Eric, note that your analysis for config=3 and config=4 are incorrect. $ load =1bs0 $ select altloc!='' and config=1 17 atoms selected $ show selected [SER]53:A.N%A #414 [SER]53:A.CA%A #416 [SER]53:A.C%A #418 [SER]53:A.O%A #420 [SER]53:A.CB%A #422 [SER]53:A.OG%A #424 [ARG]361:A.N%D #2737 [ARG]361:A.CA%D #2739 [ARG]361:A.C%D #2741 [ARG]361:A.O%D #2743 [ARG]361:A.CB%D #2745 [ARG]361:A.CG%D #2747 [ARG]361:A.CD%D #2749 [ARG]361:A.NE%D #2751 [ARG]361:A.CZ%D #2753 [ARG]361:A.NH1%D #2755 [ARG]361:A.NH2%D #2757
"config = 1" for biomodels resets the configuration per group. So since SER53 has A and B, and ARG361 has D and E, "config=1" allows A for SER53 and D for ARG361. That is, the first option in each group. If you want that to operate differently, you will need to do it manually. On Tue, Jul 28, 2015 at 12:10 PM, Robert Hanson <hans...@stolaf.edu> wrote: > 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 > > -- 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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