[Molvis-list] Re: Molvis-list Digest, Vol 23, Issue 1
Richard Sheehan
sheehan_rs at yahoo.com
Thu Sep 7 13:48:36 EDT 2006
I just thought that there wasn't much discussion on
molecular modelling of biological compounds. This
seemed kind of strange to me; but since I'm a novice
in this arena, I was just sitting around watching for
a while.
I have now subscribe to the JMOL uses list to
hopefully learn a bit more about this field and what
is going on with molecular modelling.
--- molvis-list-request at bioinformatics.org wrote:
> Send Molvis-list mailing list submissions to
> molvis-list at bioinformatics.org
>
> To subscribe or unsubscribe via the World Wide Web,
> visit
>
>
https://bioinformatics.org/mailman/listinfo/molvis-list
> or, via email, send a message with subject or body
> 'help' to
> molvis-list-request at bioinformatics.org
>
> You can reach the person managing the list at
> molvis-list-owner at bioinformatics.org
>
> When replying, please edit your Subject line so it
> is more specific
> than "Re: Contents of Molvis-list digest..."
>
>
> Today's Topics:
>
> 1. Recent MolVis articles in BAMBEd (Eric Martz)
> 2. Drop in use of this list (Eric Martz)
> 3. Re: Drop in use of this list (Dan Bolser)
> 4. Re: Drop in use of this list (Timothy
> Driscoll)
>
>
>
----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 06 Sep 2006 17:34:20 -0400
> From: Eric Martz <emartz at microbio.umass.edu>
> Subject: [Molvis-list] Recent MolVis articles in
> BAMBEd
> To: molvis-list at bioinformatics.org
> Cc: jvoet1 at swarthmore.edu, hardy at chem.umass.edu,
> voet at sas.upenn.edu,
> garman at biochem.umass.edu, theis at biochem.umass.edu
> Message-ID:
>
<5.2.0.9.2.20060906170131.02ee5ec0 at marlin.bio.umass.edu>
> Content-Type: text/plain; charset="us-ascii";
> format=flowed
>
> The journal "Biochemical and Molecular Biology
> Education" (BAMBEd,
> http://www.bambed.org/ www required) continues to
> grow and thrive under the
> editorship of Don and Judy Voet.
>
> The May/June issue includes "A new three-dimensional
> educational model kit
> for building DNA and RNA molecules: development and
> evaluation", which
> describes injection-molded plastic models with
> attention to pedagogically
> important detail. The authors are in Brazil and I
> found no mention of
> whether their models are available for purchase.
>
> The July/August issue contains three articles
> relevant to MolVis.
>
> Tim Herman and others contribute "Tactile teaching,
> exploring protein
> structure/function using physical models". They make
> a compelling case for
> the impact of physical models in learning. They have
> led exciting model
> designing collaborations between educators/students
> and researchers
> reporting cutting edge molecular structures. They
> have initiated impressive
> model-building challenges for the Science Olympiad
> competition. A cut-away
> spacefilled model of the active site of
> acetylcholinesterase combats the
> mis-impression (from ball and stick models) that
> "proteins are made mostly
> of air". Models can be borrowed by educators from
> their lending library
> (http://www.rpc.msoe.edu/cbm/lib/).
>
> Angel Herraez contributes "Biomolecules in the
> computer: Jmol to the
> rescue", introducing Jmol and arguing effectively
> for the ability of the
> Jmol java applet to replace Chime, avoiding many of
> the problematic issues
> with Chime. This is a meaty and scholarly article,
> amply illustrated, and
> including a short glossary.
>
> Finally, I personally enjoyed Howard Dintzis' "The
> wandering pathway to
> determining N to C synthesis of proteins - Some
> recollections concerning
> protein structure and biosynthesis". As a student,
> he was taught that the
> function of DNA is to maintain osmotic balance in
> the nucleus. His
> descriptions of rubbing elbows with Max Perutz, John
> Kendrew, and Francis
> Crick are fascinating, including early searches for
> mutant human proteins
> (culminating in sickle cell hemoglobin). In 1954,
> they were calculating a
> Patterson maps for heavy metal derivitives of
> myoglobin and hemoglobin on
> the vacuum-tube (valve) EDSAC 1, the most powerful
> digital computer of the
> day. Its 1 kilobyte dynamic memory utilized an iron
> pipe filled with
> mercury, in which sound waves traveling between a
> speaker and a microphone
> encoded the data!
>
> -Eric
>
> ----
> Eric Martz, Professor Emeritus, Dept Microbiology
> University of Massachusetts, Amherst MA US
> http://www.umass.edu/molvis/martz
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 06 Sep 2006 20:21:13 -0400
> From: Eric Martz <emartz at microbio.umass.edu>
> Subject: [Molvis-list] Drop in use of this list
> To: molvis-list at bioinformatics.org
> Cc: jeff at bioinformatics.org
> Message-ID:
>
<5.2.0.9.2.20060906200024.02488010 at marlin.bio.umass.edu>
> Content-Type: text/plain; charset="us-ascii";
> format=flowed
>
> Dear MolVis-List Subscribers,
>
> During 1996-2004, this list averaged 1.15
> messages/day (420/year, range
> 352-526). There was no trend in traffic despite the
> fact that in the first
> few years, there were less than half as many
> subscribers.
