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 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.
dkim at nmsu.edu