[Chimera-users] Select / Structure / secondary structure / turnbroken
Koch, O (Oliver)
oliver.koch at sp.intervet.com
Thu Nov 12 07:59:25 PST 2009
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
Dr. Oliver Koch
Intervet Innovation GmbH
55270 Schwabenheim, Germany
E-Mail: oliver.koch at sp.intervet.com
Phone: +49 (6130) 948 396
Fax: +49 (6130) 948 517
Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 Geschäftsführer: Dr. Peter Schmid
> -----Original Message-----
> From: chimera-users-bounces at cgl.ucsf.edu
> [mailto:chimera-users-bounces at cgl.ucsf.edu] On Behalf Of Elaine Meng
> Sent: Samstag, 7. November 2009 01:02
> To: 'Chimera BB'
> Cc: chimera-users at 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
> 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,
> but I don't see anything about them in the newer (3.2) format
> 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 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 at cgl.ucsf.edu
> > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
This message and any attachments are solely for the intended recipient.
If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited
-- please immediately and permanently delete.
More information about the Chimera-users