Select / Structure / secondary structure / turn broken
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
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
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi, if you need protein and protein-ligand complexes in the PDB file format that contains fully annotated turns you should try to get access to Relibase (http://www.ccdc.cam.ac.uk/products/life_sciences/relibase/). The recent version Relibase+ 3.0 contains the module Secbase which includes a complete assignment of all turns within protein structures. The TURN assignment within the original PDB files is quite fragmentary. There is a free web-access to relibase for academic user (http://relibase.ccdc.cam.ac.uk). This is not updated to Relibase 3.0 yet, but should be in the near future. Turn Classification used: "Turns revisited: A uniform and comprehensive classification of normal, open, and reverse turn families minimizing unassigned random chain portions" http://www3.interscience.wiley.com/journal/121378732/abstract "Secbase: Database Module To Retrieve Secondary Structure Elements with Ligand Binding Motifs" http://pubs.acs.org/doi/abs/10.1021/ci900202d Kind regards Oliver Dr. Oliver Koch BioChemInformatics Postdoctoral-Fellow Intervet Innovation GmbH Zur Propstei 55270 Schwabenheim, Germany E-Mail: oliver.koch@sp.intervet.com Phone: +49 (6130) 948 396 Fax: +49 (6130) 948 517 Home http://www.intervet.com Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 Geschäftsführer: Dr. Peter Schmid
-----Original Message----- From: chimera-users-bounces@cgl.ucsf.edu [mailto:chimera-users-bounces@cgl.ucsf.edu] On Behalf Of Elaine Meng Sent: Samstag, 7. November 2009 01:02 To: 'Chimera BB' Cc: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] Select / Structure / secondary structure / turnbroken
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
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
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participants (3)
-
Elaine Meng -
Koch, O (Oliver) -
Tom Goddard