Protein visualization in SGI

D. KIM dkim at nmsu.edu
Thu Oct 17 15:56:48 EST 1996

In article <mangalam-1710961158320001 at skink.bio.uci.edu> mangalam at uci.edu (Harry Mangalam) writes:
>>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.

[deleted stuff from H. M.]

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

I am confused.  RasMol for Windows, at least (and I believe therefore all 
current versions of the program) is able to "restrict" presentation of 
different portions of a molecule using different arguments to the 
"restrict" and "select" commands.  e.g. to display aa 120 - 345 only in a 
protein of 600 aa, use the command

restrict 1-119 or 346-600

This will leave only the  desired residues on the screen.

To display as "ribbon" format, use the DISPLAY -> RIBBON menu items.

To show aa 125, 300 and 380 only as spacefill in the ribbon, use:

select 125, 300, 380
and then do DISPLAY -> SPACEFILL in the menu.

It may be possible to use SELECT command with a structural argument, e.g.

select helix


select 120 - 350 and helix

and then modify the display parameters by the menu.

Do you have the manual for RASMOL 2.5?  I believe a .PS and .txt version 
is available at the same location as the program.

Daniel Kim
dkim at nmsu.edu

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