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

ilan samish ilan.samish at weizmann.ac.il
Fri Apr 21 10:38:04 EDT 2006

Hi Dan,
For cavity-type analysis you may want to use
castP (web interface): http://cast.engr.uic.edu/cast/

or the far more advanced volbl algorithm that is behind castP (linux/unix):


See additional relevant links in a course I once gave:


Ilan Samish, Ph.D.
Dept of Biochemistry & Biophysics
School of Medicine
& Dept of Chemistry
231 South 34th Street
University of Pennsylvania
Philadelphia, PA  19104-6323

Office: Chemistry, 261 Cret Wing
Tel (Saven Lab):  (215) 898 2025
Tel (DeGrado Lab):(215) 898 2322
Mobile:           (267) 334 5917
Fax:              (215) 573 6416
E-mail: samish at sas.upenn.edu

> -----Original Message-----
> From: molvis-list-bounces+trans.lab=skynet.be at bioinformatics.org
> [mailto:molvis-list-bounces+trans.lab=skynet.be at bioinformatics.org] On
> Behalf Of Dan Bolser
> Sent: 20 April 2006 13:58
> To: molvis-list at bioinformatics.org
> Subject: [Molvis-list] Measuring viruses (and other viral-like things)?
> 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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