Wow, that is really tricky. I have to completely rewrite that algorithm.
On Fri, Jul 24, 2015 at 6:46 PM, Eric Martz <ema...@microbio.umass.edu> wrote: > Hi Bob, > > The fix in Jmol from July 23 works for the first test case, 9ins, but not > for other cases. > > CASE WITH A, B, C: > > Jaim's server http://bip.weizmann.ac.il/oca-bin/altloc > 1bsz: 158 lines with alternate locations: A=74 B=74 C=10 > > $ load =1bsz > HYDROLASE 01-SEP-98 1BSZ > PEPTIDE DEFORMYLASE AS FE2+ CONTAINING FORM (NATIVE) IN COMPLE > INHIBITOR POLYETHYLENE GLYCOL > found biomolecule 1: A > found biomolecule 2: B > found biomolecule 3: C > > $ select altloc!='' > 158 atoms selected #CORRECT > $ select altloc!='' and config=1 > 74 atoms selected #CORRECT > $ select altloc!='' and config=2 > 74 atoms selected #CORRECT > $ select altloc!='' and config=3 > 6 atoms selected # WRONG, SHOULD BE 10 > $ select altloc!='' and config=4 > 0 atoms selected #CORRECT > $ select altloc!='' and not (config=1,config=2) > 10 atoms selected #CORRECT > $ select altloc!='' and config=2 and config=1 > 0 atoms selected #CORRECT > $ > > CASE WITH A, B, C, D: > > 1al4 gets this report at Jaim's server: > > > > *528 lines with alternate locations: A=238 B=244 C=34 D=12 Jmol handles it > CORRECTLY: *$ load =1al4 > ANTIBIOTIC 11-JUN-97 1AL4 > GRAMICIDIN D FROM BACILLUS BREVIS (N-PROPANOL SOLVATE) > found biomolecule 1: A, B > > $ select altloc!='' > 528 atoms selected > $ select altloc!='' and config=1 > 238 atoms selected > $ select altloc!='' and config=2 > 244 atoms selected > $ select altloc!='' and config=3 > 34 atoms selected > $ select altloc!='' and config=4 > 12 atoms selected > $ select altloc!='' and config=5 > 0 atoms selected > > SECOND CASE WITH A, B, C, D: > > > 1bs0: 34 lines with alternate locations: A=6 B=6 D=11 E=11 > > $ load =1bs0 > TRANSFERASE 31-AUG-98 1BS0 > PLP-DEPENDENT ACYL-COA SYNTHASE > found biomolecule 1: A > found biomolecule 2: A > > $ select altloc!='' > 34 atoms selected #CORRECT > $ select altloc!='' and config=1 > 0 atoms selected # WRONG, SHOULD BE 6 > $ select altloc!='' and config=2 > 0 atoms selected # WRONG, SHOULD BE 6 > $ select altloc!='' and config=3 > 11 atoms selected #CORRECT > $ select altloc!='' and config=4 > 11 atoms selected #CORRECT > $ select altloc!='' and config=5 > 0 atoms selected #CORRECT > > OUTLIER CASE WITH A-V, 22 CONFIGS! > > An excellent test case is 1zir, reported as follows by Jaim's server > *http://bip.weizmann.ac.il/oca-bin/altloc > <http://bip.weizmann.ac.il/oca-bin/altloc>* > *247 lines with alternate locations: A=65 B=64 C=9 D=9 E=4 F=4 G=11 H=11 > I=7 J=7 K=1 L=1 M=4 N=4 O=8 P=8 Q=7 R=7 S=4 T=4 U=4 V=4* > > select altloc!='' correctly reports 247. There should be nonzero config > counts up to 22! > > select altloc!='' and config=1 reports 2, but the correct count is much > more than 2, probably 65. Jmol reports only the waters, not the non-waters. > > Ditto for config=2. > > config > 2 are often zero or numbers much lower than what is in the PDB > file > > Regards, Eric > > -- 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
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