[Molvis-list] Measuring viruses (and other viral-like things)?

Herbert J. Bernstein yaya at bernstein-plus-sons.com
Sun Apr 23 10:53:44 EDT 2006

Dear Dan,

   Glad it worked.  Sorry about the Y-axis scroll bar.  Right now the scroll
bars are mapped to the nested rotations, rather than to the relevant mouse
coordinates.  I will look at making the scroll bars more intuitive.


At 1:26 PM +0100 4/23/06, Dan Bolser wrote:
>Herbert J. Bernstein wrote:
>>Dear Dan,
>>   Thank you for reporting this bug in RasMol.  I have prepared a
>>patch and a few binaries at:
>>    http://arcib.dowling.edu/software/rasmol/downloads/version_2.7.3.1/
>>The binaries were produced from the RasMol_2.7.3 kit with the patches
>>mouserun2.patch, ztrl.patch, distfix.patch applied.  At the moment
>>there are slackware 10.1 versions with and without xforms and with
>>and without shared memory (useful when using another machine as
>>the X-windows display), Mac OS X X11 and classic versions, and MS
>>Windows versions.  If you need another flavor of binary, let me
>>know and we'll work on it.
>>   Comments and suggestions would be appreciated.  There are some
>>drastic changes coming for support of WPDB, Russian (from Gregory 
>>A. Pozhvanov), Japanese (from  Mamoru Yamanishi) and OpenGL (from
>>Vassil Litchev and Enno Fennema) and it would be helpful to have
>>2.7.3 stable before we move up to 2.7.4.
>Hi, thanks very much for the speedy patch! I tried 
>'rasmol_NOXF_SHM_32BIT' on Linux 2.6.16-1.2069_FC4 i686 athlon i386 
>GNU/Linux, and it worked great.
>I had a quick look at 1c8d and measured the size of the internal 
>cavity from between 130 to 150 Ang., and the outer diameter from 
>between 230 and 280 Ang. (roughly).
>I still find the y-axis scroll bar behaves a little bit strangely 
>(regarding mouserun2.patch), with unusual 'retrograde' motion when I 
>expected smooth rotation in the y-axis.
>I am not sure how to 'probe' the other new features, so other than 
>that everything seemed to work fine in general.
>Thanks very much for all the suggestions from the list regarding the 
>problem below. I really appreciate the feedback I got from everyone 
>both on and off the list.
>All the best,
>>   Regards,
>>     Herbert
>>At 12:57 PM +0100 4/20/06, Dan Bolser wrote:
>>>Hi, I am trying to get some rough estimates for the overall 
>>>diameter and cavity size of the following 5 structures...
>>>1c8d (diameter = ~200A from the literature)
>>>1jh5 (diameter = ~ 200A from the literature)
>>>1c8n (diameter = ~ 280A from the literature)
>>>Specifically 1stm and 1hqk, for which I can't find an estimate in 
>>>the literature (admittedly only after a quick look).
>>>I decided to tried using Rasmol, starting with 1c8d. I quickly 
>>>found that I couldn't get the structures from the PQS, which 
>>>showed the correct structure (60-mer) but the link to the file was 
>>>broken. Conversely, the pdb-beta site appeared not to know about 
>>>the correct biological assembly (showing only the ASU), but gave 
>>>me the correct (60 subunit file) anyway.
>>>Using the 'pick distance' feature in Rasmol proved to be a bit 
>>>buggy, sometimes returning a 'nan' distance at the terminal 
>>>(apparently labeled correctly on the structure) but worse, 
>>>sometimes returning a distance that seemed far too small (giving 
>>>values in the range of 30 to 60 A instead of 100 to 200 A by eye).
>>>Computationally what I would like to do is fit a sphere (or an 
>>>ellipse, whichever is smaller) to the structure and minimize the 
>>>size of the sphere to enclose something like 95-99% of the atoms. 
>>>Is there any tool that I can use to do this?
>>>I am not even sure if this description makes sense, but I want to 
>>>avoid just returning the maximum distance between any two atoms, 
>>>which probably isn't a fair 'rough estimate' of the diameter of 
>>>the above molecules.
>>>Does anyone happen to know (approximately) the external and 
>>>internal diameter of these molecules? Or a (free) package that 
>>>lets me find them?
>>>Thanks for any suggestions,
>>>Molvis-list mailing list
>>>Molvis-list at bioinformatics.org
>Molvis-list mailing list
>Molvis-list at bioinformatics.org

  Herbert J. Bernstein, Professor of Computer Science
    Dowling College, Kramer Science Center, KSC 121
         Idle Hour Blvd, Oakdale, NY, 11769

               Office:  +1-631-244-3035
            Lab (KSC 020): +1-631-244-3451
                  yaya at dowling.edu

More information about the Molvis-list mailing list