one ends up with stray disulfide bonds, hydrogen bonds, or >surfaces. > >I vote for "restrict" in Jmol to hide *all* renderings. > > > >/* - - - - - - - - - - - - - - - - - - - - - - - - - - - >Protein Explorer - 3D Visualization: http://proteinexplorer.org >Workshops: http://www.umass.edu/molvis/workshop >World Index of Molecular Visualization Resources: http://molvisindex.org >ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il >Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm >PDB Lite Macromolecule Finder: http://pdblite.org >Molecular Visualization EMail List: > http://www.umass.edu/microbio/rasmol/raslist.htm > >Eric Martz, Professor Emeritus, Dept Microbiology >U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532 > http://www.umass.edu/molvis/martz >- - - - - - - - - - - - - - - - - - - - - - - - - - - */ > -- ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com References: <47243.80.58.16.235.1076895342.squirrel@www.howards.org> <4030A29D.60209@imb-jena.de> <33383.212.128.142.26.1076930485.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: [Jmol-users] Axis orientation - Step 2 Date: Mon, 16 Feb 2004 09:38:44 -0500 (EST) To: Miguel Howard Cc: jmol-users@lists.sourceforge.net, jr@imb-jena.de, rasmol@lists.umass.edu To help get us all on the same page, I have prepared a draft positioning test at: http://arcib.dowling.edu/~BernsteH/postest/ I will run rasmol for a variety of platforms (including sgi, mac and windows )through this test later today and see if we have gotten turned around on any of them. In any case it is the intention, as stated in the manual for y to be increasing going down and x to be increasing going to the right. Regards, Herbert ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Mon, 16 Feb 2004, Miguel Howard wrote: > >>So, RasMol/Chime is right-handed, but it has the +Y axis pointing > >> *down*. > >> > >> > > no, only the Windows version, > > I do not believe that it is only the Windows version. > RasMol 2.6b2 also has the +Y axis pointed down. > Since RasMol had it in this orientation, so does Chime. > > > on Irix RasMol2.7.2.1 shows up with true right-handed annotated axis > > system, but > > By 'true right-handed' I assume that you mean that +Y goes up. > > Someone else also told me that this changed in RasMol 2.7 > > At the present time I am not in a position where I can verify that with > RasMol 2.7. > > >>(Note that we are going to try to keep this relatively simple by not > >> yet introducing the issue of rotations about the axes) > >> > >> > > that is a problem, > > though rotation on x and z are as expected, y rotation is not on Irix > > (but it is in agreement with with the wrong axis annotation in RasWin) > > this should be corrected in RasMol and RasWin, too. > > We will discuss the rotation issues very soon. > > First I want to get everyone to understand the current status of Chime and > the various versions of RasMol regarding axis orientation. > > The rotation issue will be more difficult for people to understand and > will have a much larger impact on existing scripts. > > > >>What do people think we should do about it? > >> > >> 1. Maintain RasMol/Chime compatibility ... +Y points down > >> - RasMol/Chime users are used to seeing their molecules > >> in this orientation > >> - won't break existing scripts > >> - nobody really cares, just leave it alone > >> > >> > >> 2. Break RasMol/Chime compatibility ... +Y points up > >> - this is the way it should have been done in the > >> first place, we have an opportunity to fix it, > >> let's not propogate errors > >> - if someone *really* needs to see their molecules > >> in the RasMol/Chime orientation they can just do a > >> 'rotate x 180' > >> > >> > > I vote for 2 don't pollute the Jmol code with bugs. > > OK > > >> 3. Support both > >> - just add a switch/script command to Jmol > >> - it is easy to do ... Jmol already does both > >> - Q: What should the *default* orientation be? > >> - Q: What do you call this switch in a menu? > >> - Q: Any proposal for what the script command should be? > >> > > > Miguel > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- jr@imb-jena.de Importance: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Re: [Jmol-users] Axis orientation - Step 2 Date: Mon, 16 Feb 2004 16:35:13 +0100 (CET) To: rasmol@lists.umass.edu Cc: yaya@bernstein-plus-sons.com, jmol-users@lists.sourceforge.net, Herbert said: > To help get us all on the same page, I have prepared a draft > positioning test at: > > http://arcib.dowling.edu/~BernsteH/postest/ > > I will run rasmol for a variety of platforms (including sgi, mac and > windows )through this test later today and see if we have gotten > turned around on any of them. Thanks for posting this. It is helpful. There were several follow-up messages about this on jmol-users, and you may not have been copied on some critical ones. I believe that the general concensus is that the confusion is caused by a labelling error in RasWin (and possibly some older versions of RasMol). Jan says that RasWin puts the Y label at the *top* of the axis, which is actually the negative end. Nevertheless, the coordinate system *is* right-handed ... it was only a labelling issue. Jan also says that this problem does not exist in RasMol 2.7 > In any case it is the intention, > as stated in the manual for y to be increasing going down and x > to be increasing going to the right. This was actually the genesis of the discussion on jmol-users ... the fact that the +Y axis goes down. The axis orientation discussion was a prelude to the *real* discussion that we need to have about the rotations in RasMol. Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; de-AT; rv:1.6) Gecko/20040113 X-Accept-Language: de, en-us, en References: <47243.80.58.16.235.1076895342.squirrel@www.howards.org> <4030A29D.60209@imb-jena.de> <33383.212.128.142.26.1076930485.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Jan Reichert Subject: Re: [Jmol-users] Axis orientation - Step 2 Date: Mon, 16 Feb 2004 16:37:36 +0100 To: rasmol@lists.umass.edu Cc: jmol-users@lists.sourceforge.net Herbert J. Bernstein schrieb: >To help get us all on the same page, I have prepared a draft positioning >test at: > > http://arcib.dowling.edu/~BernsteH/postest/ > >I will run rasmol for a variety of platforms (including sgi, mac >and windows )through this test later today and see if we have gotten >turned around on any of them. In any case it is the intention, >as stated in the manual for y to be increasing going down and x >to be increasing going to the right. > > I would suggest to change the manual to get a right handed system timothy driscoll schrieb: >>Q: Given that there *are* existing applications and tutorials, what do you >>think we should do about this issue? >> >> >> >a right-handed orientation "seems" more natural to me, though I am >hard-pressed to explain why (I'm left-handed). > > > > >>Q: Do other molecular visualization applications have the +Y axis pointing >>upwards or downwards? >> >> >> >I can take a look... > > RasMol2.7 Irix (starts with rotate x 180) translation Y down, X right, Z to front (rotation after a rotate x 180 command! x+ y+ z- ) InsightII (starts as expected) translation: Y up, X right, Z to front (rotation x+, y+, z-) MolMol (as expected) Y up, X right, Z ? (rotation x+, y+, z+) MolScript (as expected) Y up, X right, Z ? according documentation, to the front (rotation x+, y+, z+) +rotation means right handed (as the fingers around the thumb pointing to positive values) I suggest, lets make it like MolMol and MolScript. Regards, Jan ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com References: <33609.212.128.142.26.1076945713.