Protein visualization in SGI

Harry Mangalam mangalam at uci.edu
Thu Oct 17 14:58:32 EST 1996


>a free program for SGI which allows the user to visualize only
> certain parts of a protein structure (for exemple a residue range,
> secondary structures of the same type, etc.) from the full PDB file. I
> would need also that the program allow to see the structure in a rich
> format (ribbons, balls & stick, etc) and if possible combinations of some
> of them in the same view. I have tried RasMol but aparently it's not
> possible to do both.

Setor (SGI's only - contact the Author Stephen V Evans
(evans at flint.biochm.uottawa.ca) does all this better than just about any
program I've seen.  There are others that can do it Per Kraulis's
molscript is great for generating postscript, but has no user interface to
speak of.  vmd can do a substantial amount of what you want, but Setor is
the best I've seen, (but it can't do rasmol's VERY SLICK trick of using
dssp to determine secondary structure representation.).


> I would be very interested to know if exist a protein visualization program
> which reads files that could be previously edited to set up the view (MAGE
> does it but the quality of the views is poor). The program sholud run on
> Mac or SGI. Thanks in advances for your help. Please reply these mail.

I think that Setor can do this as well, but it requires that the file be
saved in Setor format; I don't believe that PDB has such a field
specifier.

Cheers
Harry
-- 
Harry J Mangalam, MolBio+Biochem / Dev+Cell Bio, Rm 4201, BioSciII  UC Irvine, Irvine, CA, 92717, (714) 824-4824, fax (714) 824 8598




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