Re: [Jmol-users] Electron density maps in Jmol
One more thing: These files contain multiple surfaces. Just like other isosurfaces, you can select one of them out: isosurface OBJ sample.obj 3 In this case, though, if you leave the number out, you get all of them. Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 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 -- Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise -Strategies to boost innovation and cut costs with open source participation -Receive a $600 discount off the registration fee with the source code: SFAD http://p.sf.net/sfu/XcvMzF8H___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Electron density maps in Jmol
ok, that's in. I'll upload a version later this morning. These can be saved as JVXL files with a space savings of about 75%. use the OBJ keyword prior to the file name: isosurface OBJ sample.obj See attached image. Note that these can be mapped with values from another function, just like isosurface PMESH. On Thu, Feb 19, 2009 at 11:16 AM, Robert Hanson hans...@stolaf.edu wrote: Eran, I see the format described at http://www.eg-models.de/formats/Format_Obj.html It's almost a pmesh file. It would be simple enough to get Jmol to read that format using the isosurface PMESH or just the pmesh command itself. We might have to ignore a few things (texture, normals, larger polygons. Have an example file I can play with? Bob On Thu, Feb 19, 2009 at 10:30 AM, Eran Hodis eranho...@gmail.com wrote: I see. Jmol can export 3D object files such as VRML -- can it read any of these files as well? (I'm thinking that maybe I can convert my Wavefront object file into one of these filetypes and then load it into Jmol, if possible) Eran On Thu, Feb 19, 2009 at 3:48 PM, Robert Hanson hans...@stolaf.eduwrote: I have no idea... On Thu, Feb 19, 2009 at 9:46 AM, Eran Hodis eranho...@gmail.com wrote: Hi Bob, In our case it's a Wavefront object file. Eran On Thu, Feb 19, 2009 at 3:37 PM, Robert Hanson hans...@stolaf.eduwrote: obj could be anything. What is it? Electron density: I've worked out a preliminary version of electron density plotting and mapping in Jmol. It's pretty slow, because all of the occupied MOs have to be scanned. But it does work at least for RHF. I have it ignoring d and f orbitals. Bob On Thu, Feb 19, 2009 at 6:33 AM, Eran Hodis eranho...@gmail.comwrote: Thanks Bob! Another question for anyone who may know: I have a .obj file that I would like to visualize in Jmol. Is anyone aware of a way to do this (possibly by first converting it to a different format that Jmol can read)? Thanks for the help. Eran I for one would like to display isodensity surfaces for wave functions calculated with the GAMESS-US program. Jan Egon -- http://chem-bla-ics.blogspot.com/ -- Create and Deploy Rich Internet Apps outside the browser with Adobe(R)AIR(TM) software. With Adobe AIR, Ajax developers can use existing skills and code to build responsive, highly engaging applications that combine the power of local resources and data with the reach of the web. Download the Adobe AIR SDK and Ajax docs to start building applications today- http://p.sf.net/sfu/adobe-com ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Jan H. Jensen Associate Research Professor Department of Chemistry jhjen...@kemi.ku.dk University of CopenhagenPhone: +45 35 32 02 39 Universitetsparken 5FAX: +45 35 32 02 14 2100 Copenhagen Denmark http://propka.ki.ku.dk/~jhjensenhttp://propka.ki.ku.dk/%7Ejhjensen =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- -- Create and Deploy Rich Internet Apps outside the browser with Adobe(R)AIR(TM) software. With Adobe AIR, Ajax developers can use existing skills and code to build responsive, highly engaging applications that combine the power of local resources and data with the reach of the web. Download the Adobe AIR SDK and Ajax docs to start building applications today- http://p.sf.net/sfu/adobe-com ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Create and Deploy Rich Internet Apps outside the browser with Adobe(R)AIR(TM) software. With Adobe AIR, Ajax developers can use existing skills and code to build responsive, highly engaging applications that combine the power of local resources and data with the reach of the web. Download the Adobe AIR SDK and Ajax docs to start building applications today- http://p.sf.net/sfu/adobe-com ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 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
Re: [Jmol-users] Bonds not showing in Jmol 11.6 (Angel Herraez)
