[Chimera-users] Show molecular surface for one chain only

Hurt, Darrell (NIH/NIAID) [E] darrellh at niaid.nih.gov
Mon Oct 22 09:07:29 PDT 2012


Oh wait. Now I've found it. The "split" or "surfcat" commands. Sorry to bother you!




Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH

31 Center Drive, Room 3B62B, MSC 2135
Bethesda, MD 20892-2135
Office  301-402-0095
Mobile 301-758-3559
http://bioinformatics.niaid.nih.gov (Within NIH)
http://exon.niaid.nih.gov (Public)

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From: <Hurt>, Darrell Hurt <darrellh at niaid.nih.gov<mailto:darrellh at niaid.nih.gov>>
Date: Monday, October 22, 2012 11:23 AM
To: "chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>" <chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>>
Subject: Show molecular surface for one chain only

Hi Chimera folks,

I have a peptide bound to a protein. They are two separate chains in single PDB. I want to show the molecular surface for the protein, but not the peptide (to see the surface where the peptide binds to the protein). This is easy (the default, actually) for small molecules. But when I select the chain of the protein and display its surface, the surface is "broken" around the peptide and I cannot see what I want. The rest of the surface is OK, but in the area of interest, I cannot see the surface.

I tried the "Intersurf" command and it sort of works, but I want an MSMS molecular surface of the protein with the peptide sitting in it. Is there some trick for this other than separating the peptide from the protein and putting it into a separate model?

Thanks,
Darrell


Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH

31 Center Drive, Room 3B62B, MSC 2135
Bethesda, MD 20892-2135
Office  301-402-0095
Mobile 301-758-3559
http://bioinformatics.niaid.nih.gov (Within NIH)
http://exon.niaid.nih.gov (Public)

Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.



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