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

Dan Bolser dmb at mrc-dunn.cam.ac.uk
Thu Apr 20 07:57:45 EDT 2006

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 

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,


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