Unfortunately, the chain designations used by Jmol to create the complete
model,
_atom_site.label_asym_id
are not the ones you refer to with "chain=",
_atom_site.auth_asym_id
For example, in 1vu4 we have:
ATOM 68679 C CA . VAL MA 1 36 ? 215.540 621.913 480.029 1.00 0.00 ? ? ?
? ? ? 36 VAL m CA 1
"MA" is the label_asym_id; "m" is the auth_asym_id
This is just the way it is. You need to use
set chaincasesensitive true
(I'm surprised Jmol doesn't set that automatically; I thought it did)
and then refer to the author's chain designations.
load 1vu4.cif
print show('chains').join(" ")
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z a b c d e f g h i j k l
m n o p q r s t u v w x y z 0 1 2
Bob
On Thu, Aug 14, 2014 at 3:11 AM, Jaime Prilusky <
[email protected]> wrote:
> How to select chains in large structures? Testing on
> Jmol.jar 14.2.4_2014.08.03 2014-08-03 08:56
>
> We are working on 4v8m, one of the ‘large structures’ (
> ftp://ftp.wwpdb.org/pub/pdb/data/large_structures/mmCIF/4v8m.cif.gz )
> . The asymmetric unit for this structure is composed of multiple PDB
> entries: 3ZEQ, 3ZEX, 3ZEY, 3ZF7 and has 86 chains.
>
> The chain names are the following:
> A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,
> U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,
> JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,
> WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB,HB,IB,
> JB,KB,LB,MB,NB,OB,PB,QB,RB,SB,TB,UB,VB,
> WB,XB,YB,ZB,AC,BC,CC,DC,EC,FC,GC,HC
>
> The command *getProperty chaininfo* displays a long list, including the
> two character chains, which means to me that Jmol parses the mmCIF file and
> builds a data structure.
>
> Selecting one character name chains (tested a few), report *0 atoms
> selected*, like * select chain=‘A’. *Some of the two character name
> chains also report* 0 atoms*, like* select chain=‘DA'*
>
> Several of the two character name chains return something, including
> those chains that are not reported in the list of chains! The file does not
> report chain AX nor AZ, but the select chain command finds atoms associated
> to that name.
>
> $ select chain='AA'
> 47370 atoms selected
> $ select chain='AB'
> 1557 atoms selected
> $ select chain='AC'
> 1620 atoms selected
> $ select chain='AD'
> 853 atoms selected
> $ select chain='AE'
> 1300 atoms selected
> $ select chain='AX'
> 1628 atoms selected
> $ select chain=‘AZ’
> 526 atoms selected
>
> Could it be that the internal structure index is wrong? Suggestions?
>
> Jaim
> __
> Dr Jaime Prilusky
> Head Bioinformatics
> R&D Bioinformatics and Data Management
> Department of Biological Services
> Weizmann Institute of Science
> 76100 Rehovot - Israel
>
> mail: [email protected]
> tel: 972-8-9344959
> fax: 972-8-9344113
> OCA, http://oca.weizmann.ac.il (the protein structure/function database)
> Proteopedia, http://proteopedia.org (because life has more than 2D)
> ------------------------------------------------------------------------
>
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
------------------------------------------------------------------------------
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
