From: Dan G. <gez...@nd...> - 2006-06-27 19:16:34
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> http://www.stolaf.edu/people/hansonr/jmol/test/proto and let me > know if > what I have done there in relation to ellipsoids is sufficient for > you. > The basic format is: > > isosurface center {x y z} ellipsoid {cx cy cz f_ab} > > or > > isosurface center (some_atom_expression) ellipsoid {cx cy cz f_ab} Oooooo..... Ahhhhhhhhhhhh..... Very cool! --Dan *********************************************** J. Daniel Gezelter Associate Professor Department of Chemistry and Biochemistry 251 Nieuwland Science Hall University of Notre Dame Notre Dame, IN 46556-5670 phone: +1 (574) 631-7595 fax: +1 (574) 631-6652 e-mail: gez...@nd... web: http://www.nd.edu/~gezelter ************************************************ |
From: Egon W. <e.w...@sc...> - 2006-06-28 09:35:29
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On Tuesday 27 June 2006 21:16, Dan Gezelter wrote: > > http://www.stolaf.edu/people/hansonr/jmol/test/proto and let me > > know if > > what I have done there in relation to ellipsoids is sufficient for > > you. > > The basic format is: > > > > isosurface center {x y z} ellipsoid {cx cy cz f_ab} > > > > or > > > > isosurface center (some_atom_expression) ellipsoid {cx cy cz f_ab} > > Oooooo..... Ahhhhhhhhhhhh..... > > Very cool! Do I understand correctly that this also works on arbitrary points {x y z} in space? This would mean that Jmol can now render pharmacophores! Oooo.... Ahhhh.... very cool, indeed! How can a set color and transparency? Egon -- e.w...@sc... Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 |
From: Bob H. <ha...@st...> - 2006-06-28 13:07:21
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Glad you like it. Yes, arbitrary points in space; arbitrary atoms; arbitrary geometric centers of collections of atoms; arbitrary orientation of ellipsoid; arbitrary dimensions (provided a=b). colors/transparency: The simplest thing to do is to assign an arbitrary id to the isosurface: isosurface item1 center {1.0 2.0 3.0} ellipsoid {1 0 0 0.5} ..... isosurface item2 center (within(molecule,atomno=3)) scale 5.0 ellipsoid {1 0 0 0.5} .... and then refer to that using the $name notation: color $item1 transparent yellow color $item2 green some of this is done in <http://www.stolaf.edu/people/hansonr/jmol/test/proto/isosurface.htm> Bob Egon Willighagen wrote: >On Tuesday 27 June 2006 21:16, Dan Gezelter wrote: > > >>>http://www.stolaf.edu/people/hansonr/jmol/test/proto and let me >>>know if >>>what I have done there in relation to ellipsoids is sufficient for >>>you. >>>The basic format is: >>> >>> isosurface center {x y z} ellipsoid {cx cy cz f_ab} >>> >>>or >>> >>> isosurface center (some_atom_expression) ellipsoid {cx cy cz f_ab} >>> >>> >>Oooooo..... Ahhhhhhhhhhhh..... >> >>Very cool! >> >> > >Do I understand correctly that this also works on arbitrary points {x y z} in >space? > >This would mean that Jmol can now render pharmacophores! > >Oooo.... Ahhhh.... very cool, indeed! > >How can a set color and transparency? > >Egon > > > |
From: Egon W. <e.w...@sc...> - 2006-07-02 20:04:03
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On Wednesday 28 June 2006 15:11, Bob Hanson wrote: > colors/transparency: > > The simplest thing to do is to assign an arbitrary id to the isosurface: > > isosurface item1 center {1.0 2.0 3.0} ellipsoid {1 0 0 0.5} ..... > isosurface item2 center (within(molecule,atomno=3)) scale 5.0 ellipsoid > {1 0 0 0.5} .... What do I need to fill in for the dots? Nothing seems to work... > and then refer to that using the $name notation: > > color $item1 transparent yellow This crashes Jmol... in such a way that I can no longer rotate the molecule, nor can I enter new commands in the console... > color $item2 green This worked. > some of this is done in > <http://www.stolaf.edu/people/hansonr/jmol/test/proto/isosurface.htm> This seems to be down at the moment... Egon -- e.w...@sc... Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 |
From: Bob H. <ha...@st...> - 2006-07-02 21:19:46
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You want just dots? Then: isosurface delete; isosurface center {2 2 2} resolution 2 sphere 2.0 dots nofill The trick is that you need the "resolution 2" BEFORE generating the sphere, and since there is no identifier. If you provide an identifier: isosurface delete; isosurface myiso dots nofill center {2 2 2} resolution 2 sphere 2.0 then the dots/nofill can appear anywhere after that, because Jmol knows then that you are referring to THIS isosurface and not some other. Egon Willighagen wrote: >On Wednesday 28 June 2006 15:11, Bob Hanson wrote: > > >>colors/transparency: >> >>The simplest thing to do is to assign an arbitrary id to the isosurface: >> >>isosurface item1 center {1.0 2.0 3.0} ellipsoid {1 0 0 0.5} ..... >>isosurface item2 center (within(molecule,atomno=3)) scale 5.0 ellipsoid >>{1 0 0 0.5} .... >> >> > >What do I need to fill in for the dots? Nothing seems to work... > > > >>and then refer to that using the $name notation: >> >>color $item1 transparent yellow >> >> > > > >This crashes Jmol... in such a way that I can no longer rotate the molecule, >nor can I enter new commands in the console... > > > I can't imagine why that would be any problem -- maybe try that again with the latest version (10.x.18). Maybe you picked up a bad file. >>color $item2 green >> >> > >This worked. > > > >>some of this is done in >><http://www.stolaf.edu/people/hansonr/jmol/test/proto/isosurface.htm> >> >> > >This seems to be down at the moment... > > > yes, all day, unfortunately. >Egon > > > |
From: Egon W. <e.w...@sc...> - 2006-07-03 07:04:30
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On Sunday 02 July 2006 23:24, Bob Hanson wrote: > You want just dots? Then: hehehe... ummm no. Your email with the command had dots at the end, as in: > >On Wednesday 28 June 2006 15:11, Bob Hanson wrote: > >>isosurface item1 center {1.0 2.0 3.0} ellipsoid {1 0 0 0.5} ..... :) But thanx for the extra examples. I am talking with someone on pharmacophore rendering, and these use spheres and ellipsoids. <snip> > >>and then refer to that using the $name notation: > >>color $item1 transparent yellow > > > >This crashes Jmol... in such a way that I can no longer rotate the > > molecule, nor can I enter new commands in the console... > > I can't imagine why that would be any problem -- maybe try that again > with the latest version (10.x.18). Maybe you picked up a bad file. Used the latest from SVN. Will try to reproduce on an other machine. Egon -- e.w...@sc... Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 |