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From: Alan H. <he...@il...> - 2006-09-26 15:07:41
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<html> <body> Firstly, I was wrong :-) in thinking that Jmol does not have access to different ionic radii for different valence states (thanks Angel and Phillip). Bob's table radii.xls does indeed contain the various valence states. But does Jmol actually use the valence states specified in CIF files ? eg:<br> <pre>_atom_type_oxidation_number As3- -3. Na1+ 1. </pre>For example, as Angel's table shows:<a href="http://biomodel.uah.es/jmol/radii/jmol_radii.en.html" eudora="autourl"> http://biomodel.uah.es/jmol/radii/jmol_radii.en.html</a><br> there should be a big difference between As-3 <br> <a href="http://icsd.ill.fr/icsd/index.php?action=Search&elements=as-3" eudora="autourl"> http://icsd.ill.fr/icsd/index.php?action=Search&elements=as-3</a> <br> as in Na3As, and As+3 as in CsAs4F13<br> <a href="http://icsd.ill.fr/icsd/index.php?action=Search&elements=as%2B3" eudora="autourl"> http://icsd.ill.fr/icsd/index.php?action=Search&elements=as%2B3<br> </a>I have taken those examples because there can be no doubt about the valence state of As, it is clearly marked in the CIF files, and these files are freely available from the demo WWW version of ICSD.<br><br> For CIF files, Jmol draws As-3 with much the same radius as As+3. I suspect it is using the uncharged atom radius, so As-3 and As+3 are drawn the same size, intermediate between Na+1 and Cs+1<br><br> Alan.<br> BTW, David Brown tells me that the best values for ionic radii are still those of Shannon and Prewitt 1969, Acta Cryst. B25, 925-946 (for oxides) and Shannon 1976 Acta Cryst. A32, 751-767 (for halides), so I guess the values in Jmol are fine (I haven't checked).<br> </body> <br> <div>_____________________________________________________________</div> <div>Dr Alan Hewat, ILL Grenoble, FRANCE<he...@il...>fax+33.476.20.76.48</div> <div>+33.476.20.72.13 (.26 Mme Guillermet) <a href="http://www.ill.fr/dif/people/hewat/" EUDORA=AUTOURL> http://www.ill.fr/dif/people/hewat/</a></div> <div>_____________________________________________________________</div> </html> |
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From: Rolf H. <rh...@fl...> - 2006-09-26 14:59:12
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Bob Hanson wrote: >Jmol users interested in using Jmol for more than viewing: > >I have added some new command-line options. > >What do you think of this? (Using the applicatoin from a Windows command prompt) > > >Create a JVXL file directly >--------------------------- > > Jmol -ionx iso.spt myfile.xyz > myfile.jvxl > >where: > > -i,--silent silent startup operation > -o,--noconsole no console -- all output to sysout > -n,--nodisplay no display (much faster) > -x,--exit run script and exit > > iso.spt is: > > isosurface solvent;show isosurface > > >creates a JVXL solvent surface file. > > > <snip> >You get the idea. I just uploaded the code; coming in 10.9.66; suggestions? > > This is really great! As someone who works with Unix/Linux systems for more than ten years I highly appreciate the power of command-line tools (without disregarding that of mouse-driven tools). Currently we are using rasmol as command-line tool to build our site environment database (a database containing a list of residues inside a specific distance for all active sites named in PDB files from the Protein Data Bank). I have not tried it yet but I guess we could now use Jmol for this instead. Currently we are generating all automatically generated images for our PDB atlas pages (http://www.fli-leibniz.de/IMAGE.html) using rasmol as command-line tool. Most of the currently manually generated images are created already using our Jmol viewer. We would really prefer to use Jmol also for the automatic image generation. Q: Is it already possible or might it be possible in the future to export a script generated view as an image file with Jmol as a command-line tool? Regards, Rolf |
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From: Rolf H. <rh...@fl...> - 2006-09-26 11:58:58
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Bob Hanson wrote: >Rolf Huehne wrote: > >>Bob Hanson wrote: >> >> >>>OK, First thing I saw when I opened a console: >>> >>>FileManager opening >>>http://moleculesinmotion.com/Jmol10962/authored/scripts/all_off.spt >>>ScriptException:SET ECHO must follow, not precede, model loading >>> Script line:set echo off >>> File:authored/scripts/all_off.spt Line number:44 >>> >>>Are you trying to put out an echo message to the blank applet before >>>loading a molecule? This we cannot do (because there is no "frame" to >>>hold the echo information). >>> >>> >>This used to work with older versions like 10.00.36 or 10.2. >> >> >I don't think so. Have you tried it? This is a fundamental limitation of >echo that