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: [Jmol-users] Axis orientation - Step 2 Date: Mon, 16 Feb 2004 10:47:04 -0500 (EST) To: rasmol@lists.umass.edu Cc: jmol-users@lists.sourceforge.net, jr@imb-jena.de RasMol 2.6 is not the current version, and it is not very productive to work from that as a base, nor does it make sense to drop back and fix problems in such an old version. The best current release is RasMol 2.7.2.1. I am working on a final clean up to 2.7.2 that will be released shortly as 2.7.2.1.1. Then I will incorporate the next round of improvements into 2.7.3. If there is a problem with axis labelling, I will be happy to fix it in 2.7.3, but first we need to know for sure what we want to do. I believe most users are used to the coordinate system in the manual in which the Y axis goes down and the X axis run to the right. Is there some disagreement about that? -- Herbert ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Mon, 16 Feb 2004, Miguel Howard wrote: > Herbert said: > > > To help get us all on the same page, I have prepared a draft > > positioning test at: > > > > http://arcib.dowling.edu/~BernsteH/postest/ > > > > I will run rasmol for a variety of platforms (including sgi, mac and > > windows )through this test later today and see if we have gotten > > turned around on any of them. > > Thanks for posting this. It is helpful. > > There were several follow-up messages about this on jmol-users, and you may > not have been copied on some critical ones. > > I believe that the general concensus is that the confusion is caused by > a labelling error in RasWin (and possibly some older versions of RasMol). > > Jan says that RasWin puts the Y label at the *top* of the axis, which > is actually the negative end. > > Nevertheless, the coordinate system *is* right-handed ... it was only a > labelling issue. > > Jan also says that this problem does not exist in RasMol 2.7 > > > > In any case it is the intention, > > as stated in the manual for y to be increasing going down and x > > to be increasing going to the right. > > This was actually the genesis of the discussion on jmol-users ... the fact > that the +Y axis goes down. > > The axis orientation discussion was a prelude to the *real* discussion > that we need to have about the rotations in RasMol. > > > Miguel > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- jr@imb-jena.de Importance: Normal References: <33609.212.128.142.26.1076945713.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Re: [Jmol-users] Axis orientation - Step 2 Date: Mon, 16 Feb 2004 17:45:32 +0100 (CET) To: rasmol@lists.umass.edu Cc: yaya@bernstein-plus-sons.com, jmol-users@lists.sourceforge.net, Herbert, > RasMol 2.6 is not the current version, and it is not very productive to > work from that as a base, In general I agree that people should use the current version of OpenRasMol. However, in my particular case I have two special reasons for running 2.6: 1. My primary motivation for working on Jmol is to build a Chime replacement. Since 2.6 was the basis for Chime, I think it makes sense for me to use it. 2. I have recently had the need to look at the source code in order to understand the rules for hydrogen bonding. Since the 2.6 source code is in the public domain, I can read the source code without infringing upon any licensing issues. I am not doing any real *work* with RasMol :-) > nor does it make sense to drop back > and fix problems in such an old version. I agree. > The best current release is > RasMol 2.7.2.1. I am working on a final clean up to 2.7.2 that will be > released shortly as 2.7.2.1.1. Then I will incorporate > the next round of improvements into 2.7.3. If there is a problem > with axis labelling, I will be happy to fix it in 2.7.3, but first we > need to know for sure what we want to do. Jan indicated that the labelling was *not* an issue in 2.7.? on Irix. He indicated that the Y axes labelling was a problem with RasWin. He did not say which version. (For my part, I don't understand the RasMol lineage/progeny well enough to know where RasWin fits in relative to RasMol 2.6 or 2.7 :-) > I believe most users are used > to the coordinate system in the manual in which the Y > axis goes down and the X axis run to the right. Is there some > disagreement about that? I will address this in a separate email. Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com References: <33609.212.128.142.26.1076945713.squirrel@www.howards.org> <33624.212.128.142.26.1076949932.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: [Jmol-users] Axis orientation - Step 2 Date: Mon, 16 Feb 2004 12:08:53 -0500 (EST) To: Miguel Howard Cc: rasmol@lists.umass.edu, jmol-users@lists.sourceforge.net, jr@imb-jena.de The only possible license conflict in using RasMol 2.7 as a base would be if you were planning to make a non-open-source derivative. Is jmol changing from being open source? If you are concerned about the different license wording used for RasMol, we will be able to move over to the GPL once we have excised the GIF code. Richard Stallman has agreed that the CIF code does not create a conflict. Your real problem arises if you download and use Chime. The MDL license forbids reverse engineering. Use of 2.6 as a base will just create yet another slightly different variant of RasMol and propogate some rather arcane bugs for a few more years. Regards, Herbert P.S. I have corrected a couple of typos on the postest page. As part of a right-handed system, the Z axis should run from the front to the back, not the back to the front. ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Mon, 16 Feb 2004, Miguel Howard wrote: > Herbert, > > > RasMol 2.6 is not the current version, and it is not very productive to > > work from that as a base, > > In general I agree that people should use the current version of OpenRasMol. > > However, in my particular case I have two special reasons for running 2.6: > 1. My primary motivation for working on Jmol is to build > a Chime replacement. Since 2.6 was the basis for Chime, > I think it makes sense for me to use it. > 2. I have recently had the need to look at the source code > in order to understand the rules for hydrogen bonding. > Since the 2.6 source code is in the public domain, I > can read the source code without infringing upon any > licensing issues. > > I am not doing any real *work* with RasMol :-) > > > > nor does it make sense to drop back > > and fix problems in such an old version. > > I agree. > > > The best current release is > > RasMol 2.7.2.1. I am working on a final clean up to 2.7.2 that will be > > released shortly as 2.7.2.1.1. Then I will incorporate > > the next round of improvements into 2.7.3. If there is a problem > > with axis labelling, I will be happy to fix it in 2.7.3, but first we > > need to know for sure what we want to do. > > Jan indicated that the labelling was *not* an issue in 2.7.? on Irix. > > He indicated that the Y axes labelling was a problem with RasWin. He did > not say which version. > > (For my part, I don't understand the RasMol lineage/progeny well enough to > know where RasWin fits in relative to RasMol 2.6 or 2.7 :-) > > > > I believe most users are used > > to the coordinate system in the manual in which the Y > > axis goes down and the X axis run to the right. Is there some > > disagreement about that? > > I will address this in a separate email. > > > > Miguel > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com References: <33609.212.128.142.26.1076945713.squirrel@www.howards.org> <33624.212.128.142.26.1076949932.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: [Jmol-users] Axis orientation - Step 2 Date: Mon, 16 Feb 2004 12:13:39 -0500 (EST) To: rasmol@lists.umass.edu Cc: jmol-users@lists.sourceforge.net, jr@imb-jena.de RasWin is just the name of the Winodws executable of RasMol. Most of the code for the Windows, Mac and X-Windows versions of RasMol is identical. So there is a RasWin for each version of RasMol. ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Mon, 16 Feb 2004, Miguel Howard wrote: > > (For my part, I don't understand the RasMol lineage/progeny well enough to > know where RasWin fits in relative to RasMol 2.6 or 2.7 :-) > > Miguel > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: <33609.212.128.142.26.1076945713.squirrel@www.howards.org> <33624.212.128.142.26.1076949932.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Re: [Jmol-users] Axis orientation - Step 2 Date: Mon, 16 Feb 2004 18:49:32 +0100 (CET) To: yaya@bernstein-plus-sons.com Cc: rasmol@lists.umass.edu, jmol-users@lists.sourceforge.net, jr@imb-jena.de Herbert said: > The only possible license conflict in using RasMol 2.7 as a base would > be if you were planning to make a non-open-source derivative. Is jmol > changing from being open source? We've had this discussion before ... There are no plans to change Jmol from being open source. > If you are concerned about the > different license wording used for RasMol, we will be able to move over > to the GPL once we have excised the GIF code. Richard Stallman has > agreed that the CIF code does not create a conflict. Per our email exchanges last year, I am not comfortable using the 2.7 code until it is available under a GPL license. This is especially the case because of the history of the RasMol licensing terms. And because you indicated that the GIF code was a particular problem with the GPL terms. I believe that you previously indicated that you were hoping that your students could get most of the work done during the Fall of 2003. Once OpenRasMol is available under GPL I will be eager to use it. > Your real problem arises if you download and use Chime. The MDL > license forbids reverse engineering. Thank you. I am aware of the MDL licensing terms. > Use of 2.6 as a base will just create yet another slightly different > variant of RasMol and propogate some rather arcane bugs for a few > more years. I appreciate your concern. I am comfortable that I am using 2.6 as a reference, not as a base. Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- jr@imb-jena.de Importance: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: +Y axis orientation Date: Mon, 16 Feb 2004 19:13:11 +0100 (CET) To: rasmol@lists.umass.edu Cc: yaya@bernstein-plus-sons.com, jmol-users@lists.sourceforge.net, Herbert said: > I believe most users are used > to the coordinate system in the manual in which the Y > axis goes down and the X axis run to the right. Is there some > disagreement about that? I wouldn't say that there is *disagreement* ... but I would say that the fact that the +Y axis points down was an unfortunate choice. We have been discussing this on the jmol-users mailing list as a smaller group prior to bringing it to the broader rasmol list. I believe that an outsider or newcomer taking a look at this would naturally assume that the +Y axis points up: - effectively all 2D graphs have +Y pointing upwards - 3D graphs in math textbooks have the +Y axis pointing upwards and the +Z axis coming out of the page - OpenGL has the +Y axis pointing up - VRML has the +Y axis pointing up It is true that most computer windowing systems have the increasing Y axis going down the page. But in my opinion we should insulate the end-users from this technical artifact. Our discussion has been whether Jmol should: 1. maintain RasMol/Chime compatibility and keep +Y going down 2. drop compatibility and make +Y point up 3. offer a backward-compatibility switch/setting in order to support both axis orientations. In general, those who have voiced opinions on jmol-users have advocated options 2 or 3. I was more comfortable having the initial discussion on jmol-users with a smaller group of people. But, we got 'sidetracked' because of confusion caused by erroneous Y axis labelling in some version of RasWin ... Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com References: <47243.80.58.16.235.1076895342.squirrel@www.howards.org> <4030A29D.60209@imb-jena.de> <33383.212.128.142.26.1076930485.squirrel@www.howards.org> <4030E3C0.3090309@imb-jena.de> ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: [Jmol-users] Axis orientation - Step 2 Date: Mon, 16 Feb 2004 13:30:34 -0500 (EST) To: rasmol@lists.umass.edu Cc: jmol-users@lists.sourceforge.net > RasMol2.7 Irix (starts with rotate x 180) translation Y down, X right, > Z to front (rotation after a rotate x 180 command! x+ y+ z- ) I have just done a clean recompile and install of the SGI version of release 2.7.2.1.1. I get a right-handled system with Z running into the screen, Y running down the screen and X running from left to right. Is there a Z-inversion happening somewhere to produce the left-handed "RasMol2.7 Irix" display? -- Herbert ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Mon, 16 Feb 2004, Jan Reichert wrote: > Herbert J. Bernstein schrieb: > > >To help get us all on the same page, I have prepared a draft positioning > >test at: > > > > http://arcib.dowling.edu/~BernsteH/postest/ > > > >I will run rasmol for a variety of platforms (including sgi, mac > >and windows )through this test later today and see if we have gotten > >turned around on any of them. In any case it is the intention, > >as stated in the manual for y to be increasing going down and x > >to be increasing going to the right. > > > > > I would suggest to change the manual to get a right handed system > > timothy driscoll schrieb: > > >>Q: Given that there *are* existing applications and tutorials, what do you > >>think we should do about this issue? > >> > >> > >> > >a right-handed orientation "seems" more natural to me, though I am > >hard-pressed to explain why (I'm left-handed). > > > > > > > > > >>Q: Do other molecular visualization applications have the +Y axis pointing > >>upwards or downwards? > >> > >> > >> > >I can take a look... > > > > > RasMol2.7 Irix (starts with rotate x 180) translation Y down, X right, > Z to front (rotation after a rotate x 180 command! x+ y+ z- ) > InsightII (starts as expected) translation: Y up, X right, Z to front > (rotation x+, y+, z-) > MolMol (as expected) Y up, X right, Z ? (rotation x+, y+, z+) > MolScript (as expected) Y up, X right, Z ? according documentation, to > the front (rotation x+, y+, z+) > > +rotation means right handed (as the fingers around the thumb pointing > to positive values) > > I suggest, lets make it like MolMol and MolScript. > Regards, Jan > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Re: [Jmol-users] Axis orientation - Step 2 Date: Mon, 16 Feb 2004 20:13:50 +0100 (CET) To: yaya@bernstein-plus-sons.com Cc: rasmol@lists.umass.edu > I have just done a clean recompile and install of the SGI version of > release 2.7.2.1.1. I get a right-handled system with Z running into > the screen, Y running down the screen and X running from left to > right. > > Is there a Z-inversion happening somewhere to produce the left-handed > "RasMol2.7 Irix" display? Herbert, I did not interpret Jan's message as saying that he saw a left-handed RasMol 2.7 Irix display. On the contrary, Jan was quite clear that the system was always right-handed, and that this RasWin issue was just a labelling problem. He did not say which version of RasWin. What may have caused some of the confusion is that I believe that that Jan is advocating a change to make the default +Y axis orientation point upwards. Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com References: <60349.80.58.16.235.1076958830.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: [Jmol-users] Axis orientation - Step 2 Date: Mon, 16 Feb 2004 14:32:22 -0500 (EST) To: rasmol@lists.umass.edu > RasMol2.7 Irix (starts with rotate x 180) translation Y down, X right, > Z to front (rotation after a rotate x 180 command! x+ y+ z- ) is a left-handed system. You have to put Z into the screen (to the back) to get a right-handed system. That is what RasMol produces. All you need to do if you like to have Y up and Z out is the rotate around X by 180, which can be done trivially at startup. ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Mon, 16 Feb 2004, Miguel Howard wrote: > > I have just done a clean recompile and install of the SGI version of > > release 2.7.2.1.1. I get a right-handled system with Z running into > > the screen, Y running down the screen and X running from left to > > right. > > > > Is there a Z-inversion happening somewhere to produce the left-handed > > "RasMol2.7 Irix" display? > > Herbert, > > I did not interpret Jan's message as saying that he saw a left-handed > RasMol 2.7 Irix display. > > On the contrary, Jan was quite clear that the system was always > right-handed, and that this RasWin issue was just a labelling problem. He > did not say which version of RasWin. > > What may have caused some of the confusion is that I believe that that Jan > is advocating a change to make the default +Y axis > orientation point upwards. > > > Miguel > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.5) Gecko/20031007 X-Accept-Language: de,en References: <47243.80.58.16.235.1076895342.squirrel@www.howards.org> <4030A29D.60209@imb-jena.de> <33383.212.128.142.26.1076930485.squirrel@www.howards.org> <4030E3C0.3090309@imb-jena.de> ++++------+------+------+------+------+------+------+------+------+------+ From: Jan Reichert Subject: Re: [Jmol-users] Axis orientation - Step 2 Date: Mon, 16 Feb 2004 20:37:10 +0100 To: rasmol@lists.umass.edu Herbert J. Bernstein wrote: >>RasMol2.7 Irix (starts with rotate x 180) translation Y down, X right, >>Z to front (rotation after a rotate x 180 command! x+ y+ z- ) >> >> Y down, X right, Z to front is right handed, but the rotation around the Z-axis is not. > >I have just done a clean recompile and install of the SGI version of >release 2.7.2.1.1. I get a right-handled system with Z running into >the screen, Y running down the screen and X running from left to right. > > yes, this is the start orientation in RasMol2.7.2.1, too ("rotate x 180" different from the orientation I expect a PDB file to show up in a molecular graphics program) look at published images from molecules, e.g. in the discussion of the poplar plastocyanin 1plc they call the flat surface with [His]87 near the copper the northern surface, but in RasMol2.7 it is "rotate x 180" and the acidic patch around [TYR]83 is shown on nearly every published plastocyanin image on the right side. So a RasMol user starts up with an unexpected view, when he has read a paper and starts RasMol to compare. I agree with Miguel, that it is better to change the RasMol documentation and start with Y up and X right Z out of the plain because the authors of the PDB files often deposited them with this orientation in mind. >Is there a Z-inversion happening somewhere to produce the left-handed >"RasMol2.7 Irix" display? > > no, not on Irix, only in RasWin2.7.2.1 the label of the Y axis is on the opposite side, which looks like left-handed, but translation indicates the right right-handed internal orientation. Regards, Jan >-- Herbert >===================================================== > Herbert J. Bernstein, Professor of Computer Science > Dowling College, Kramer Science Center, KSC 121 > Idle Hour Blvd, Oakdale, NY, 11769 > > +1-631-244-3035 > yaya@dowling.edu >===================================================== > >On Mon, 16 Feb 2004, Jan Reichert wrote: > > > >>Herbert J. Bernstein schrieb: >> >> >> >>>To help get us all on the same page, I have prepared a draft positioning >>>test at: >>> >>> http://arcib.dowling.edu/~BernsteH/postest/ >>> >>>I will run rasmol for a variety of platforms (including sgi, mac >>>and windows )through this test later today and see if we have gotten >>>turned around on any of them. In any case it is the intention, >>>as stated in the manual for y to be increasing going down and x >>>to be increasing going to the right. >>> >>> >>> >>> >>I would suggest to change the manual to get a right handed system >> >>timothy driscoll schrieb: >> >> >> >>>>Q: Given that there *are* existing applications and tutorials, what do you >>>>think we should do about this issue? >>>> >>>> >>>> >>>> >>>> >>>a right-handed orientation "seems" more natural to me, though I am >>>hard-pressed to explain why (I'm left-handed). >>> >>> >>> >>> >>> >>> >>>>Q: Do other molecular visualization applications have the +Y axis pointing >>>>upwards or downwards? >>>> >>>> >>>> >>>> >>>> >>>I can take a look... >>> >>> >>> >>> >>RasMol2.7 Irix (starts with rotate x 180) translation Y down, X right, >>Z to front (rotation after a rotate x 180 command! x+ y+ z- ) >>InsightII (starts as expected) translation: Y up, X right, Z to front >> (rotation x+, y+, z-) >>MolMol (as expected) Y up, X right, Z ? (rotation x+, y+, z+) >>MolScript (as expected) Y up, X right, Z ? according documentation, to >>the front (rotation x+, y+, z+) >> >>+rotation means right handed (as the fingers around the thumb pointing >>to positive values) >> >>I suggest, lets make it like MolMol and MolScript. >>Regards, Jan >> >> >> >> >> >-----------------------------------------------------ra > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com References: <47243.80.58.16.235.1076895342.squirrel@www.howards.org> <4030A29D.60209@imb-jena.de> <33383.212.128.142.26.1076930485.squirrel@www.howards.org> <4030E3C0.3090309@imb-jena.de> <40311BE6.7040206@imb-jena.de> ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: [Jmol-users] Axis orientation - Step 2 Date: Mon, 16 Feb 2004 15:28:32 -0500 (EST) To: rasmol@lists.umass.edu The initial orientation, Y down, X right, Z into the screen (not Z to the front) is right-handed, so the rotation around the Z-axis is right-handed as well. Unless someone has an example of an image coming up differently on some platform using RasMol 2.7, I don't think we should change the current default code. However, if there is a significant demand, I will be happy to include a command-line option to specify a initial screen orientation. I would appreciate suggestion on the way to interact with, say, the reset command to provide the best interaction with existing scripts. With so many users already working with the current initial orientation (X to the right, Y down, Z into the screen) it would be unwise to make a different orientation the default. -- HJB ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Mon, 16 Feb 2004, Jan Reichert wrote: > Herbert J. Bernstein wrote: > > >>RasMol2.7 Irix (starts with rotate x 180) translation Y down, X right, > >>Z to front (rotation after a rotate x 180 command! x+ y+ z- ) > >> > >> > Y down, X right, Z to front is right handed, but the rotation around the > Z-axis is not. > > > > >I have just done a clean recompile and install of the SGI version of > >release 2.7.2.1.1. I get a right-handled system with Z running into > >the screen, Y running down the screen and X running from left to right. > > > > > yes, this is the start orientation in RasMol2.7.2.1, too ("rotate x 180" > different from the orientation I expect a PDB file to show up in a > molecular graphics program) > look at published images from molecules, e.g. in the discussion of the > poplar plastocyanin 1plc they call the flat surface with [His]87 near > the copper the northern surface, but in RasMol2.7 it is "rotate x 180" > and the acidic patch around [TYR]83 is shown on nearly every published > plastocyanin image on the right side. So a RasMol user starts up with an > unexpected view, when he has read a paper and starts RasMol to compare. > I agree with Miguel, that it is better to change the RasMol > documentation and start with Y up and X right Z out of the plain because > the authors of the PDB files often deposited them with this orientation > in mind. > > >Is there a Z-inversion happening somewhere to produce the left-handed > >"RasMol2.7 Irix" display? > > > > > no, not on Irix, only in RasWin2.7.2.1 the label of the Y axis is on the > opposite side, which looks like left-handed, but translation indicates > the right right-handed internal orientation. > Regards, Jan > > >-- Herbert > >===================================================== > > Herbert J. Bernstein, Professor of Computer Science > > Dowling College, Kramer Science Center, KSC 121 > > Idle Hour Blvd, Oakdale, NY, 11769 > > > > +1-631-244-3035 > > yaya@dowling.edu > >===================================================== > > > >On Mon, 16 Feb 2004, Jan Reichert wrote: > > > > > > > >>Herbert J. Bernstein schrieb: > >> > >> > >> > >>>To help get us all on the same page, I have prepared a draft positioning > >>>test at: > >>> > >>> http://arcib.dowling.edu/~BernsteH/postest/ > >>> > >>>I will run rasmol for a variety of platforms (including sgi, mac > >>>and windows )through this test later today and see if we have gotten > >>>turned around on any of them. In any case it is the intention, > >>>as stated in the manual for y to be increasing going down and x > >>>to be increasing going to the right. > >>> > >>> > >>> > >>> > >>I would suggest to change the manual to get a right handed system > >> > >>timothy driscoll schrieb: > >> > >> > >> > >>>>Q: Given that there *are* existing applications and tutorials, what do you > >>>>think we should do about this issue? > >>>> > >>>> > >>>> > >>>> > >>>> > >>>a right-handed orientation "seems" more natural to me, though I am > >>>hard-pressed to explain why (I'm left-handed). > >>> > >>> > >>> > >>> > >>> > >>> > >>>>Q: Do other molecular visualization applications have the +Y axis pointing > >>>>upwards or downwards? > >>>> > >>>> > >>>> > >>>> > >>>> > >>>I can take a look... > >>> > >>> > >>> > >>> > >>RasMol2.7 Irix (starts with rotate x 180) translation Y down, X right, > >>Z to front (rotation after a rotate x 180 command! x+ y+ z- ) > >>InsightII (starts as expected) translation: Y up, X right, Z to front > >> (rotation x+, y+, z-) > >>MolMol (as expected) Y up, X right, Z ? (rotation x+, y+, z+) > >>MolScript (as expected) Y up, X right, Z ? according documentation, to > >>the front (rotation x+, y+, z+) > >> > >>+rotation means right handed (as the fingers around the thumb pointing > >>to positive values) > >> > >>I suggest, lets make it like MolMol and MolScript. > >>Regards, Jan > >> > >> > >> > >> > >> > >-----------------------------------------------------ra > > > > > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal References: <47243.80.58.16.235.1076895342.squirrel@www.howards.org> <4030A29D.60209@imb-jena.de> <33383.212.128.142.26.1076930485.squirrel@www.howards.org> <4030E3C0.3090309@imb-jena.de> <40311BE6.7040206@imb-jena.de> ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: Re: [Jmol-users] Axis orientation - Step 2 Date: Mon, 16 Feb 2004 21:34:42 +0100 (CET) To: rasmol@lists.umass.edu >>>RasMol2.7 Irix (starts with rotate x 180) translation Y down, X >>> right, Z to front (rotation after a rotate x 180 command! x+ y+ z- >>> ) >>> >>> > Y down, X right, Z to front is right handed, Jan, what you have just described is a left-handed system. thumb -> +X index -> +Y middle -> +Z > but the rotation around the Z-axis is not. I believe that the rotations in RasMol are not consistently right-handed. > I agree with Miguel, that it is better to change the RasMol > documentation and Just to clarify ... I have not advocated making *any* changes to RasMol documention or RasMol. It would not be my place to do so. I *did* ask the question in the context of *Jmol* because: - the default orientation of +Y going down seems unnatural to me - the rotations are not consistently right-handed So, in the context of Jmol, I have raised the question of whether it is appropriate to propogate these characteristics. And, if we want to make changes, whether or not we should have a switch to maintain backward-compatibility. >>Is there a Z-inversion happening somewhere to produce the left-handed >> "RasMol2.7 Irix" display? >> >> > no, not on Irix, only in RasWin2.7.2.1 the label of the Y axis is on the > opposite side, which looks like left-handed, but translation indicates > the right right-handed internal orientation. Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Importance: Normal ++++------+------+------+------+------+------+------+------+------+------+ From: Miguel Howard Subject: RasMol rotations about axes Date: Tue, 17 Feb 2004 01:37:23 +0100 (CET) To: jmol-users@lists.sourceforge.net, rasmol@lists.umass.edu Summary ======= I may be wrong on this, so I need people to check my work ... It looks to me like the RasMol rotations about axes are not consistently right-handed. We need to discuss this and try to figure out what to do about it ... if anything ... whether or not it is something we need to *fix* in Jmol. The bad news is that changing the rotation behavior would break every script that uses the 'rotate y ' command or the Chime 'move' command. The good news is that the repair is quite easy. Should Jmol be 100% RasMol/Chime compatible? Should Jmol only support a fully right-handed system? Can't we have both? Detail ====== I think we have the general understanding that the axis orientation in RasMol is right-handed. With the default orientation of having - +X to the right - +Y going down - +Z into the screen The general feeling from the jmol-users seems to be that we should offer the option of having +Y go up and +Z come out of the screen. Many think that this is a more natural orientation that is adopted by math textbooks, OpenGL, VRML, etc. Now, we need to talk about the rotations. As I understand it, a right-handed rotation should be counter-clockwise when the viewer is positioned on the + axis and is looking towards the origin. To visualize it with your hand ... - with your right hand - extend your thumb - curl your fingers - point your thumb at your nose - you are looking at the origin from the + end of the axis - your fingers are pointing in the direction of the rotation I believe that this is consistent with Anthony Stone's previous email to jmol-users. Let's look at the axis rotations in RasMol ... load someMolecule set axes on rotate x 10 You then need to take the mouse and wiggle it a little. I observe that the +Z axis (which is in the back) comes up. Point your thumb to the right with your fingers curled. The fingers are curling up from the back. This means that RasMol did a right-handed rotation around the X axis. Good. Let's skip to the Z axis reset rotate z 10 I observe that the +X drops on the right. The +Z axis goes into the screen. Point your right thumb into the screen. Your fingers are curling down on the right. RasMol is doing a right-hand rotation around the Z axis. Good. Finally, let's look at the Y axis reset rotate y 10 I observe that the +Z axis at the back moves to the left. The +Y axis points down, so point your right thumb down. Fingers are curling around back to the *right* ... but +Z moved to the *left*. Huh? Try it with your left hand. Thumb down, fingers curl to the left, +Z moved to the left ... it sure looks like to me that RasMol is doing a left-hand rotation around the Y axis. I have looked at this several dozen times over the past 6 months. At first I wasn't confident of my observations, but now I have convinced myself. But I may be wrong ... I certainly have struggled with this 'handedness' stuff :-) Q: Please post some independent confirmations telling me that you concur ... or explaining my error :-) Q: I have not tried this in Chime ... can someone check it out and confirm that it behaves the same way? Q: Can someone also confirm that the chime 'move' command about the y axis is also left-handed? Unfortunately, this has pretty big implications for someone who has a large investment in existing scripts (Eric?). It means that all moves and rotates around the Y axis need to be negated. At least it isn't difficult. My goal for Jmol has been to get as close as possible to 100% RasMol/Chime script compatibility, to ease the migration path for people who have existing scripts. But this might be a pretty big change for people who have an investment in tutorials/courseware. As I see it, the options are pretty similar to the Axis Orientation question: 1. Jmol should only support RasMol/Chime rotations - people have made an investment in existing RasMol/Chime scripts - it works fine, leave it alone - people are used to seeing it behave this way - it doesn't really matter, no one has looked at it for years so nobody really cares 2. Jmol should be completely right-handed - the system should be consistently right-handed - the fact that y rotates backwards is a design flaw that should be corrected, not propogated - people have been confused by this for years - noone is going to use existing scripts anyway - OR, those who have scripts can easily change them - OR, just write a script converter that will fix existing scripts ... just negate the parameter to 'rotate y ' and 'move x z ...' commands 3. Jmol should offer both - it is easy to support both Q: What should the default orientation be in Jmol? Q: What should the script command be to change the setting? Q: Is this *exactly* the same switch that controls the Y axis orientation? I am interested in your thoughts and feedback. Thanks, Miguel ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- Content-disposition: inline User-Agent: Mutt/1.5.1i References: <50647.80.58.16.235.1076978243.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Wayne M Barnes Subject: Re: RasMol rotations about axes Date: Mon, 16 Feb 2004 19:14:12 -0600 To: rasmol@lists.umass.edu Thank you Miguel; that was fun. On my Rasmol 2.6, the command set axes on puts X and Z at their positive ends, but Y at the top, which you say is negative. [Why does the Y axis point down, anyway. If it pointed up, the rotations would be fine.] If you want Y to point down, this axis label Y should be down there, too. - Wayne On Tue, Feb 17, 2004 at 01:37:23AM +0100, Miguel Howard wrote: > Summary > ======= > I may be wrong on this, so I need people to check my work ... > > It looks to me like the RasMol rotations about axes are not consistently > right-handed. [message cut here] -- Wayne M. Barnes, Ph.D. wayne@barnes1.wustl.edu Biochemistry Dept. 8231 fax: 314.754.9556 Washington Univ. Medical School ph: 314.362.3351 660 South Euclid Ave., St. Louis, MO 63110 http://barnes1.wustl.edu Just plain Taq is old tech anymore. ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- X-X-Sender: yaya@epsilon.pair.com References: <50647.80.58.16.235.1076978243.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: "Herbert J. Bernstein" Subject: Re: RasMol rotations about axes Date: Mon, 16 Feb 2004 20:15:41 -0500 (EST) To: rasmol@lists.umass.edu Cc: jmol-users@lists.sourceforge.net Dear Miguel, I think you are right. Once again, the best fix would be a command line switch. Changing the default would break lots of scripts. Clearly Jmol is an independent program and its developers can do whatever they think best, but with over a million existing rasmol users worldwide, providing them with a program that works in a similar fashion when they are using a browser might be a good idea. Regards, Herbert ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Tue, 17 Feb 2004, Miguel Howard wrote: > Summary > ======= > I may be wrong on this, so I need people to check my work ... > > It looks to me like the RasMol rotations about axes are not consistently > right-handed. > > We need to discuss this and try to figure out what to do about it ... if > anything ... whether or not it is something we need to *fix* in Jmol. > > The bad news is that changing the rotation behavior would break every > script that uses the 'rotate y ' command or the Chime 'move' > command. The good news is that the repair is quite easy. > > Should Jmol be 100% RasMol/Chime compatible? > Should Jmol only support a fully right-handed system? > Can't we have both? > > > Detail > ====== > I think we have the general understanding that the axis orientation in > RasMol is right-handed. With the default orientation of having > - +X to the right > - +Y going down > - +Z into the screen > > The general feeling from the jmol-users seems to be that we should offer > the option of having +Y go up and +Z come out of the screen. Many think > that this is a more natural orientation that is adopted by math > textbooks, OpenGL, VRML, etc. > > > > Now, we need to talk about the rotations. > > As I understand it, a right-handed rotation should be counter-clockwise > when the viewer is positioned on the + axis and is looking towards the > origin. > > To visualize it with your hand ... > - with your right hand > - extend your thumb > - curl your fingers > - point your thumb at your nose > - you are looking at the origin from the + end of the axis > - your fingers are pointing in the direction of the rotation > > I believe that this is consistent with Anthony Stone's previous email to > jmol-users. > > Let's look at the axis rotations in RasMol ... > > load someMolecule > set axes on > rotate x 10 > > You then need to take the mouse and wiggle it a little. I observe that > the +Z axis (which is in the back) comes up. > > Point your thumb to the right with your fingers curled. The fingers are > curling up from the back. This means that RasMol did a right-handed > rotation around the X axis. Good. > > Let's skip to the Z axis > > reset > rotate z 10 > > I observe that the +X drops on the right. The +Z axis goes into the > screen. Point your right thumb into the screen. Your fingers are curling > down on the right. RasMol is doing a right-hand rotation around the Z > axis. Good. > > Finally, let's look at the Y axis > > reset > rotate y 10 > > I observe that the +Z axis at the back moves to the left. The +Y axis > points down, so point your right thumb down. Fingers are curling around > back to the *right* ... but +Z moved to the *left*. Huh? > > Try it with your left hand. Thumb down, fingers curl to the left, +Z > moved to the left ... it sure looks like to me that RasMol is doing a > left-hand rotation around the Y axis. > > > > I have looked at this several dozen times over the past 6 months. At > first I wasn't confident of my observations, but now I have convinced > myself. But I may be wrong ... I certainly have struggled with this > 'handedness' stuff :-) > > Q: Please post some independent confirmations telling me that you concur ... > or explaining my error :-) > > Q: I have not tried this in Chime ... can someone check it out and > confirm that it behaves the same way? > > Q: Can someone also confirm that the chime 'move' command about the y > axis is also left-handed? > > > Unfortunately, this has pretty big implications for someone who has a > large investment in existing scripts (Eric?). It means that all moves and > rotates around the Y axis need to be negated. At least it isn't difficult. > > My goal for Jmol has been to get as close as possible to 100% RasMol/Chime > script compatibility, to ease the migration path for people who have > existing scripts. But this might be a pretty big change for people who > have an investment in tutorials/courseware. > > As I see it, the options are pretty similar to the Axis Orientation > question: > > 1. Jmol should only support RasMol/Chime rotations > - people have made an investment in existing > RasMol/Chime scripts > - it works fine, leave it alone > - people are used to seeing it behave this way > - it doesn't really matter, no one has looked > at it for years so nobody really cares > > 2. Jmol should be completely right-handed > - the system should be consistently right-handed > - the fact that y rotates backwards is a design > flaw that should be corrected, not propogated > - people have been confused by this for years > - noone is going to use existing scripts anyway > - OR, those who have scripts can easily change them > - OR, just write a script converter that will > fix existing scripts ... just negate the parameter > to 'rotate y ' and 'move x z ...' > commands > > 3. Jmol should offer both > - it is easy to support both > Q: What should the default orientation be in Jmol? > Q: What should the script command be to change > the setting? > Q: Is this *exactly* the same switch that controls > the Y axis orientation? > > > > I am interested in your thoughts and feedback. > > > Thanks, > Miguel > > > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; fr-FR; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: fr-fr, fr References: <50647.80.58.16.235.1076978243.