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

[Trans-Laboratory -- Chemical Analysis Service Provider --]

Hello Dan,

Yes there is an application free of charge found at
http://www.yasara.org/index.html that will do what you would like and much
more, e.g. superpose (recently somebody asked about this as well), align,
etc.  This is an excellent application full of good features developed by U.
Graz -Austria- and Radbound Nijmegen -Netherlands-.  In addition, up to date
I have not seen another application with prettier rendering than this one.
Only thing to do is to register and ask for the application.

For example I took 1c8d (must download the file to local disc because I have
not seen a direct link import function to RCSB as in spdbv) and although I
do not know from where you look at the cavity, I measure the distance where
it looked narrowest between N-Asp240 and N-Thr476 with "Analyze Geometry"
and obtained 168,91 nm, N-Gly242 and N-Asp 475 = 164,06 nm and N-Gly242 and
N-Asp477 = 193,66 nm; it took less than 10 minutes.  Worth trying it!

Hope this helps,

Ricardo A. Correa C.
Molecular Biology Amateur


Trans-Laboratory 
Chemical Analysis Service Provider 
Rue François Stroobant 41 
1050 Brussels - Belgium 
e-mail   	: 	trans.lab at skynet.be
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-----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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