Dear Pymol users,

I am very pleased with Pymol as a visualization tool for the generation of publication quality images, but I am having a problem with one aspect of the problem.  I am working with several PDB files that do not have embedded secondary structure assignments.  I have been trying to render these structures as cartoon diagrams, and as you might expect, the secondary structures are not revealed unless you tell the program where they exist.  One option is the command: util.ss.  As is mentioned in the manual this is not a reliable assignment algorithm.  I have confirmed this problem with several of my PDB files. The assignments do not match those found by other programs.  So I am in search of a solution.  Can one manually create a secondary structure assignment matrix to insert into the PDB file?  I must admit that as a novice I do not understand the formatting of the secondary structure matrices that I have seen embedded  in some PDB files.  Is there a resource somewhere that explains the formatting of such a matrix?  Alternatively, is there a manual series of Pymol commands to directly assign secondary structure for a protein for insertion into the .pml script file?  Even better, is there a separate program that can assign secondary structure and then allow you to save the revised PDB file with the secondary structure assignments inserted into the PDB output.  I would be willing to accept any of the above!!  One further consideration:  I have limited accessibility to unix-based programs.  I am presently running Pymol on a Mac under X-windows (it works great by the way, although rather slow).  Replies for workarounds should please take into account that alternative programs should be available to a windows or preferably a Mac environment.  

Thanks, and I hope that there is a solution.

-Kelley      


Dr. Kelley Moremen
Associate Professor
Complex Carbohydrate Research Center
Department of Biochemistry and Molecular Biology
University of Georgia, Athens, GA 30602-7229
Office (706) 542-1705    Fax: (706) 542-1759
Email: moremen@arches.uga.edu
(send email with large attachments to: moremen@bmb.uga.edu)
Website: http://bmbiris.bmb.uga.edu/moremen/lab/