Frank, That PDB file has bogus/inconsistent segment identifiers that are screwing up atomic ordering (since atoms are sorted into segments by default).
set ignore_pdb_segi before loading the pdb file and then everything should work file. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Frank Dressel > Sent: Thursday, January 19, 2006 7:36 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] selection disordered > > Hi there, > > i have the following problem: selecting all ca atoms in chain > A of 1ao0 the amino acids in the selection are disordered > with respect to their occurrence in the protein. > > After loading the protein i tried the following: > > numbers=[] > iterate (chain a)&(name ca),(numbers.append(resi)) > print numbers > > And what i get is the following: > > ['56', '1', '2', '3', '4', '5', '6', '7', '8', '9', '10', > '11', '12', '13', '14', '15', '16', '17', '18', '19', '20', > '21', '22', '23', '24', '25', '26', '27','28', '29', '30', > '31', '32', '33', '34', '35', '36', '37', '38', '39', '40', > '41', '42', '43', '44', '45', '46', '47', '48', '49', '50', > '51', '52', '53', '54', '55', '57', '58', '59', '60', '61', ...] > > So the 56th amino acid is BEFORE the first one. Whats going wrong? > > Thanks: > > Frank > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep > through log files for problems? Stop! Download the new AJAX > search engine that makes searching your log files as easy as > surfing the web. DOWNLOAD SPLUNK! > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=103432&bid=230486&; > dat=121642 > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > >
