Thanks, Bob! --Chuck ----- Original Message ----- From: Robert Hanson To: Charles Harrison Shubert ; jmol-users@lists.sourceforge.net Sent: Wednesday, August 11, 2010 12:19 AM Subject: Re: [Jmol-users] BUG: Parallel isosurfaces changed between RC26 and12.0.2
This is fixed. http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip and 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 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 $ ------------------------------------------------------------------------------ The Palm PDK Hot Apps Program offers developers who use the Plug-In Development Kit to bring their C/C++ apps to Palm for a share of $1 Million in cash or HP Products. Visit us here for more details: http://p.sf.net/sfu/dev2dev-palm _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- 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 ------------------------------------------------------------------------------ This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- 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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