has been around forever. Without a model loaded there cannot >be an Echo object (currently). I assure you, if there is no model >loaded, there is no Frame object, and absolutely nothing -- not even the >Jmol frank -- is put to the screen. > >The only thing that is different now is that you get a message saying >that it won't work. If you want to send your web page a message, you can >use the "message" command, but not the "echo" command. > > I investigated this a bit more and must admit that I wasn't precise enough. The piece of code that is used with version 10.00.36 at our site looks essentially like this: zap; echo "set echo top left; echo "Loading PDB file, please wait..."; refresh; load ... This code is sent to Jmol when reloading the PDB file into our interface (see for example "http://www.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=1deh", script triggered by pressing for example the 'PROSITE' standard view button at the top). As you might remember from one of my recent previous posts I modified 'Jmol.js' by adding an 'echo "Please Wait...";' to all scripts send to Jmol. So this second echo command would be executed before the above one. At this time there is already a file loaded, so that the "Please Wait..." message is (apparently) always shown. But I am quite sure that at least sometimes the 'LoadingPDB file...' message also appears with version 10.00.36. For version 10.9.65, which I am currently testing with our interface, I removed the 'zap' from the script to get rid of the exception that breaks the script. Fortunately the echo messages written prior to the 'load' command are not wiped out, so that now always both messages appear. (only in my development version, not at the URL provided above) So for my purposes this would be sufficient, if the 'zap' isn't really necessary at this point. During the first loading of the file the message is not that essential, because applet loading is going on before and the user isn't expected to be as impatient as after pressing a button. You might be wondering why the file is reloaded for the standard views. One reason is that it is the only way I know of, that fully resets all (?) settings. Since our interface provides many possibilities to manipulate settings this seems to be essential. The other reason is that with the 'Model' standard view (appearing only for NMR structures or others with multiple models, e.g.: "http://www.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=1a3p") a different file is needed in many cases. >>I guess it has something to do with the new capabilities of the 'echo' >>command. Although I think these capabilities might be useful, it will be >>a major drawback if one can't display any more a message prior to >>loading. Especially loading large or multiple frame structures can take >>quite a while and the user tends to be impatient if nothing happens for >>a while... >> >> >> >Enter this as a feature request, please. I certainly think it could be >useful. > > I just submitted it. Regards, Rolf |
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From: Bob H. <ha...@st...> - 2006-09-25 21:54:48
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OK, I hereby institute a new file format. "isotope-xyz" -- XYZI -- (or, if you prefer, "Hanson's format") same as XYZ, but you can use an isotope number prefix to the element symbol: 13C 12C 2H etc. :) Nicolas Vervelle wrote: >I think that we should not modify standard file formats to add our own >features. >We should keep the formats as they are supposed to exists without addition. > >Bob Hanson wrote: > > >>no, of course not. This would be, ah, xyzi ! >> >>Nicolas Vervelle wrote: >> >> >> >> >>>Bob Hanson wrote: >>> >>> >>> >>> >>> >>>>Does anyone know what different file formats use to designate isotopes? >>>>I guess PDB uses "D" but what about other isotopes. >>>> >>>>I'm thinking of extending the XYZ reader to accept them like this: >>>> >>>>13C 3.4 5.6 7.8 >>>>C 2.3 4.4 4.4 >>>>12C 3.2 3.3 3.3 >>>> >>>>Then at least we can have something to work with. >>>> >>>> >>>> >>>> >>>> >>>> >>>Are you sure that the XYZ format is supposed to have isotopes number ? >>> >>>Nico >>> >>> >>>------------------------------------------------------------------------- >>>Take Surveys. Earn Cash. Influence the Future of IT >>>Join SourceForge.net's Techsay panel and you'll get the chance to share your >>>opinions on IT & business topics through brief surveys -- and earn cash >>>http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >>>_______________________________________________ >>>Jmol-users mailing list >>>Jmo...@li... >>>https://lists.sourceforge.net/lists/listinfo/jmol-users >>> >>> >>> >>> >>> >>------------------------------------------------------------------------- >>Take Surveys. Earn Cash. Influence the Future of IT >>Join SourceForge.net's Techsay panel and you'll get the chance to share your >>opinions on IT & business topics through brief surveys -- and earn cash >>http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >>_______________________________________________ >>Jmol-users mailing list >>Jmo...@li... >>https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> >> >> >> >> > >------------------------------------------------------------------------- >Take Surveys. Earn Cash. Influence the Future of IT >Join SourceForge.net's Techsay panel and you'll get the chance to share your >opinions on IT & business topics through brief surveys -- and earn cash >http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > |
