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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