Re: [Jmol-users] Jmol-users Digest, Vol 110, Issue 3

[Craig T Martin]

Dear all

   I am trying to take some pages created more than 5 years ago in Jmol and 
bring them up to modern JSmol/Jmol standards. I’m now using the most recent 
Jmol release, and using the Jmol2.js adapter routines. I’ve got that running 
fine with a simple test page, but have not been successful with my more complex 
pages.

  In particular, my “complex” page does a lot of javascript rendering of the 
HTML, through calls in the Header section, followed by a call at the end of the 
HTML body (this allows a common framework from my own javascript library, but 
includes simple user HTML).

  As you can see in the code below, what I would like to do is to load my Jmol 
applet into a DIV after the page/document has fully loaded. I create (not 
shown) a DIV dedicated to the applet and I do the call to jmolApplet into a 
variable. Finally, after the page has loaded, I’m trying to load that variable 
into that existing DIV. Everything is working fine, but nothing loads into the 
DIV. No error messages (though I may not know everywhere to look for those).

Any advice here? If you want to play with the page, it can be found at
>

And the older, functioning (and Java-only) page at
>

Thanks,

Craig Martin

// ===
//Global variable
var StoredCodeJmol;

//Writes to DIV JAppDIV, previously prepared
function AfterLoaded() {
$('#JAppDIV').html(StoredCodeJmol);
}

// Set to call above after the document is fully loaded/rendered
$(document).ready(function(){AfterLoaded()});

// Temporarily turn off direct writing
jmolSetDocument(0);

StoredCodeJmol = jmolApplet([1.0,1.0], LoadScript);

//Restore direct writing by Jmol.js calls
jmolSetDocument(document);
// ===

I do get the following in the console, if that’s helpful
=
[Log] JSmol load jmolApplet0 loadClazz... (JSmol.min.js, line 273)
[Log] JSmol load jmolApplet0 start applet... (JSmol.min.js, line 273)
[Log] JSmol exec jmolApplet0 loadClazz null -- OK (JSmol.min.js, line 272)
[Log] xhr.open async=false url=../jsmol/j2s/core/package.js (JSmol.min.js, line 
178)
[Log] xhr.open async=false url=../jsmol/j2s/core/package.js (JSmol.min.js, line 
178)
[Log] xhr.open async=false url=../jsmol/j2s/core/corejmol.z.js (JSmol.min.js, 
line 178)
[Log] xhr.open async=false url=../jsmol/j2s/java/net/UnknownServiceException.js 
(JSmol.min.js, line 178)
[Log] xhr.open async=false url=../jsmol/j2s/J/io/JmolBinary.js (JSmol.min.js, 
line 178)
[Log] xhr.open async=false url=../jsmol/j2s/J/g3d/PrecisionRenderer.js 
(JSmol.min.js, line 178)
=
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Re: [Jmol-users] bug: config=1

[Eric Martz]

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 
To: Robert Hanson 



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 
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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