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From: Bob H. <ha...@st...> - 2006-09-25 21:53:00
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>-- new command line options allow silent, no-display operation > > -o,--noconsole no console -- all output to sysout > -i,--silent silent startup operation > -n,--nodisplay no display > -x,--exit run script and exit > > > that last one is not obvious. Instead of -s myfile.spt you use -x myfile.spt Why not just -x -s myfile.spt ? you ask? Because -x by itself could not possibly be any use, so it replaces the "s" instead of just adding on to it. All negotiable. This is just a first try. Bob > >------------------------------------------------------------------------- >Take Surveys. Earn Cash. Influence the Future of IT >Join SourceForge.net's Techsay panel and you'll get the chance to share your >opinions on IT & business topics through brief surveys -- and earn cash >http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > |
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From: Nicolas V. <nve...@cl...> - 2006-09-25 21:51:34
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I think that we should not modify standard file formats to add our own features. We should keep the formats as they are supposed to exists without addition. Bob Hanson wrote: > no, of course not. This would be, ah, xyzi ! > > Nicolas Vervelle wrote: > > >> Bob Hanson wrote: >> >> >> >>> Does anyone know what different file formats use to designate isotopes? >>> I guess PDB uses "D" but what about other isotopes. >>> >>> I'm thinking of extending the XYZ reader to accept them like this: >>> >>> 13C 3.4 5.6 7.8 >>> C 2.3 4.4 4.4 >>> 12C 3.2 3.3 3.3 >>> >>> Then at least we can have something to work with. >>> >>> >>> >>> >> Are you sure that the XYZ format is supposed to have isotopes number ? >> >> Nico >> >> >> ------------------------------------------------------------------------- >> Take Surveys. Earn Cash. Influence the Future of IT >> Join SourceForge.net's Techsay panel and you'll get the chance to share your >> opinions on IT & business topics through brief surveys -- and earn cash >> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >> _______________________________________________ >> Jmol-users mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> >> > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys -- and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > |
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From: Nicolas V. <nve...@cl...> - 2006-09-25 21:49:22
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Jmol 10.9.66 will be available for download at http://www.jmol.org/files/ in a few minutes. Please test and report problems on sourceforge tracker. What's new: -- new command history for applet and app - holds last 100 either from the menu, from buttons, from entering at the console. -- fix for alpha polymer -- fix for not loading files with spaces -- new command line options allow silent, no-display operation -o,--noconsole no console -- all output to sysout -i,--silent silent startup operation -n,--nodisplay no display -x,--exit run script and exit |
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From: Bob H. <ha...@st...> - 2006-09-25 21:48:48
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no, of course not. This would be, ah, xyzi ! Nicolas Vervelle wrote: >Bob Hanson wrote: > > >>Does anyone know what different file formats use to designate isotopes? >>I guess PDB uses "D" but what about other isotopes. >> >>I'm thinking of extending the XYZ reader to accept them like this: >> >>13C 3.4 5.6 7.8 >>C 2.3 4.4 4.4 >>12C 3.2 3.3 3.3 >> >>Then at least we can have something to work with. >> >> >> >Are you sure that the XYZ format is supposed to have isotopes number ? > >Nico > > >------------------------------------------------------------------------- >Take Surveys. Earn Cash. Influence the Future of IT >Join SourceForge.net's Techsay panel and you'll get the chance to share your >opinions on IT & business topics through brief surveys -- and earn cash >http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > |
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From: Nicolas V. <nve...@cl...> - 2006-09-25 21:45:28
