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

Herbert J. Bernstein yaya at bernstein-plus-sons.com
Sat Apr 22 21:46:00 EDT 2006

Dear Dan,

   Thank you for reporting this bug in RasMol.  I have prepared a
patch and a few binaries at:


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.


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 
>Thanks for any suggestions,
>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

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