Thanks, Angel. I checked over the alignment of the pdb data and, though there wasn't anything obviously wrong, deleting some unnecessary data solved the problem. I wonder why Jmol 11.2 was happy with the data as it was, but Jmol 11.4 and 11.6 didn't like it? Thanks again Ewen -Original Message- From: jmol-users-requ...@lists.sourceforge.net [mailto:jmol-users-requ...@lists.sourceforge.net] Sent: 13 February 2009 16:20 To: jmol-users@lists.sourceforge.net Subject: Jmol-users Digest, Vol 33, Issue 19 Send Jmol-users mailing list submissions to jmol-users@lists.sourceforge.net To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/jmol-users or, via email, send a message with subject or body 'help' to jmol-users-requ...@lists.sourceforge.net You can reach the person managing the list at jmol-users-ow...@lists.sourceforge.net When replying, please edit your Subject line so it is more specific than Re: Contents of Jmol-users digest... Today's Topics: 1. Re: script [file-name] LINE n (Robert Hanson) 2. Mac OS X (Amal CHLYEH) 3. Re: Mac OS X (Egon Willighagen) 4. Re: Bonds not showing in Jmol 11.6 (Angel Herraez) 5. Re: Mac OS X (Amal CHLYEH) 6. Re: Mac OS X (Angel Herraez) 7. Re: Mac OS X (Rolf Huehne) 8. Re: Mac OS X (Egon Willighagen) 9. Re: Mac OS X (Paul Pillot) -- Message: 1 Date: Fri, 13 Feb 2009 08:11:13 -0600 From: Robert Hanson hans...@stolaf.edu Subject: Re: [Jmol-users] script [file-name] LINE n To: jmol-users@lists.sourceforge.net Message-ID: ba9c0bd60902130611y5cb0c598r18d991d45206c...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 script myfile.spt LINES 1 - 100 On Fri, Feb 13, 2009 at 6:02 AM, Jan H. Jensen jhjen...@kemi.ku.dk wrote: script [file-name] LINE n seems to only execute line n, rather than starting the script at line n. Is there a way to invoke the latter? Best regards, Jan -- =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Jan H. Jensen Associate Research Professor Department of Chemistry jhjen...@kemi.ku.dk University of CopenhagenPhone: +45 35 32 02 39 Universitetsparken 5FAX: +45 35 32 02 14 2100 Copenhagen Denmark http://propka.ki.ku.dk/~jhjensen http://propka.ki.ku.dk/%7Ejhjensen =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- -- Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise -Strategies to boost innovation and cut costs with open source participation -Receive a $600 discount off the registration fee with the source code: SFAD http://p.sf.net/sfu/XcvMzF8H ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 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 -- next part -- An HTML attachment was scrubbed... -- Message: 2 Date: Fri, 13 Feb 2009 14:03:24 +0100 From: Amal CHLYEH am.chl...@gmail.com Subject: [Jmol-users] Mac OS X To: jmol-users@lists.sourceforge.net Message-ID: 337706c6-4f0e-41ab-94c4-89250782b...@gmail.com Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Bonjour, je voudrais utiliser un ligiciel de visualisation des mol?cules en 3D mais je ne trouve rien qui puisse aller avec Mac OS X. Pouvez vous m'indiquer un site o? je pourrai trouver cela ? D'avance merci Pr. Amal CHLYEH Universit? Cadi Ayyad Facult? des Sciences MarrakechMAROC -- Ce message a ?t? v?rifi? par MailScanner pour des virus ou des polluriels et rien de suspect n'a ?t? trouv?. MailScanner remercie transtec pour son soutien. -- Message: 3 Date: Fri, 13 Feb 2009 15:30:17 +0100 From: Egon Willighagen egon.willigha...@gmail.com Subject: Re: [Jmol-users] Mac OS X To: jmol-users@lists.sourceforge.net Message-ID: 6aeb064b0902130630t38b8b9edg567653707d142...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi Amal, 2009/2/13 Amal CHLYEH am.chl...@gmail.com: je voudrais utiliser un ligiciel de visualisation des mol?cules en 3D mais je ne trouve rien qui puisse aller avec Mac OS X. Pouvez vous m'indiquer un site o? je pourrai trouver cela ? Jmol should not have trouble to run on OS/X; we have been using it inside Bioclipse for a long
[Jmol-users] Vibrations in Jmol
I would like to use the scale factor for vibrations to demonstrate the classical turning points of a vibration. I am not sure how to read the documentation: Adjusts the scale of the vector independently of the vibration motion Does a scale factor of 1.0 simply scale each vector by 1.0, or is each atom displaced one unit in the direction of each vector? Are the vectors scaled by the inverse square root of the atomic mass (technically needed to make the units come out right, but rarely done). Best regards, Jan -- =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Jan H. Jensen Associate Research Professor Department of Chemistry jhjen...@kemi.ku.dk University of CopenhagenPhone: +45 35 32 02 39 Universitetsparken 5FAX: +45 35 32 02 14 2100 Copenhagen Denmark http://propka.ki.ku.dk/~jhjensen =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- -- Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise -Strategies to boost innovation and cut costs with open source participation -Receive a $600 discount off the registration fee with the source code: SFAD http://p.sf.net/sfu/XcvMzF8H ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Bonds not showing in Jmol 11.6 (Angel Herraez)
Folks, Please don't send the entire list digest as part of your reply to the list. Thanks, Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 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 -- Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise -Strategies to boost innovation and cut costs with open source participation -Receive a $600 discount off the registration fee with the source code: SFAD http://p.sf.net/sfu/XcvMzF8H___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
