Subject: summary of software to view metal centres of proteins

From: "chinmoy ranjan" <[email-masked]>
Date: Sat, 31 Mar 2001 20:05:00 +0530

Dear CClers,

Few days earlier Ihad posted a message. I n responce I got the following
info . Thanks for the suggesstions.
The following is the list of suggesstions that I recieved:

Dear CCLers,
 I am trying to see the exact architecture of active site of a protein .

Could any one tell me any software or tool (preferably free )through
which I could view the exact metal centre of the protein. I tried to
edit the PDB file and view the metal centre using rasmol but without
much success.
 Thanks in advance.

Greetings,

The program Ligplot from the Thorton lab prepares a nice schematic
drawing
in 2D showing the protein environment of a ligand (reading the info from 
a PDB file).

The URL I have (it is olda - may have been changed) is
http://www.biochem.ucl.ac.uk/~mcdonald/

Mihaly Mezei, Dept. of Physiology & Biophysics, Mount Sinai School of =
Medicine
           Voice: (212) 241-2186     Fax: (212) 860-3369|
WWW: http://adsr13.mssm.edu/domains/dept/facultyInfo.epl?objname=physbio&user=mezeim01

Ranjan,

I guess VMD should do the job. I am pretty sure it is a freeware,
you may want to check that. Normally, InsightII or Quanta does this
effectively, these are not freeware though..
Another possibility is PDB viewer.

Lakshmi
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Jim Kress:

WebLabViewerLite (
http://www.msi.com/life/products/weblab/viewer/register/lite/download_lite.html )
VMD ( http://www.ks.uiuc.edu/Research/vmd/ )
gOpenMol ( http://laaksonen.csc.fi/gopenmol/gopenmol.html   )

Jim

Dear Chinmoy,

You can try WebLab:
It is free, run on PC-Windows and you can download it from:
www.msi.com
Bye
Marco

CHINMOY RANJAN
INDIAN INSTITUTE OF TECHNOLOGY
KANPUR