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[Jmol-developers] [ jmol-Bugs-2639278 ] Measuring again
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From: SourceForge.net <no...@so...> - 2009-02-26 14:16:08
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Bugs item #2639278, was opened at 2009-02-25 18:57 Message generated for change (Settings changed) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2639278&group_id=23629 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Open Resolution: Fixed Priority: 5 Private: No Submitted By: Rene Kanters (rkanters) Assigned to: Nobody/Anonymous (nobody) Summary: Measuring again Initial Comment: I just realized that in the latest build I obtained (it had been a while since I update my jmol sources) the measuring is completely strange. I currently can only measure angles (earlier I could do only bond lengths). And an additional change is that the measuring only happens for the atoms in the first model. If one opens a file with multiple models (e.g. the new enediyne,out from the qchem Jmol-datafiles) and pick model 9, do some measurements: none show up there but if you go back to model 1 the values show up. Also the values in the measurements are really only valid for model 1 (not for model 9) that was selected when doing the measurements. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-02-26 08:14 Message: Rene, I've decided to consider this a bug and have fixed it. Try it now. The original measure syntax, with just numbers, was never adapted after it was made possible to load multiple models. (I can hardly remember when that wasn't possible!) It seems reasonable to me to adapt that syntax to allow selecting of the first atom in each case in the CURRENTLY VISIBLE FRAME SET - which might be more than one model, but most of the time will be just one. Check the SVN. Bob ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-02-26 07:51 Message: This is proper behavior. See the documentation on MEASURE: "If neither ALL nor ALLCONNECTED is present, only the first matching atom in the entire model set (all frames, so probably the first frame) is matched in each atom expression." ---------------------------------------------------------------------- Comment By: Rene Kanters (rkanters) Date: 2009-02-26 07:02 Message: I forgot to mention that the version of Jmol I just built reads: Jmol Version 11.7.27_dev 2009-02-25 19:48, so I assume I have the latest one. ---------------------------------------------------------------------- Comment By: Rene Kanters (rkanters) Date: 2009-02-26 06:58 Message: I just updated my Jmol environment with SVN and after rebuilding Jmol from scratch I still have the problem. The version you provide in the zip file does not have the updated QchemReader in it, so I can not open the files I need to look at (and measure distances and angles). Currently measure seems to only measure atoms in the first model, even when a different model is selected. For instances if you open the attached enediyne.out file (which I added the Jmol-datafiles SVN repository in the qchem directory as well). you can do in the script window a measure 7 9 and get the proper value. If you then go to model 5, do a measure 7 9: nothing happens (viewing model 1 will show that that measure was erased) doing another measure 7 9 in model 5 will not show it in model 5 but turn it back on in model 1.... File Added: enediyne.out ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-02-26 05:54 Message: Yes -- it's related to the other problem just fixed. Should be fine now. The measureallmodels setting is also working fine. The SVN is updated, and this is also available at http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip It will be part of Jmol 11.7.27 -- broken in 11.7.24 on Feb. 4. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2639278&group_id=23629 |