help HOMOLOGY

HABERMANN at AIMP.UNA.AC.AT HABERMANN at AIMP.UNA.AC.AT
Wed Mar 17 09:09:00 EST 1993


Angelo writes:

>I am trying to build up a good working model for a single chain antibody
>(variable regions of the light and heavy linked by a peptide linker)
>using the HOMOLOGY program within INSIGHT (Biosym).  I am able to
>transfer SCR (struc. conserved region) coordinates the sequence of my
>interest.  My question is that whether its possible to truncate the
>sequnce of an existing pdb file to be displayed as a truncated protein?
>(for eg. even if I use the display command to show only the part of the
>protein on screen, I always get the full protein sequence information on
>screen when I invoke the extract sequnce command)
>One way to get around that problem I think is to edit and delete the
>unnecessary sequnce coordinates in the pdb file before displaying it on
>screen.  Does that make sense or is there any easy ways of doing the
>same thing.  Since i don't know much about editing pdb files, can
>someone out there help me doing it.
>I am using homology program within Insight 2.0 in a silicon graphic work
>station.
>Thanks in advance

>Angelo           

I quite don't understand, why you have problems with the whole sequence being displayed. 
Once you have transferred the SCR's of the homologous protein to your own sequence, 
the pdb_file isn't with the whole coordinate set isn't of great interest any more. apart 
from that, the variable, non_homologous regions are not really in the way. 
anyhow, to answer your question: it doesn't help to just NOT DISPLAY the regions you don't need.
 even if you save them as not displayed, they will always be present in the file. 
what you could do is to delete them with the RESIDUE_DELETE command in the BIOPOLYMER module, 
alternatively, you could simply edit the pdb_file and cut out the regions, that do not interest you. 

good luck
bianca

habermann at aimp.una.ac.at



More information about the Proteins mailing list