This is fixed. http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zipand
http://chemapps.stolaf.edu/jmol/docs/examples-12/new.htm
version=12.1.4
# new feature: isosurface display within 2.0 {atomset} -- renderable subset
of isosurface
# new feature: isosurface display all
# bug fix: CRYSTAL reader orientation error
# bug fix: show INFO not showing COMPND record text
# bug fix: isosurface LATTICE {x y z} should be relative to current UNITCELL
# bug fix: broken selectExtended mode
# bug fix: some isosurface display properties not generalized to wildcard
# bug fix: Parallel processing not creating process-specific copies of
shapes
# bug fix: load unitcell for slab/polymer should allow 0, not just -1 in b
and c
# bug fix: diastereomer check still checking stereochemistry
# bug fix: SMILES generator should not produce stereochemistry for RX2R'
-Bob
On Mon, Aug 9, 2010 at 10:03 AM, Robert Hanson <hans...@stolaf.edu> wrote:
> Perhaps. But really I suspect it's something different. The isosurfaces
> should be completely different objects -- they are initiated independently
> and then merged at parallel function exit.
>
> I'm headed in to where my MacBook is now.
>
> On Mon, Aug 9, 2010 at 6:00 AM, Charles Shubert <cshub...@mit.edu> wrote:
>
>> Hi Bob,
>>
>> Sounds like the conference was a success.
>>
>> As I noted in an earlier email, I'm generating the script and I don't
>> exactly know when a particular script will be generated, so I then to
>> sprinkle extra "subset"s and "select"s around to make sure that I know the
>> selection state when I send a script to the Jmol interpreter.
>>
>> The important thing with this problem is to have multiple chains. I tend
>> to use 1A3N (hemoglobin) because it has 4. I'm guessing that some of the
>> recently added isosurface variables are either not being initialized or
>> being overwritten when a parallel process executes. It has a
>> not-thread-safe quality about it.
>>
>> I hope you got some vacation in,
>>
>> --Chuck
>>
>> ----- Original Message -----
>> *From:* Robert Hanson <hans...@stolaf.edu>
>> *To:* jmol-users@lists.sourceforge.net
>> *Sent:* Monday, August 09, 2010 1:15 AM
>> *Subject:* Re: [Jmol-users] BUG: Parallel isosurfaces changed between
>> RC26 and12.0.2
>>
>> Sorry for the delay -- was at the BCCE conference --
>>
>> "subset" and "select" are global settings -- you wouldn't want any of that
>> in the process blocks. In addition, unless you have previously used subset,
>> issuing it here has no effect. Just put it before the first process{}
>> command.
>>
>> Also, select here has no effect on the isosurface command, since you have
>> a select option there. And "A" is probably not defined anyway, so that's why
>> you are getting 0 atoms selected.
>>
>> I'll check on my MacBook when I return to my office, as it uses 2
>> processors and this laptop doesn't.
>>
>> Bob
>>
>>
>> On Thu, Aug 5, 2010 at 1:45 PM, Charles Harrison Shubert <
>> cshub...@mit.edu> wrote:
>>
>>> BUG: Parallel isosurfaces changed between RC26 and 12.0.2
>>>
>>> This looks to me like the cutoff, min, max variables are probably not
>>> being initialized in the parallel threads as I would expect the parser to
>>> whine if my syntax needed new extra stuff.
>>>
>>> When I run the following:
>>>
>>> load "/Users/cshubert/Downloads/1A3N.pdb";
>>>
>>> parallel makeIsos{
>>> process{ subset; select {A and PROTEIN}; isoSurface surfaceA
>>> select(within(chain,*:A)) ignore (within(chain,not *:A)) VDW 96 % color
>>> TRANSLUCENT 0.0 [192,208,255] FILL;}
>>> process{ subset; select {B and PROTEIN}; isoSurface surfaceB
>>> select(within(chain,*:B)) ignore (within(chain,not *:B)) VDW 96 % color
>>> TRANSLUCENT 0.0 [176,255,176] FILL;}
>>> process{ subset; select {C and PROTEIN}; isoSurface surfaceC
>>> select(within(chain,*:C)) ignore (within(chain,not *:C)) VDW 96 % color
>>> TRANSLUCENT 0.0 [255,192,200] FILL;}
>>> process{ subset; select {D and PROTEIN}; isoSurface surfaceD
>>> select(within(chain,*:D)) ignore (within(chain,not *:D)) VDW 96 % color
>>> TRANSLUCENT 0.0 [255,255,128] FILL;}
>>> };
>>> set multiProcessor true; show mulitProcessor;
>>> makeIsos;
>>> subset;
>>>
>>>
>>> In RC 26 I get isosurfaces being drawn for the 4 chains of this
>>> hemoglobin molecule and the following console output:
>>>
>>> $
>>>
>>> multiProcessor = true
>>> mulitprocessor = <not defined>
>>> 0 atoms selected
>>> 0 atoms selected
>>> 0 atoms selected
>>> 0 atoms selected
>>> surfaced created with cutoff=0.0; number of isosurfaces = 1
>>> surfaceb created with cutoff=0.0; number of isosurfaces = 1
>>> surfacec created with cutoff=0.0; number of isosurfaces = 1
>>> surfacea created with cutoff=0.0; number of isosurfaces = 1
>>> $
>>>
>>> In 12.0.2 I don't get the isosurfaces for the chains and I get the
>>> following console output:
>>>
>>> $
>>>
>>> multiProcessor = true
>>> mulitprocessor = <not defined>
>>> 0 atoms selected
>>> 0 atoms selected
>>> 0 atoms selected
>>> 0 atoms selected
>>> surfacea created with cutoff=NaN min=0.0 max=0.0; number of isosurfaces
>>> = 0
>>> $
>>>
>>>
>>>
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>>>
>>
>>
>> --
>> Robert M. Hanson
>> Professor of Chemistry
>> St. Olaf College
>> 1520 St. Olaf Ave.
>> Northfield, MN 55057
>> http://www.stolaf.edu/people/hansonr
>> phone: 507-786-3107
>>
>>
>> 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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>>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> 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
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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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