[Chimera-users] Select / Structure / secondary structure / turn broken

[Elaine Meng]

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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