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Bob Hanson wrote: > Does anyone know what different file formats use to designate isotopes? > I guess PDB uses "D" but what about other isotopes. > > I'm thinking of extending the XYZ reader to accept them like this: > > 13C 3.4 5.6 7.8 > C 2.3 4.4 4.4 > 12C 3.2 3.3 3.3 > > Then at least we can have something to work with. > Are you sure that the XYZ format is supposed to have isotopes number ? Nico |
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From: Bob H. <ha...@st...> - 2006-09-25 21:37:32
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Does anyone know what different file formats use to designate isotopes? I guess PDB uses "D" but what about other isotopes. I'm thinking of extending the XYZ reader to accept them like this: 13C 3.4 5.6 7.8 C 2.3 4.4 4.4 12C 3.2 3.3 3.3 Then at least we can have something to work with. Bob |
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From: Bob H. <ha...@st...> - 2006-09-25 21:28:49
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I think the 10.9.65 LOAD command is broken. This will be fixed in 10.9.66 Bob Hanson wrote: > Nico, > > oops, can you just quick recompile and put it out as 10.9.65? I don't > think an announcement is necessary; I just noticed _H was not working, > and also added _2H, _3H I have to go to work, will only be able to do it this evening. Nico > > Bob > > Nicolas Vervelle wrote: > >> Hi, >> >> Jmol 10.9.65 is available for download at http://www.jmol.org/files >> Please test as much as you can, v11.0 should be released in a near >> future. >> >> Nico >> >> 10.9.65 contains mostly minor improvements, some without any external >> effect (hopefully!) >> >> 10.9.65 >> >> - revamped CIF reader (should not be any different for users) >> - popup menu select-->hetero-->By HETATM >> - fixed exit;/quit; for script interruption >> - new D,T colors (still tentative) >> - simplified LOAD command syntax -- no "" necessary for filename >> >> load #reloads current file >> load myfile.cif 3 #loads just the third model load myfile.cif {1 1 >> 1} #load the 555 unit cell and applies symmetry >> load myfile.cif 3 {1 1 1} #loads the 3rd model and applys symmetry >> for 555 >> load "my file.cif" # quotes required if a space is present >> load "" {1 1 1} # reloads the current file with a different unit >> cell range >> >> Bob >> >> >> >> >> >> >> >> ------------------------------------------------------------------------- >> >> Take Surveys. Earn Cash. Influence the Future of IT >> Join SourceForge.net's Techsay panel and you'll get the chance to >> share your >> opinions on IT & business topics through brief surveys -- and earn cash >> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >> >> _______________________________________________ >> Jmol-users mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > > |
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From: Bob H. <ha...@st...> - 2006-09-25 20:18:35
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This is the sort of thing I built the new data command for. Customizable data sets. Let's think about that. Alan Hewat wrote: >Angel, thanks for pointing me to this table, which seems very complete. >Tomorrow I will check how the ionic radius changes when I change the >valence specified in the CIF file. Perhaps it is to do with file formats >as you suggest. >Alan. > >Angel Herraez said: > > >>Alan, check values not in radii.xls, but in the source, >>http://svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/viewer/JmolConstants.java?view=markup >>that's where Jmol takes them from. >> >>Maybe something changed along versions (it shouldn't, I think). I'll try >>to see my periodic table >>using 10.9.... no, it's got the same aspect. I think it must be a question >>of file formats (pdb, mol) specifying charges in different ways >> >> >_____________________________________________________________ >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/ >_____________________________________________________________ > > >------------------------------------------------------------------------- >Take Surveys. Earn Cash. Influence the Future of IT >Join SourceForge.net's Techsay panel and you'll get the chance to share your >opinions on IT & business topics through brief surveys -- and earn cash >http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > |
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From: Alan H. <he...@il...> - 2006-09-25 20:11:23
