Dan, Yes, those files aren't really valid PDBs, but you can probably solve this by assigning a distinct chain to the waters and rebuilding:
alter hoh/, chain='X' sort Cheers, Warren -- mailto:war...@delsci.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Daniel Rigden > Sent: Friday, July 16, 2004 3:14 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] sequence viewer problem on some PDB files > > Hi > > It looks to me as if there is a glitch in the sequence viewer > for some PDB files like 4PFK. The symptom is that waters get > mixed up among the protein sequences as in the snapshot here > > http://pcwww.liv.ac.uk/~drigden/dross.png > > If you write the structure out again you get things like this > > ATOM 40 N GLY 5 20.601 -28.694 4.635 1.00 > 37.79 > 4PFK N > ATOM 41 CA GLY 5 19.386 -28.380 5.423 1.00 > 41.21 > 4PFK C > ATOM 42 C GLY 5 19.278 -26.841 5.426 1.00 > 42.59 > 4PFK C > ATOM 43 O GLY 5 20.254 -26.164 5.038 1.00 > 43.67 > 4PFK O > HETATM 44 O HOH 5 4.786 -19.354 8.074 1.00 > 34.51 > 4PFK O > HETATM 45 O HOH 6 7.048 -4.823 8.185 1.00 > 20.29 > 4PFK O > ATOM 46 N VAL 6 18.116 -26.349 5.824 1.00 > 38.63 > 4PFK N > ATOM 47 CA VAL 6 17.842 -24.904 5.901 1.00 > 33.77 > 4PFK C > ATOM 48 C VAL 6 16.826 -24.721 7.009 1.00 > 35.07 > 4PFK C > ATOM 49 O VAL 6 15.935 -25.593 7.057 1.00 > 37.40 > 4PFK O > ATOM 50 CB VAL 6 17.427 -24.327 4.537 1.00 > 31.75 > 4PFK C > ATOM 51 CG1 VAL 6 16.199 -24.987 3.908 1.00 > 28.52 > 4PFK C > ATOM 52 CG2 VAL 6 17.323 -22.819 4.592 1.00 > 25.99 > 4PFK C > TER 53 VAL 6 > HETATM 54 O HOH 7 7.246 -12.026 8.967 1.00 > 16.51 > 4PFK O > ATOM 55 N LEU 7 16.985 -23.701 7.817 1.00 > 35.71 > 4PFK N > ATOM 56 CA LEU 7 16.018 -23.467 8.906 1.00 > 38.35 > 4PFK C > > After playing a bit it seems as if it applies particularly to > old, non-standard PDB files where > > a) Protein and HETATMs have the same chain ID (in the case of > 4pfk, chain ID is blank for both) > b) Water numbering overlaps protein residue numbering > > Wish I'd noticed this one yesterday too... > > Cheers > > Dan > > > -- > Dr Daniel John Rigden Tel:(+44) 151 795 4467 > School of Biological Sciences FAX:(+44) 151 795 4414 > Room 101, Biosciences Building > University of Liverpool > Crown St., > Liverpool L69 7ZB, U.K. > > > > ------------------------------------------------------- > This SF.Net email is sponsored by BEA Weblogic Workshop FREE > Java Enterprise J2EE developer tools! > Get your free copy of BEA WebLogic Workshop 8.1 today. > http://ads.osdn.com/?ad_id=4721&alloc_id=10040&op=click > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >