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

Dan Bolser dmb at mrc-dunn.cam.ac.uk
Sun Apr 23 08:26:00 EDT 2006

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)
>> 1stm
>> 1hqk
>> 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,
>> Dan.
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