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Angel, thanks for pointing me to this table, which seems very complete. Tomorrow I will check how the ionic radius changes when I change the valence specified in the CIF file. Perhaps it is to do with file formats as you suggest. Alan. Angel Herraez said: > Alan, check values not in radii.xls, but in the source, > http://svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/viewer/JmolConstants.java?view=markup > that's where Jmol takes them from. > > Maybe something changed along versions (it shouldn't, I think). I'll try > to see my periodic table > using 10.9.... no, it's got the same aspect. I think it must be a question > of file formats (pdb, mol) specifying charges in different ways _____________________________________________________________ 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/ _____________________________________________________________ |
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From: Bob H. <ha...@st...> - 2006-09-25 19:58:47
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Try the file, and if you can't color partialCharges then let me know. Bob rspinney wrote: >I think your method works well. Will it support other files formats which >include partial charges? > >Rick Spinney > > > >------------------------------------------------------------------------- >Take Surveys. Earn Cash. Influence the Future of IT >Join SourceForge.net's Techsay panel and you'll get the chance to share your >opinions on IT & business topics through brief surveys -- and earn cash >http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > |
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From: Bob H. <ha...@st...> - 2006-09-25 19:57:28
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Comments appreciated on the D/T colors now at http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/new.htm These are the light yellow variety. Bob |
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From: Bob H. <ha...@st...> - 2006-09-25 19:55:59
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feature request. Alan Hewat wrote: >I found Bob's table radii.xls and notice that if you ask for "spacefill ionic" jmol tries to use the ionic radius for the valence state listed in the CIF file. If it doesn't find that valence state in the table, it apparently uses the van der Waals radius. Since radii.xls only contains one valence state for each atom, jmol will sometimes fail to find the appropriate ionic radius and use instead a mixture of ionic and very different van der Waals radii. > >1) Can we eventually use our own table of radii ? >2) If jmol doesn't find the right valence state in the table, perhaps it should use the radius for a neighbouring valence state rather than the van der Waals radius ? >3) I will try to suggest a more complete table of empirical ionic radii with the help of I.David Brown. > >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/ >_____________________________________________________________ > > >------------------------------------------------------------------------- >Take Surveys. Earn Cash. Influence the Future of IT >Join SourceForge.net's Techsay panel and you'll get the chance to share your >opinions on IT & business topics through brief surveys -- and earn cash >http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > |
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From: Bob H. <ha...@st...> - 2006-09-25 19:55:34
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feature request Alan Hewat wrote: >Eric Martz wrote: > > >>I am unable to do a pure zoom without inadvertantly rotating around Z. Frustrating! >> >> > >PC middle-mouse dragging works fine in 10.9.65 with little/no interaction between zoom and z-rotation. >But on the same subject, it would be nice if dragging left+right buttons would do x-y displacements (in addition to Ctrl-Alt-drag). >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/ >_____________________________________________________________ > > >------------------------------------------------------------------------- >Take Surveys. Earn Cash. Influence the Future of IT >Join SourceForge.net's Techsay panel and you'll get the chance to share your >opinions on IT & business topics through brief surveys -- and earn cash >http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > |
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From: Angel H. <ang...@ua...> - 2006-09-25 19:27:59
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Alan, check values not in radii.xls, but in the source, http://svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/viewer/JmolConstants.java?vie w=markup that's where Jmol takes them from. Maybe something changed along versions (it shouldn't, I think). I'll try to see my periodic table using 10.9.... no, it's got the same aspect. I think it must be a question of file formats (pdb, mol) specifying charges in different ways |
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From: Bob H. <ha...@st...> - 2006-09-25 19:15:48
