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 (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) ------------------------------------------------------------------------
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