OK, I get it. Have to catch a plane, though.... Will upload later today. On Tue, Jul 28, 2015 at 11:05 AM, Robert Hanson <hans...@stolaf.edu> wrote:
> 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 > > -- 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