>
> Last year, the traffic dropped to 1/3 of the
> previous level (132 in 2005,
> 0.36/day). In the first half of 2006, there were 89
> messages (about 0.5
> messages/day).
>
> The number of subscribers plateaued at about 600
> from 2001 through 2004,
> but has now grown to 740.
>
> I suspect that the dizzying level of traffic on the
> jmol-users list, and
> the well-justified excitement about Jmol, has
> diverted some traffic from
> molvis-list. I myself am working more and more with
> Jmol.
>
> Of course, modest traffic is not necessarily bad,
> especially if the quality
> of, and interest in message content is high.
>
> As a reminder, quoting from our website
>
(http://bioinformatics.org/mailman/listinfo/molvis-list):
>
> "Molvis-list is for discussion of molecular
> visualization software,
> especially free software and its uses in education,
> such as MDL Chime,
> Protein Explorer, and RasMol, among many. Technical
> questions, "How do I
> ...", comparisons between software packages, or
> questions about pros and
> cons, are welcome. Discussions may include molvis
> packages that have their
> own dedicated email lists, such as Jmol or DeepView,
> although technical
> questions about those packages should be sent to
> their dedicated lists.
> Discussions may also include commercial molvis
> software packages.
>
> Subscribers with commercial affiliations are
> welcome. Advertising is
> prohibited, but occasional, brief, low-key
> announcements of commercial
> products of interest to the subscribership are
> welcome, as are
> announcements of relevant meetings, positions
> available or sought."
>
> Feel free to use this list! Ideas to increase the
> usefulness of this list
> are welcome!
>
> I'd like to extend my heartfelt appreciation to Tim
> Driscoll, who has
> kindly taken over the day to day maintenance of this
> list on a volunteer
> basis for the past couple of years. His work
> consists mostly of deleting
> spam, thereby sparing us from all receiving it -- so
> I'm sure you
> appreciate him too!
>
> -Eric (who founded this list in 1995)
>
>
> /* - - - - - - - - - - - - - - - - - - - - - - - - -
> - -
> Eric Martz, Professor Emeritus, Dept Microbiology
> U Mass, Amherst -- http://www.umass.edu/molvis/martz
>
> Biochem 3D Education Resources http://MolviZ.org
> See 3D Molecules, Install Nothing! -
> http://firstglance.jmol.org
> Protein Explorer - 3D Visualization:
> http://proteinexplorer.org
> Workshops: http://workshops.proteinexplorer.org
> World Index of Molecular Visualization Resources:
> http://molvisindex.org
> ConSurf - Find Conserved Patches in Proteins:
> http://consurf.tau.ac.il
> Atlas of Macromolecules:
> http://atlas.proteinexplorer.org
> PDB Lite Macromolecule Finder: http://pdblite.org
> Molecular Visualization EMail List (molvis-list):
>
>
http://bioinformatics.org/mailman/listinfo/molvis-list
> - - - - - - - - - - - - - - - - - - - - - - - - - -
> - */
>
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 07 Sep 2006 15:58:58 +0100
> From: Dan Bolser <dmb at mrc-dunn.cam.ac.uk>
> Subject: Re: [Molvis-list] Drop in use of this list
> To: "Molecular Visualization, especially in
> education with freeware"
> <molvis-list at bioinformatics.org>
> Message-ID: <450033B2.5000302 at mrc-dunn.cam.ac.uk>
> Content-Type: text/plain; charset=ISO-8859-1;
> format=flowed
>
> Eric Martz wrote:
> > Dear MolVis-List Subscribers,
> >
> > During 1996-2004, this list averaged 1.15
> messages/day (420/year, range
> > 352-526). There was no trend in traffic despite
> the fact that in the
> > first few years, there were less than half as many
> subscribers.
> >
> > Last year, the traffic dropped to 1/3 of the
> previous level (132 in
> > 2005, 0.36/day). In the first half of 2006, there
> were 89 messages
> > (about 0.5 messages/day).
> >
> > The number of subscribers plateaued at about 600
> from 2001 through 2004,
> > but has now grown to 740.
> >
> > I suspect that the dizzying level of traffic on
> the jmol-users list, and
> > the well-justified excitement about Jmol, has
> diverted some traffic from
> > molvis-list. I myself am working more and more
> with Jmol.
> >
> > Of course, modest traffic is not necessarily bad,
> especially if the
> > quality of, and interest in message content is
> high.
> >
> > As a reminder, quoting from our website
> >
>
(http://bioinformatics.org/mailman/listinfo/molvis-list):
> >
> > "Molvis-list is for discussion of molecular
> visualization software,
> > especially free software and its uses in
> education, such as MDL Chime,
> > Protein Explorer, and RasMol, among many.
