noting -- still no luck uploading changes... Subversion status for j* projects
SourceForge Allura-backed Subversion for j* projects – i.e. SVN repos where project-name starts with the letter “j” – is temporarily offline pending data restoration. On Tue, Jul 28, 2015 at 12:06 PM, Robert Hanson <hans...@stolaf.edu> wrote: > 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 > > -- 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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