From: Bob H. <ha...@st...> - 2008-03-15 13:12:40
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Jmol Developers, I have uploaded Jmol 11.5.16 -- Nico, please release 11.5.16 and 11.4.0 The big new thing is the ability to delete individual models. You do this by selecting ATOMS, and then Jmol deletes all models involving the selected atoms. For example: load files "caffeine.xyz" "1crn.pdb" load append "1blu.pdb" zap 1.1 # remove caffeine zap 2.1 # remove 1crn.pdb Individual models or sets of models from within a set of models in a file may be zapped: load cyclohexane_movie.xyz zap model < 10, model > 15 This was VERY complicated, but in the end it boiled down to just two new general methods (ArrayUtil.deleteElements and BitSetUtil.deleteBits) and then thorough application of those two methods. I'm not sure I found all the necessary points to apply these methods. I would really appreciate some major testing on this. Who can help? We need to produce model sets involving multiple models with every possible feature (polyhedra, cartoons, dots, draw, etc.) and then delete a model somewhere in the middle of the set, save the state, restore the state, save the state again, and restore the state again to see if we get exactly the same state as we started with. Dots, for example, I haven't tested at all. I just don't have time this morning to work on this anymore, but I'm confident enough that it is basically OK to release it now and let others play with it. Please do! Bob # new feature: zap {atom expression} # zaps models associated with given atoms. # use "show models" to see what models are present, then zap them with their # file.model number: # # zap 1.1,2.1 # these two models deleted # zap atomIndex=0 # ALL ATOMS IN FIRST MODEL deleted # # Note that file.model numbers do not change after this. # So if initially there were two files loaded # # zap 1.1 # # removes the first model and leaves the second as "2.1" # # NEEDS THOROUGH TESTING, particularly in regard to saving/restoring the state -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 |
From: Bob H. <ha...@st...> - 2008-03-15 20:39:50
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Correction. In 11.5.16, in fact, dots weren't zapped properly. Also, for that version you have to specify full models using the file.model notation, not just subsets of the models. This is corrected for 11.5.17. Bob Bob Hanson wrote: > Jmol Developers, > > I have uploaded Jmol 11.5.16 -- Nico, please release 11.5.16 and 11.4.0 > > The big new thing is the ability to delete individual models. You do > this by selecting ATOMS, and then Jmol deletes all models involving > the selected atoms. For example: > > load files "caffeine.xyz" "1crn.pdb" > load append "1blu.pdb" > > zap 1.1 # remove caffeine > zap 2.1 # remove 1crn.pdb > > Individual models or sets of models from within a set of models in a > file may be zapped: > > load cyclohexane_movie.xyz > zap model < 10, model > 15 > > > This was VERY complicated, but in the end it boiled down to just two > new general methods (ArrayUtil.deleteElements and > BitSetUtil.deleteBits) and then thorough application of those two > methods. > > I'm not sure I found all the necessary points to apply these methods. > I would really appreciate some major testing on this. Who can help? We > need to produce model sets involving multiple models with every > possible feature (polyhedra, cartoons, dots, draw, etc.) and then > delete a model somewhere in the middle of the set, save the state, > restore the state, save the state again, and restore the state again > to see if we get exactly the same state as we started with. > > Dots, for example, I haven't tested at all. I just don't have time > this morning to work on this anymore, but I'm confident enough that it > is basically OK to release it now and let others play with it. Please do! > > Bob > > > # new feature: zap {atom expression} # zaps models associated with > given atoms. > # use "show models" to see what models are present, then zap them > with their > # file.model number: > # > # zap 1.1,2.1 # these two models deleted > # zap atomIndex=0 # ALL ATOMS IN FIRST MODEL deleted > # > # Note that file.model numbers do not change after this. > # So if initially there were two files loaded > # > # zap 1.1 > # > # removes the first model and leaves the second as "2.1" > # > # NEEDS THOROUGH TESTING, particularly in regard to saving/restoring > the state > > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 |