Subject: Re: CCL:Simple program for editing protein structure

From: "Nick Rhodes" <[email-masked]>
Date: Fri, 14 Jan 2000 10:20:13 -0000

Hi Bjoern,

Take a look at the Swiss PDB viewer:

	http://www.expasy.ch/spdbv/mainpage.html

It does most of the things I want and seems pretty robust, I use it under NT but 
there's an IRIX version - and it's free!

Description (taken from the site):

Swiss-PdbViewer is an application that provides a user friendly interface allowing 
to analyse several proteins at the same time. The proteins can be superimposed 
in order to deduce structural alignments and compare their active sites or any 
other relevant parts. Amino acid mutations, H-bonds, angles and distances 
between atoms are easy to obtain thanks to the intuitive graphic and menu 
interface.  

Moreover, Swiss-PdbViewer is tightly linked to Swiss-Model, an automated 
homology modelling server running in the Geneva Glaxo Welcome Experimental 
Research.  

Working with these two programs greatly reduces the amount of work necessary 
to generate models, as it is possible to thread a protein primary sequence onto a 
3D template and get an immediate feedback of how well the threaded protein will 
be accepted by the reference structure before submitting a request to build 
missing loops and refine sidechain packing.  

Swiss-PdbViewer can also read electron density maps, and provides various tools 
to build into the density.  

In addition, various modelling tools are integrated and command files for popular 
energy minimisation packages can be generated.  

Finally, as a special bonus, POV-Ray scenes can be generated from the current 
view in order to make stunning ray-traced quality images. An example can be 
found here.  

good luck

Nick

*****************************************************************
Nick Rhodes, Chemical Information Systems Research Group, 
Department of Information Studies, University of Sheffield, 
Regent Court, 211 Portobello Street, Sheffield, 
South Yorkshire, S1 4DP, United Kingdom.

---

From: "Rzepa, Henry" <[email-masked]>
Date: Fri, 14 Jan 2000 08:28:34 +0000

>One of the more useful simple tools I've found for this is a custom
>version of Rasmol, from the UC Berkely Chem. Dept.; there are MacOS and
>Wintel versions of executable programs.  The URL is:
>
>	http://mc2.CChem.Berkeley.EDU/Rasmol/
>
>The major changes vs. the standard Rasmol are:
>
>- ability to load more than one molecule
>- ability to rotate torsions and change conformations

The above relates to RasMol V2.5 and 2.6b

I think one should also point out that the  "un-enhanced" RasMol
(I suppose the  "official" version) has reached  Version 2.7.1, and
can be found at 

http://www.bernstein-plus-sons.com/software/rasmol/

It, inter alia, supports mmCIF as well as the older  PDB formats. 

Henry Rzepa. +44 (0)20 7594 5774 (Office) +44 (0)20 7594 5804 (Fax)
Dept. Chemistry, Imperial College, London, SW7  2AY, UK. 
http://www.ch.ic.ac.uk/rzepa/