From: Alan H. <he...@il...> - 2007-04-25 14:46:11
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At 17:40 18/04/2007, Bob Wrote: >I saw the zeolite case as a nice opportunity to try a few new things. The new features are indeed much better than what I previously used in ICSD to represent cavities eg see: http://icsd.ill.fr/icsd/cifdraw.php?&id[]=43790 But this brings us back to a question from last August about "deleting" atoms. Zeolites are often reported with their cavities full of other atoms (eg water). To draw the cavities correctly you need to be able to select (eg with the mouse) and hide/delete these junk atoms for the purpose of constructing the cavities. (Yes I know you can't actually delete them from the input file with Jmol; but you can already make them invisible or of zero radius, though that doesn't seem to be sufficient for the purpose of ignoring them for the construction of cavities). I have other problems with zeolites in that the technique for constructing coordination polyhedra from CIF files, which consists of including all the surrounding cells but making them invisible, takes a lot of time if the cell is large. I really don't need complete surrounding cells to construct coordination polyhedra, just the immediate surroundings would do, which should be faster for large structures. (Yes, I can get around this by dumping just the atoms of interest into a PDB or XYZ file, but that is ugly). Alan. BTW Christian, the new jmol drawings in your Zeolite Atlas look great. Congrats to you and Bob. _____________________________________________________________ Dr Alan Hewat, ILL Grenoble, FRANCE<he...@il...>fax+33.476.20.76.48 +33.476.20.72.13 (.26 Mme Guillermet) http://www.ill.fr/dif/people/hewat/ _____________________________________________________________ |
From: Alan H. <he...@il...> - 2007-04-25 16:16:09
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At 17:04 25/04/2007, Bob wrote: >If isosurface ignore(xxxxx) .... >does not do the job for cavities, then that is a bug. Oops :-) Selecting and hiding unwanted atoms and then using: isosurface ignore(hidden) minset 1000 INTERIOR cavity 1.0 sasurface 0.2; works fine eg http://icsd.ill.fr/icsd/cifdraw.php?&id[]=70186 I should have remembered that since I have already used "isosurface ignore(xxx)" Alan. _____________________________________________________________ Dr Alan Hewat, ILL Grenoble, FRANCE<he...@il...>fax+33.476.20.76.48 +33.476.20.72.13 (.26 Mme Guillermet) http://www.ill.fr/dif/people/hewat/ _____________________________________________________________ |
From: Alan H. <he...@il...> - 2007-04-26 08:50:12
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BTW Christian, you indicated that you have solved the problem of using different colors for frontlit/backlit isosurfaces as in http://www.ethlife.ethz.ch/e/articles/sciencelife/zeolithim5.html How do you define your two isosurfaces ? Alan. At 19:36 23/04/2007, Christian Baerlocher wrote: >>>- would it be possible for the surfaces to change not only the >>>lighting between front and back but also the color? I know, I could >>>mimic this by generating a second surface further in, but a simple >>>command frontcolor/backcolor would of course be simpler... >>(Bob replied) no, I don't think so. The two colors have to be the same. > >I added a option for two surfaces. This again works only well for >large/medium pores. _____________________________________________________________ Dr Alan Hewat, ILL Grenoble, FRANCE<he...@il...>fax+33.476.20.76.48 +33.476.20.72.13 (.26 Mme Guillermet) http://www.ill.fr/dif/people/hewat/ _____________________________________________________________ |
From: Bob H. <ha...@st...> - 2007-04-25 15:04:09
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If isosurface ignore(xxxxx) .... does not do the job for cavities, then that is a bug. Alan Hewat wrote: >At 17:40 18/04/2007, Bob Wrote: > > > >>I saw the zeolite case as a nice opportunity to try a few new things. >> >> > >The new features are indeed much better than what I previously used in ICSD to represent cavities eg see: http://icsd.ill.fr/icsd/cifdraw.php?&id[]=43790 But this brings us back to a question from last August about "deleting" atoms. > >Zeolites are often reported with their cavities full of other atoms (eg water). To draw the cavities correctly you need to be able to select (eg with the mouse) and hide/delete these junk atoms for the purpose of constructing the cavities. (Yes I know you can't actually delete them from the input file with Jmol; but you can already make them invisible or of zero radius, though that doesn't seem to be sufficient for the purpose of ignoring them for the construction of cavities). > >I have other problems with zeolites in that the technique for constructing coordination polyhedra from CIF files, which consists of including all the surrounding cells but making them invisible, takes a lot of time if the cell is large. I really don't need complete surrounding cells to construct coordination polyhedra, just the immediate surroundings would do, which should be faster for large structures. (Yes, I can get around this by dumping just the atoms of interest into a PDB or XYZ file, but that is ugly). > > > I understand. Let's see how this would work and see if there are any major issues. Four options: a) the unwanted atoms are never delivered by the reader in the first place. b) the unwanted atoms are filtered out when the "real" atom set is created from the set of atoms that were read. c) user has a "delete atoms" option, and atoms are actually permanently removed. d) user has a "delete atoms" option, and deleted atoms are tagged but still present. Issues: 1) how to handles references to deleted atoms. 2) how to handle the "state" in order to preserve and reproduce the changes. If option a or b is chosen, it shouldn't be too difficult to do this. Bob >Alan. >BTW Christian, the new jmol drawings in your Zeolite Atlas look great. Congrats to you and Bob. > >_____________________________________________________________ >Dr Alan Hewat, ILL Grenoble, FRANCE<he...@il...>fax+33.476.20.76.48 >+33.476.20.72.13 (.26 Mme Guillermet) http://www.ill.fr/dif/people/hewat/ >_____________________________________________________________ > > >------------------------------------------------------------------------- >This SF.net email is sponsored by DB2 Express >Download DB2 Express C - the FREE version of DB2 express and take >control of your XML. No limits. Just data. Click to get it now. >http://sourceforge.net/powerbar/db2/ >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > |