Dear Bob, Thank you for a prompt reply. It does work when using the proper chain identifier. Regards, Jaim
On Aug 14, 2014, at 4:32 PM, Robert Hanson <[email protected]<mailto:[email protected]>> wrote: 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]<mailto:[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]<mailto:[email protected]> tel: 972-8-9344959 fax: 972-8-9344113 OCA, http://oca.weizmann.ac.il<http://oca.weizmann.ac.il/> (the protein structure/function database) Proteopedia, http://proteopedia.org<http://proteopedia.org/> (because life has more than 2D) ------------------------------------------------------------------------ ------------------------------------------------------------------------------ _______________________________________________ Jmol-users mailing list [email protected]<mailto:[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]<mailto:[email protected]> https://lists.sourceforge.net/lists/listinfo/jmol-users
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