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let me know if you think this is not working correctly. Phillip Barak wrote: >----- Original Message ----- >From: Alan Hewat <he...@il...> > > >>Angel, that is a beautiful illustration in 10.00.36. In particular it >>shows Mn+++ smaller than O-- and N--- But when I draw Hollandite >>(NH4)Mn8O16 with ionic radii in 10.9.65 >>http://icsd.ill.fr/icsd/cifdraw.php?&id[]=38457 >>the Mn+++ are more than twice the size of the other ions. I assume >>thatthis is because Mn+++ is not listed in radii.xls so I suppose >>that jmol >>defaults to van de Waals (or neutral atoms?). >> >> > >Alan, the code for Mn+++ is in JmolConstants.java, as Angel says: > > 919 (25 << 4) + (2 + 4), // 25,2,0.8,"Mn" > 920 (25 << 4) + (3 + 4), // 25,3,0.66,"Mn" > 921 (25 << 4) + (4 + 4), // 25,4,0.6,"Mn" > 922 (25 << 4) + (7 + 4), // 25,7,0.46,"Mn" > > > >>Phillip, if you used Shannon's ionic radii that should be fine, but >>in the >>table radii.xls I only saw one valence state listed for each ion. >> >> > >I'm looking at a file, crystal_ionic-radii.xls, that was distributed >with the src code, at least in previous versions of Jmol, and it has >multiple oxidation states for ions...that was the purpose of adding >ionic radii, of course, to improve autobonding of inorganic substances >and to make spacefill ionic possible. > > > >>In fact it would be possible to calculate the Brown-Shannon valence >>sumfrom the interatomic distances and adjust the ionic radius >>appropriatelyfor each ion for a given structure, but maybe this can >>be left to jmol >>12.00 :-) Jmol 11.00 is pretty complete as it is. >> >> > >We too left the calculation of the coordination number--and the use of >the Shannon radii--until a later date :-) > >--Phillip Barak > > > > > >------------------------------------------------------------------------- >Take Surveys. Earn Cash. Influence the Future of IT >Join SourceForge.net's Techsay panel and you'll get the chance to share your >opinions on IT & business topics through brief surveys -- and earn cash >http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > |
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From: Bob H. <ha...@st...> - 2006-09-25 19:14:31
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for ionic not found, we could default to the closest known ion charge -- at least X 3+ will be small, if not small enough, if X 2+ is present. Angel Herraez wrote: >Alan, > > > >>I found Bob's table radii.xls and notice that if you ask for "spacefill ionic" >>jmol tries to use the ionic radius for the valence state listed in >>the CIF file. If it doesn't find that valence state in the table, >>it apparently uses the van der Waals radius. Since radii.xls only >>contains one valence state for each atom, jmol will sometimes fail >>to find the appropriate ionic radius and use instead a mixture of >>ionic and very different van der Waals radii. >> >> > >My recollection (may be wrong) was that atomic radius is used, not >vdW, if the ionic state is not found. I haven't checked it, though. >Take a look at >http://biomodel.uah.es/jmol/radii/jmol_radii.en.html >which may be of help to you. > >I also think there is provision for more than one ionic state per >element (as shown in the periodic table above) > > > >------------------------------------------------------------------------- >Take Surveys. Earn Cash. Influence the Future of IT >Join SourceForge.net's Techsay panel and you'll get the chance to share your >opinions on IT & business topics through brief surveys -- and earn cash >http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > |
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From: Phillip B. <pw...@wi...> - 2006-09-25 19:12:19
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----- Original Message ----- From: Alan Hewat <he...@il...> > > Angel, that is a beautiful illustration in 10.00.36. In particular it > shows Mn+++ smaller than O-- and N--- But when I draw Hollandite > (NH4)Mn8O16 with ionic radii in 10.9.65 > http://icsd.ill.fr/icsd/cifdraw.php?&id[]=38457 > the Mn+++ are more than twice the size of the other ions. I assume > thatthis is because Mn+++ is not listed in radii.xls so I suppose > that jmol > defaults to van de Waals (or neutral atoms?). Alan, the code for Mn+++ is in JmolConstants.java, as Angel says: 919 (25 << 4) + (2 + 4), // 25,2,0.8,"Mn" 920 (25 << 4) + (3 + 4), // 25,3,0.66,"Mn" 921 (25 << 4) + (4 + 4), // 25,4,0.6,"Mn" 922 (25 << 4) + (7 + 4), // 25,7,0.46,"Mn" > Phillip, if you used Shannon's ionic radii that should be fine, but > in the > table radii.xls I only saw one valence state listed for each ion. I'm looking at a file, crystal_ionic-radii.xls, that was distributed with the src code, at least in previous versions of Jmol, and it has multiple oxidation states for ions...that was the purpose of adding ionic radii, of course, to improve autobonding of inorganic substances and to make spacefill ionic possible. > In fact it would be possible to calculate the Brown-Shannon valence > sumfrom the interatomic distances and adjust the ionic radius > appropriatelyfor each ion for a given structure, but maybe this can > be left to jmol > 12.00 :-) Jmol 11.00 is pretty complete as it is. We too left the calculation of the coordination number--and the use of the Shannon radii--until a later date :-) --Phillip Barak > |
