Dear Bob:
Update on these bugs:
The current bug was introduced between Jan 22 and Feb 10.
14.3.2_2015.01.22 still has the bug where it counts *.cb from config=1
in config=2. It does not have the config=1 bug.
14.3.12_2015.02.10 has the *.cb bug fixed, but introduced the config=1 bug.
Simple test:
load =9ins
select config=1
print {selected}.count
select altloc!='' and config=1 and config=2
print {selected}.count
The correct counts are 484 and 0.
*.cb bug count gives 446 (should be 484).
config=1 bug gives 8 (should be 0).
Eric
-------- Forwarded Message --------
Subject: Fwd: bug: config=1
Date: Sat, 18 Jul 2015 19:30:35 -0400
From: Eric Martz <ema...@microbio.umass.edu>
To: Robert Hanson <hans...@stolaf.edu>
Hi, Bob, I'm forwarding this directly to you since sourceforge seems to
have been down for hours.
I love the pivot thing for the list of elements, but I'll need this bug
fixed before I can release the next version of FirstGlance (not urgent).
Regards, Eric
-------- Forwarded Message --------
Subject: bug: config=1
Date: Sat, 18 Jul 2015 17:09:08 -0400
From: Eric Martz <ema...@microbio.umass.edu>
To: jmol-users@lists.sourceforge.net
Testing Jmol 14.3.14_2015.07.09 I find what appears to me to be a bug.
Transcript, with my comments added after #.
The correct number of altloc atoms in 9ins can be verified by entering
the PDB code here:http://bip.weizmann.ac.il/oca-bin/altloc (thanks to
Jaime Prilusky).
There are 48 in each of configs 1 and 2.
$ load =9ins
HORMONE 23-OCT-91 9INS
MONOVALENT CATION BINDING IN CUBIC INSULIN CRYSTALS
found biomolecule 1: A, B
found biomolecule 2: A, B
$ select all
532 atoms selected $ CORRECT
$ select altloc=''
436 atoms selected # CORRECT: 532 - (48 + 48) = 436.
$ select config=1
446 atoms selected # WRONG. CORRECT VALUE IS 436 + 48 = 484.
$ select altloc!=''
96 atoms selected # CORRECT: 48 + 48 = 96.
$ select altloc!='' and config=1
10 atoms selected # WRONG. CORRECT VALUE IS 48.
I have tried extracting just one or two amino acids into a PDB file, but
I have not come up with a simple example that elicits this bug.
Another example is 1bsz, where Jaime's counter reports 74 atoms in each
of configs 1 and 2, and 10 atoms in config 3:
$ 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=''
4272 atoms selected # CORRECT: 4430 - (74 + 74 + 10) = 4272.
$ select config=1
4287 atoms selected # WRONG: 4272 + 74 = 4346.
$ select altloc!=''
158 atoms selected # CORRECT: 74 + 74 + 10 = 158.
$ select altloc!='' and config=1
15 atoms selected # WRONG. SHOULD BE 74.
------------
While investigating this, I noticed that Jmol 14.3.7_2014.09.20 (which I
am currently using in FirstGlance) incorrectly counts carbon beta atoms
(*.cb) from config=1 in the config=2 count. This bug appears to be fixed
in 14.3.14_2015.07.09.
-Eric
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