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**
* *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
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