VMD-L Mailing List

From: Adrian Kaats (akaats_at_yahoo.ca)
Date: Tue Oct 31 2006 - 12:22:19 CST

Hi,

I have read the posts concerning the use of mono2poly.tcl to create biological unit coordiante files, and it works great in most cases. Unfortunately, there are some PDB files that do not seem to contain appropriate instructions for creating the biological unit and therefore do not work with mono2poly.tcl (example Ompf Porin 2OMF from RCSB). However, RCSB does provide a .pdb containing the coordinates for the biological unit - this file can be downloaded by clicking on 'Biological Unit Coordinates' under 'Download Files' on the left panel of the structure viewer.

MY PROBLEM:

When I load the 'Biological Unit Coordinates' file in VMD I can't get it to show the entire unit - it will only show the assymetric unit (please try this with the biological unit coordinates file for Ompf). It should be noted that both Rasmol and KiNG will display the entire biological unit, so there is nothing wrong with the coordinates file.

Does anybody know how to get VMD to display the entire biological unit?

Thanks,

Adrian Kaats

Graduate student
Department of Biomedical Engineering
McGill University
Montreal, Quebec
Canada

                 
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