[Chimera-users] Select / Structure / secondary structure / turnbroken

[Koch, O (Oliver)]

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 at sp.intervet.com
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> -----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 
> 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 at cgl.ucsf.edu
> > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 
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