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From: Bob H. <ha...@st...> - 2006-09-25 19:11:16
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Rolf Huehne wrote: >Bob Hanson wrote: > > >>OK, First thing I saw when I opened a console: >> >>FileManager opening >>http://moleculesinmotion.com/Jmol10962/authored/scripts/all_off.spt >>ScriptException:SET ECHO must follow, not precede, model loading >> Script line:set echo off >> File:authored/scripts/all_off.spt Line number:44 >> >>Are you trying to put out an echo message to the blank applet before >>loading a molecule? This we cannot do (because there is no "frame" to >>hold the echo information). >> >> >> >> >This used to work with older versions like 10.00.36 or 10.2. > > I don't think so. Have you tried it? This is a fundamental limitation of echo that has been around forever. Without a model loaded there cannot be an Echo object (currently). I assure you, if there is no model loaded, there is no Frame object, and absolutely nothing -- not even the Jmol frank -- is put to the screen. The only thing that is different now is that you get a message saying that it won't work. If you want to send your web page a message, you can use the "message" command, but not the "echo" command. >I guess it has something to do with the new capabilities of the 'echo' >command. Although I think these capabilities might be useful, it will be >a major drawback if one can't display any more a message prior to >loading. Especially loading large or multiple frame structures can take >quite a while and the user tends to be impatient if nothing happens for >a while... > > Enter this as a feature request, please. I certainly think it could be useful. >Q: Wouldn't it be possible to retain a (supplementary) basic 'echo' >command like that in older versions that allows placing something like a >"Please Wait..." message before loading? > > > Maybe Version 9 had this --- certainly not 10. Miguel? >Regards, >Rolf > >------------------------------------------------------------------------- >Take Surveys. Earn Cash. Influence the Future of IT >Join SourceForge.net's Techsay panel and you'll get the chance to share your >opinions on IT & business topics through brief surveys -- and earn cash >http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > |
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From: Bob H. <ha...@st...> - 2006-09-25 19:00:25
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Jmol users interested in using Jmol for more than viewing:
I have added some new command-line options.
What do you think of this? (Using the applicatoin from a Windows command prompt)
Create a JVXL file directly
---------------------------
Jmol -ionx iso.spt myfile.xyz > myfile.jvxl
where:
-i,--silent silent startup operation
-o,--noconsole no console -- all output to sysout
-n,--nodisplay no display (much faster)
-x,--exit run script and exit
iso.spt is:
isosurface solvent;show isosurface
creates a JVXL solvent surface file.
Create a JVXL file directly
---------------------------
Jmol -ionx mo.spt myfile.xyz > myfile.jvxl
where mo.spt is:
mo 12; show mo
creates a JVXL file of the 12th MO.
Create a list of measurements
-----------------------------
Jmol -ionx measure.spt myfile.xyz > measure.txt
where measure.spt is:
measure allconnected (*) (*);show measurements
generates a list of measurements.
measure.txt now contains (tab-separated):
Measurement Information
distance 1.1217928 0.112 nm H 1 #1 C 10 #10
distance 1.4158994 0.142 nm N 2 #2 C 6 #6
distance 1.3865448 0.139 nm N 2 #2 C 7 #7
...
Anything that can be "shown" can be dumped to a file this way.
Check CIF file symmetry
-----------------------
Jmol -ionx symmetry.spt myfile.cif > symmetry.txt
where symmetry.spt is:
show unitcell;show symmetry;show spacegroup;
symmetry.txt now contains:
a=9.8737, b=9.8737, c=2.8518999, alpha=90.0, beta=90.0, gamma=90.0
Symmetry Information:
model #1; name=75539-ICSD
Spacegroup: I 4/m
Number of symmetry operations: 16
Symmetry Operations:
x,y,z
-y,x,-z
y,-x,-z
x,y,-z
-x,-y,-z
y,-x,z
-y,x,z
-x,-y,z
-y+1/2,x+1/2,-z+1/2
y+1/2,-x+1/2,-z+1/2
x+1/2,y+1/2,-z+1/2
-x+1/2,-y+1/2,-z+1/2
y+1/2,-x+1/2,z+1/2
-y+1/2,x+1/2,z+1/2
-x+1/2,-y+1/2,z+1/2
x+1/2,y+1/2,z+1/2
Hermann-Mauguin symbol: I 4/m
international table number: 87
Hall symbol: -I 4
primitive Hall symbol: P 4z 1n -1
lattice type: -I: centrosymmetric body-centered
rotation term 1
input code: 4; primitive code: 4z
order: 4; axisType: z
operator: -y,x,z
Seitz matrix:
{ 0 -1 0 0 }
{ 1 0 0 0 }
{ 0 0 1 0 }
{ 0 0 0 1 }
etc., etc.
Here's a list of the SHOW command options that might be of particular
interest:
show file
show isosurface
show measurements
show mo
show model
show pdbheader
show spacegroup
show symmetry
show unitcell
oh, and anything you can get from getProperty will do the same:
getProperty fileContents
------------------------
getproperty fileContents "http://www.rcsb.org/pdb/files/1DPO.pdb"
saves 1DPO.pdb on your hard drive.
getProperty auxiliaryInfo
-------------------------
auxiliaryinfo {
someModelsHaveFractionalCoordinates true,
someModelsHaveSymmetry true,
someModelsHaveUnitcells true,
models [{
symmetryOperations
["x,y,z","-y,x,-z","y,-x,-z","x,y,-z","-x,-y,-z","y,-x,z","-y,x,z","-x,-y,z","-y+1/2,x+1/2,-z+1/2","y+1/2,-x+1/2,-z+1/2","x+1/2,y+1/2,-z+1/2","-x+1/2,-y+1/2,-z+1/2","y+1/2,-x+1/2,z+1/2","-y+1/2,x+1/2,z+1/2","-x+1/2,-y+1/2,z+1/2","x+1/2,y+1/2,z+1/2"],
structuralFormula "(N H4) Mn8 O16",
symmetryCount 16,
presymmetryAtomCount 4,
presymmetryAtomIndex 0,
formula "H4 Mn8 N1 O16",
notionalUnitcell
[9.8737,9.8737,2.8518999,90.0,90.0,90.0,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN],
spaceGroup "I 4/m",
chemicalName "Ammonium manganese oxide (1/8/16)",
coordinatesAreFractional true,
latticeDesignation ""
}]
}
getProperty atomInfo
--------------------
element "hydrogen"
visible true
model 1
radius 0.5
visibilityFlags 13
clickabilityFlags 12
bondCount 1
atomno 1
elemno 1
z 0.0
y 0.0
x 2.4571667
You get the idea. I just uploaded the code; coming in 10.9.66; suggestions?
Bob
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From: Alan H. <he...@il...> - 2006-09-25 18:41:59
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Angel Herraez said: > My recollection (may be wrong) was that atomic radius is used, not > vdW, if the ionic state is not found. I haven't checked it, though. > Take a look at > http://biomodel.uah.es/jmol/radii/jmol_radii.en.html Angel, that is a beautiful illustration in 10.00.36. In particular it shows Mn+++ smaller than O-- and N--- But when I draw Hollandite (NH4)Mn8O16 with ionic radii in 10.9.65 http://icsd.ill.fr/icsd/cifdraw.php?&id[]=38457 the Mn+++ are more than twice the size of the other ions. I assume that this is because Mn+++ is not listed in radii.xls so I suppose that jmol defaults to van de Waals (or neutral atoms?). Phillip, if you used Shannon's ionic radii that should be fine, but in the table radii.xls I only saw one valence state listed for each ion. In fact it would be possible to calculate the Brown-Shannon valence sum from the interatomic distances and adjust the ionic radius appropriately for each ion for a given structure, but maybe this can be left to jmol 12.00 :-) Jmol 11.00 is pretty complete as it is. 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/ _____________________________________________________________ |
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From: Alan H. <he...@il...> - 2006-09-25 17:39:02
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Bob Hanson said:
> load hollandite.cif {3 3 3};restrict cell=666;unitcell {1 1 1}
> select cell=666 and not _N;
> isosurface delete select(selected) ignore(not selected and cell=666)
> solvent 0.0
Yep. I got that too when I excluded N. But I would like to see some space
when I didn't exclude N. There are holes for unlocated H around that N.
Thanks for the explanation of the +x.x.
> we could just add
> vdw xx%
Yes, that would be useful, or even better to be able to use the ionic
radii (see later).
Many thanks. 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/
_____________________________________________________________
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