> Technical questions, "How do I
> > ...", comparisons between software packages, or
> questions about pros and
> > cons, are welcome. Discussions may include molvis
> packages that have
> > their own dedicated email lists, such as Jmol or
> DeepView, although
> > technical questions about those packages should be
> sent to their
> > dedicated lists. Discussions may also include
> commercial molvis software
> > packages.
> >
> > Subscribers with commercial affiliations are
> welcome. Advertising is
> > prohibited, but occasional, brief, low-key
> announcements of commercial
> > products of interest to the subscribership are
> welcome, as are
> > announcements of relevant meetings, positions
> available or sought."
> >
> > Feel free to use this list! Ideas to increase the
> usefulness of this
> > list are welcome!
> >
> > I'd like to extend my heartfelt appreciation to
> Tim Driscoll, who has
> > kindly taken over the day to day maintenance of
> this list on a volunteer
> > basis for the past couple of years. His work
> consists mostly of deleting
> > spam, thereby sparing us from all receiving it --
> so I'm sure you
> > appreciate him too!
>
> How much spam gets through the members list? (Or is
> this an 'anyone can
> post' list?)
>
>
>
> I wonder if anyone can tell me how to select only
> the 'aligned' residues
> in pymol after running the 'align x, y' command?
>
> I see that atoms (and distinct residues?) are
> rejected during the
> alignment, but how can I 'see' them?
>
> Cheers,
>
> Dan.
>
>
>
> > -Eric (who founded this list in 1995)
> >
> >
> > /* - - - - - - - - - - - - - - - - - - - - - - - -
> - - -
> > Eric Martz, Professor Emeritus, Dept Microbiology
> > U Mass, Amherst --
> http://www.umass.edu/molvis/martz
> >
> > Biochem 3D Education Resources http://MolviZ.org
> > See 3D Molecules, Install Nothing! -
> http://firstglance.jmol.org
> > Protein Explorer - 3D Visualization:
> http://proteinexplorer.org
> > Workshops: http://workshops.proteinexplorer.org
> > World Index of Molecular Visualization Resources:
> http://molvisindex.org
> > ConSurf - Find Conserved Patches in Proteins:
> http://consurf.tau.ac.il
> > Atlas of Macromolecules:
> http://atlas.proteinexplorer.org
> > PDB Lite Macromolecule Finder: http://pdblite.org
> > Molecular Visualization EMail List (molvis-list):
> >
>
http://bioinformatics.org/mailman/listinfo/molvis-list
> > - - - - - - - - - - - - - - - - - - - - - - - - -
> - - */
> >
> > _______________________________________________
> > Molvis-list mailing list
> > Molvis-list at bioinformatics.org
> >
>
https://bioinformatics.org/mailman/listinfo/molvis-list
>
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 7 Sep 2006 11:43:07 -0400
> From: Timothy Driscoll <molvisions at mac.com>
> Subject: Re: [Molvis-list] Drop in use of this list
> To: "Molecular Visualization, especially in
> education with freeware"
> <molvis-list at bioinformatics.org>
> Message-ID:
> <3AFF11E7-1450-4110-B4EE-AB092174D72D at mac.com>
> Content-Type: text/plain; charset=US-ASCII;
> delsp=yes; format=flowed
>
> On Sep 7, 2006, at 10:58 AM, Dan Bolser wrote:
>
> > Eric Martz wrote:
> >> His work consists mostly of deleting spam,
> thereby sparing us
> >> from all receiving it -- so I'm sure you
> appreciate him too!
> >
> > How much spam gets through the members list? (Or
> is this an 'anyone
> > can post' list?)
> >
>
> howdy,
>
> this list is live-moderated (which means a moderator
> must approve
> every message before it is broadcast, and every
> subscription request
> before it is activated). our policy is that only
> subscribers are
> allowed to post. occasionally, we will allow a
> relevant post from a
> non-subscriber; however, this is strongly
> discouraged because it is
> extra work for the moderators. especially since...
>
> the amount of spam sent to the list has risen
> dramatically in the
> past few months. fortunately, such messages are
> manually identified
> and discarded before they hit the list, so nobody is
> the wiser
> (except the moderators, who like to complain about
> that sort of
> thing ;-).
>
>
> warm regards,
>
> tim
> --
> Timothy Driscoll em:
> molvis at vbi.vt.edu
> Virginia Bioinformatics Institute ph:
> 540-231-3007
> Bioinformatics I: M-1 im:
> molvisions
> Washington St., Blacksburg, VA 24061
>
> "Anyone who considers arithmetical methods of
> producing random digits
> is, of course, in a state of sin." - J von Neumann
>
>
>
>
>
> ------------------------------
>
> _______________________________________________
> Molvis-list mailing list
> Molvis-list at bioinformatics.org
>
https://bioinformatics.org/mailman/listinfo/molvis-list
>
>
> End of Molvis-list Digest, Vol 23, Issue 1
> ******************************************
>
__________________________________________________
Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around
http://mail.yahoo.com
More information about the Molvis-list
mailing list