Hi Haixin, Tom is exactly right -- residues are only assigned as "turn" automatically if they are in TURN records in the input PDB file (just like SHEET and HELIX records control what is "strand" and "helix" respectively). If you mean that everything in a protein that is not helix/strand should be considered "turn," you could select that with sel protein & ~ helix & ~ strand (where "helix" is the same as ":/isHelix" etc.) Actually, you could just manually assign those residues the isTurn attribute, and then "Select... Structure... secondary structure... turn" will get what you wanted it to. You could assign the isTurn attribute with the following command: setattr r isTurn true protein & ~ helix & ~ strand After that assignment you could also use "turn" in commands (or equivalently, :/isTurn): color green turn TURN records are described for PDB version 2.3 format, <http://www.wwpdb.org/documentation/format23/sect5.html> but I don't see anything about them in the newer (3.2) format description: <http://www.wwpdb.org/documentation/format32/sect5.html> I didn't find anything at wwpdb that said "PDB files no longer have TURN records" so I am not sure of their current status. However, even in the older version of the PDB, they were not very common. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Nov 6, 2009, at 3:20 PM, Tom Goddard wrote:
Hi Haixin,
I suspect "turn" doesn't just mean not helix and not sheet but I don't know. Others in my lab will know so I've forwarded your question to the Chimera mailing list so they can answer.
If you want to select all residues that are neither helix nor sheet you can use the command:
select ~ :/isHelix :/isSheet
Tom
-------- Original Message -------- From: Haixin Sui To: 'Thomas Goddard' Date: 11/6/09 2:27 PM
Tom,
How have you been?
This email is to report a small bug I experienced. The "select"-> "structure"->"secondary structure" -> "turn" function is not working. It worked for selection of "helix" and "strand". Selection of "turn" is the only one does not work. I am using chimera alpha version 1.3( build 2577) 2008/12/09 00:54:36 on a laptop PC running Windows XP.
While I have a lot of different molecules aligned in a map, this selection function is very useful for me. Any suggestion?
Best regards from
Haixin
-- Haixin Sui Research Scientist IV Wadsworth Center Empire State Plaza P.O. Box 509 Albany, NY 12201-0509
Assistant Professor SUNY-Albany School of Public Health Department of Biomedical Sciences
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