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Jean-Philippe Demers Subject: Re: RasMol rotations about axes Date: Tue, 17 Feb 2004 00:16:27 -0500 To: rasmol@lists.umass.edu --Boundary_(ID_726NahPBNJd/sVmUAG8zDw) Hello! This has been my first appearance in the list for months; I've begun my B.Sc an it takes a lot of time/work... Since the beginning of Jmol development, it's not the first time that there's a struggle between changing the current Rasmol scripting language and keeping it as it is. First, there was the insertion code, and then it's the axis orientation and who knows what will be next. In fact, as the Jmol code gets written, it is normal that some features seem (to the development team at least) to be better designed in another way than they were in Chime/Rasmol. There are advantages to keep the current scripting format (backward compatibility with previous material so no need to modify this material, people are used to it...) as well as to change it (more logical/intuitive approach, more similar to what is used elsewhere in science and computing, better implementation of a feature, and not carrying a flaw that was in a previous software). There is the third option for Jmol to be able to interpret two scripting languages that has not been discussed a lot. It's certain that there are some disadvantages to that: need for a more complex interpreter, need for a mechanism to distinguish the two scripting language, more hassle for the script developer. However, in my mind, two facts stand clear. First, there is too much stuff out there that already uses the Chime/Rasmol scripting language so that we can say, "no one is going to use existing scripts anyway". Of course, it would be easy to modify the current scripts - I guess there will code to change anyway when we will definitely move to Jmol - but how time and labour-consuming this will be! Second fact, there will be a demand for the addition of new features to Jmol and, along with each new feature, there will be a new command added to the scripting language (and the new command will generate a syntax error if run in Chime/Rasmol). Here I discuss some ways this option could be implemented in Jmol. First, a script has an effect either on the molecule display or on the "state" of the molecule in the software memory. If two languages are supported, they can have a direct effect on the molecule; this choice would require two interpreters. Alternatively, one language could be translated into the other and the latter will affect the loaded molecule. (Interestingly, it is stated in the Chime documentation that CSML (a mere scripting language) is supported by Chime, in addition to Rasmol scripts. A CSML script is just translated into a Rasmol script and then sent to be executed). This choice would require only a script interpreter, but also a translator. It is also now a good time to think about the evolution of Jmol. I take as an asset that the development of Jmol will be rapid and continuous: addition of several features but nothing can be done perfectly at first, so there will be adjustments made to the implemented features. How can the scripting language used by Jmol cope with that? Should a script specify the version of the language in which it is written? Nevertheless, HTML has the !DOCTYPE tag to identify the version of the language used. However, it would be cumbersome to have an interpreter or a translation if there are dozens of versions of different languages. This brings us to the second problem: how to tell which language or which version a script uses. This reminds me that Mr. Bernstein had suggested to implement a command switch, a compromise that IMO does not solve the problems involved: It would add a new command (for sure not recognized by Chime, which could even less interpret the other scripting language) and would allow the sudden switching of language into a script, a situation that could introduce some confusion in the coding and interpretation of scripts. For the two facts stated below, it would not be a good idea to make a compromise language that would mix new and old, apples and oranges :-) . A solution could be to include the script specifications as comments at the beginning of the script. Another solution could be to handle each format differently. Each format could have its own file extension and MIME type. I don't know yet how scripts are handled in Jmol but there could be a way of telling the script specifications to the applet, with a PARAM tag for instance. This was my two cents; I hope it will help the development of Jmol or that it will create more debates among us, Rasmolers, Chimeleons and Jmolers. Jean-Philippe Demers Herbert J. Bernstein a écrit: >Dear Miguel, > > I think you are right. Once again, the best fix would be a >command line switch. Changing the default would break lots >of scripts. > > Clearly Jmol is an independent program and its developers >can do whatever they think best, but with over a million >existing rasmol users worldwide, providing them with >a program that works in a similar fashion when they are >using a browser might be a good idea. > > Regards, > Herbert > > --Boundary_(ID_726NahPBNJd/sVmUAG8zDw)-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; de-AT; rv:1.6) Gecko/20040113 X-Accept-Language: de, en-us, en References: <47243.80.58.16.235.1076895342.squirrel@www.howards.org> <4030A29D.60209@imb-jena.de> <33383.212.128.142.26.1076930485.squirrel@www.howards.org> <4030E3C0.3090309@imb-jena.de> <40311BE6.7040206@imb-jena.de> <41808.80.58.16.235.1076963682.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Jan Reichert Subject: Re: [Jmol-users] Axis orientation - Step 2 Date: Tue, 17 Feb 2004 08:14:26 +0100 To: rasmol@lists.umass.edu Miguel Howard schrieb: >>>>RasMol2.7 Irix (starts with rotate x 180) translation Y down, X >>>>right, Z to front (rotation after a rotate x 180 command! x+ y+ z- >>>>) >>>> >>>> >>>> >>>> >>Y down, X right, Z to front is right handed, >> >> > >Jan, what you have just described is a left-handed system. > > thumb -> +X > index -> +Y > middle -> +Z > > you are right, but I think I get confused myself because the slab method to detect z movements is difficult to interpret (I think there are bugs with this function (I noticed that only translate z -50, which I used first, but neither -40 nor -60 results in something which may be interpreted), I tried again on RasWin2.7.2.1 and Irix RasMol2.7.2.1 loading a second molecule into the scene and then try relative translate z motions, and it looks really right-handed. > > > >>but the rotation around the Z-axis is not. >> >> > >I believe that the rotations in RasMol are not consistently right-handed. > > > > >>I agree with Miguel, that it is better to change the RasMol >>documentation and >> >> > >Just to clarify ... I have not advocated making *any* changes to RasMol >documention or RasMol. It would not be my place to do so. > > that is true >I *did* ask the question in the context of *Jmol* because: > - the default orientation of +Y going down seems unnatural to me > - the rotations are not consistently right-handed > >So, in the context of Jmol, I have raised the question of whether it is >appropriate to propogate these characteristics. And, if we want to make >changes, whether or not we should have a switch to maintain >backward-compatibility. > > > > and I suggest, to alter this in future RasMol versions and hence, change the documentation. Regards, Jan > > >>>Is there a Z-inversion happening somewhere to produce the left-handed >>>"RasMol2.7 Irix" display? >>> >>> >>> >>> >>no, not on Irix, only in RasWin2.7.2.1 the label of the Y axis is on the >> opposite side, which looks like left-handed, but translation indicates >>the right right-handed internal orientation. >> >> > > >Miguel > > > ----------------------------------------------------------------rasmol-+ To change your address, unsubscribe, view previous messages/history, receive messages as weekly digests, or for any other information about the RasMol EMail List, please go to http://www.umass.edu/microbio/rasmol/raslist.htm ----------------------------------------------------------------rasmol-- User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; de-AT; rv:1.6) Gecko/20040113 X-Accept-Language: de, en-us, en References: <50647.80.58.16.235.1076978243.squirrel@www.howards.org> ++++------+------+------+------+------+------+------+------+------+------+ From: Jan Reichert Subject: Re: RasMol rotations about axes Date: Tue, 17 Feb 2004 09:08:15 +0100 To: rasmol@lists.umass.edu Herbert J. Bernstein schrieb: >Dear Miguel, > > I think you are right. Once again, the best fix would be a >command line switch. Changing the default would break lots >of scripts. > > Clearly Jmol is an independent program and its developers >can do whatever they think best, but with over a million >existing rasmol users worldwide, providing them with >a program that works in a similar fashion when they are >using a browser might be a good idea. > > I agree, although I had loved the idea to get both programs totally right-handed and upside up. There is an other problem with the RasMol translate, it only translates in % of the view, especially since RasMol is able to load and manipulate up to 5 different molecules, it would be very useful to allow translation in A units e.g. translate x 50.0 would translate the selected molecule 50 A to the right side, not half out of the viewing area. > Regards, > Herbert >===================================================== > Herbert J. Bernstein, Professor of Computer Science > Dowling College, Kramer Science Center, KSC 121 > Idle Hour Blvd, Oakdale, NY, 11769 > > +1-631-244-3035 > yaya@dowling.edu >===================================================== > >On Tue, 17 Feb 2004, Miguel Howard wrote: > > > >>Summary >>======= >>I may be wrong on this, so I need people to check my work ... >> >>It looks to me like the RasMol rotations about axes are not consistently >>right-handed. >> >>We need to discuss this and try to figure out what to do about it ... if >>anything ... whether or not it is something we need to *fix* in Jmol. >> >>The bad news is that changing the rotation behavior would break every >>script that uses the 'rotate y ' command or the Chime 'move' >>command. The good news is that the repair is quite easy. >> >>Should Jmol be 100% RasMol/Chime compatible? >> >> grr, yes >>Should Jmol only support a fully right-handed system? >>Can't we have both? >> >> interpreter switches like #!RasMol -version 2.7 in contrast to #!Jmol -version 10 >> >>Detail >>====== >>I think we have the general understanding that the axis orientation in >>RasMol is right-handed. With the default orientation of having >> - +X to the right >> - +Y going down >> - +Z into the screen >> >>The general feeling from the jmol-users seems to be that we should offer >>the option of having +Y go up and +Z come out of the screen. Many think >>that this is a more natural orientation that is adopted by math >>textbooks, OpenGL, VRML, etc. >> >> >> >>Now, we need to talk about the rotations. >> >>As I understand it, a right-handed rotation should be counter-clockwise >>when the viewer is positioned on the + axis and is looking towards the >>origin. >> >>To visualize it with your hand ... >> - with your right hand >> - extend your thumb >> - curl your fingers >> - point your thumb at your nose >> - you are looking at the origin from the + end of the axis >> - your fingers are pointing in the direction of the rotation >> >>I believe that this is consistent with Anthony Stone's previous email to >>jmol-users. >> >>Let's look at the axis rotations in RasMol ... >> >> load someMolecule >> set axes on >> rotate x 10 >> >>You then need to take the mouse and wiggle it a little. I observe that >>the +Z axis (which is in the back) comes up. >> >>Point your thumb to the right with your fingers curled. The fingers are >>curling up from the back. This means that RasMol did a right-handed >>rotation around the X axis. Good. >> >>Let's skip to the Z axis >> >> reset >> rotate z 10 >> >>I observe that the +X drops on the right. The +Z axis goes into the >>screen. Point your right thumb into the screen. Your fingers are curling >>down on the right. RasMol is doing a right-hand rotation around the Z >>axis. Good. >> >>Finally, let's look at the Y axis >> >> reset >> rotate y 10 >> >>I observe that the +Z axis at the back moves to the left. The +Y axis >>points down, so point your right thumb down. Fingers are curling around >>back to the *right* ... but +Z moved to the *left*. Huh? >> >>Try it with your left hand. Thumb down, fingers curl to the left, +Z >>moved to the left ... it sure looks like to me that RasMol is doing a >>left-hand rotation around the Y axis. >> >> you are right I had got mad on xyz here as with the translation, it is x+ y- z+ for rotation, too, using Irix RasMol2.7.2.1. >> >> >>I have looked at this several dozen times over the past 6 months. At >>first I wasn't confident of my observations, but now I have convinced >>myself. But I may be wrong ... I certainly have struggled with this >>'handedness' stuff :-) >> >>Q: Please post some independent confirmations telling me that you concur ... >>or explaining my error :-) >> >> you are right >>Q: I have not tried this in Chime ... can someone check it out and >>confirm that it behaves the same way? >> >>Q: Can someone also confirm that the chime 'move' command about the y >>axis is also left-handed? >> >> >>Unfortunately, this has pretty big implications for someone who has a >>large investment in existing scripts (Eric?). It means that all moves and >>rotates around the Y axis need to be negated. At least it isn't difficult. >> >>My goal for Jmol has been to get as close as possible to 100% RasMol/Chime >>script compatibility, to ease the migration path for people who have >>existing scripts. But this might be a pretty big change for people who >>have an investment in tutorials/courseware. >> >>As I see it, the options are pretty similar to the Axis Orientation >>question: >> >> 1. Jmol should only support RasMol/Chime rotations >> - people have made an investment in existing >> RasMol/Chime scripts >> - it works fine, leave it alone >> - people are used to seeing it behave this way >> - it doesn't really matter, no one has looked >> at it for years so nobody really cares >> >> #!RasMol >> 2. Jmol should be completely right-handed >> - the system should be consistently right-handed >> - the fact that y rotates backwards is a design >> flaw that should be corrected, not propogated >> - people have been confused by this for years >> - noone is going to use existing scripts anyway >> - OR, those who have scripts can easily change them >> - OR, just write a script converter that will >> fix existing scripts ... just negate the parameter >> to 'rotate y