Re: [Jmol-users] visualizing molecular orbitals in molden format
Thanks a lot, Bob ! This is working nicely :-) Best, Max On 13. 05. 13 00:13, Robert Hanson wrote: OK, the Molden reader should work up to orbital type i. (Untested past g.) Anything past f will be ignored. Assumptions here: type spherical/cartesian: G 9/15, H 11/21, I 13/28 (all ignored) http://chemapps.stolaf.edu/jmol/jmol-13.1.16_2013.05.12a.zip Bob On Sun, May 12, 2013 at 12:41 PM, Latévi Max LAWSON DAKU max.law...@unige.ch mailto:max.law...@unige.ch wrote: Dear Bob, I have been able to generate an input file, in molden format, which can be viewed with molden/gmolden-5.0 (geometry and MOs). Trying to open it with Jmol-13.0.14 fails with the following error message script ERROR: Error reading file at line 442: g 2 1.00 8 for file /tmp/molden.inp type Molden load molden.inp which may correspond to the fact that g functions are not supported. Do you have time to look at this ? If so, the file, compressed, (molden.inp.gz) can be downloaded at the following address This file (molden.inp.gz) can be found at the a http://dl.free.fr/muBvAUeyr All the best, Max On 03. 05. 13 14:47, Robert Hanson wrote: On Thu, May 2, 2013 at 2:40 PM, Latévi Max LAWSON DAKU max.law...@unige.ch mailto:max.law...@unige.ch wrote: On 02. 05. 13 19:34, Robert Hanson wrote: Max, Dear Bob, I thank you a lot for your kind reply. Well, there are a couple problems with the Malden reader -- requiring no blank line after [GTO] is an easy fix; g orbitals not implemented (easily fixed). Maybe a bigger issue (not solvable, probably). Q: Are you OK with ignoring the g orbitals? Yes. They should contribute little to the molecular orbitals, which I am interested in. Actually, if proceeding so, would it possible to ignore 'h' and 'i' functions as well ? sure. What are the number of orbitals in h/i cartesian/spherical sets? There seems to be something I'm missing. There are only 492 listed MO coefficients, but there are 711 listed atomic orbitals. 711 = 166 s + 84 p(x3) + 34 d(x5) + 15 f(x7) + 2 g(x10) Those numbers should match. (NEED to match.) Q: So what is 492? This really is the number of basis functions: the basis set is made of 492 contracted Gaussian functions, consisting each in a linear combination of some of the 711 primitive Gaussian functions. I guess that the manner in which the MOs are listen takes the contractions into account. I don't see it. Please explain this particular file set in detail. There 301 Gaussian sets listed, not 492. 301 = 166 s + 84 p + 34 d + 15 f + 2 g For example: s 22 1.00 4316265.0001.00 646342.4000.00 147089.7000.00 41661.5200.00 13590.7700.00 4905.7500.00 1912.746 tel:1912.7460.00 792.60430000.00 344.80650000.00 155.89990000.00 72.23091000.00 32.72506000.00 15.66762000.00 7.50348300.00 4.68440000.00 3.31222300.00 1.55847100.00 1.22040000.00 0.68391400.00 0.14675700.00 0.07058300.00 0.03144900.00 Each set may have more than one directional component, thus we have total number of independent coefficients: 711 = 166 s + 84 p(x3) + 34 d(x5) + 15 f(x7) + 2 g(x10) How do you figure that there are only 492 MO coefficients? -- Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net mailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now.
Re: [Jmol-users] a new logo-banner-icon for Jmol + JSmol
supreme! On Mon, May 13, 2013 at 5:13 AM, Angel Herráez angel.herr...@uah.es wrote: Hello Jmolers Saturday had an artistic flavor and today I am offering you a set of new Jmol and JSmol logos or banners and an icon for the Jmol application. http://biomodel.uah.es/Jmol/logos/ If you like, you are welcome to use them in your pages. I am proposing this to be the official icon and logo for J(S)mol 13.1, if accepted it will soon go into the website and the Wiki (Home page and Recycling Corner) Enjoy! Angel · Dr. Angel Herráez Bioquímica y Biología Molecular, Dep. Biología de Sistemas, Universidad de Alcalá 28871 Alcalá de Henares (Madrid) -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department 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 -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] a new logo-banner-icon for Jmol + JSmol
Very nice!! Jaim __ Dr Jaime Prilusky Head Bioinformatics RD Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel mail: jaime.prilu...@weizmann.ac.il tel: 972-8-9344959 fax: 972-8-9344113 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) On May 13, 2013, at 1:13 PM, Angel Herráez angel.herr...@uah.es wrote: Hello Jmolers Saturday had an artistic flavor and today I am offering you a set of new Jmol and JSmol logos or banners and an icon for the Jmol application. http://biomodel.uah.es/Jmol/logos/ If you like, you are welcome to use them in your pages. I am proposing this to be the official icon and logo for J(S)mol 13.1, if accepted it will soon go into the website and the Wiki (Home page and Recycling Corner) Enjoy! Angel · Dr. Angel Herráez Bioquímica y Biología Molecular, Dep. Biología de Sistemas, Universidad de Alcalá 28871 Alcalá de Henares (Madrid) --J(S)mol_logos13.png Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] visualizing molecular orbitals in molden format
On 13. 05. 13 12:38, Robert Hanson wrote: My pleasure. It's a fix for 13.0 and 13.1. :-) It so comfortable to use the MO command from the console ;-) A couple of chemistry questions: Q: Why in this Fe(NCH)6 complex are there only 19 occupied orbitals? They look great, but aren't there far more valence electrons? Many of them look like core orbitals. I count at least 60 valence electrons just in HCN. So where are they? (Only 38 electrons accounted for?) There are 107 electrons. The MOs are in fact displayed by blocks, according to their symmetry: Ag orbitals come first, then those of B3u, B2u, B1g, B1u, B2g, B3g and finally Au symmetry (grep Sym molden.inp). This in ok in that the number of MOs of a given symmetry can be read in the main Dalton2011 output. Q: Why are the doubly-occupied orbitals labeled Alpha? Aren't alpha/beta orbitals singly occupied? These MOs are obtained from a restricted-open-shell (actually, ROHF) calculation calculations, and the spin-up and spin-down spinorbitals have the same spatial parts. In this case, as you noticed, the molden driver in Dalton2011 simply outputs the MOs only once, with the right occupation numbers and labeling them Alpha. The Spin= (Alpha|Beta) entry seems required by molden when specifying MOs. Please do not hesitate for any other question you may have. Best, Max Bob On Mon, May 13, 2013 at 2:59 AM, Latévi Max LAWSON DAKU max.law...@unige.ch mailto:max.law...@unige.ch wrote: Thanks a lot, Bob ! This is working nicely :-) Best, Max On 13. 05. 13 00:13, Robert Hanson wrote: OK, the Molden reader should work up to orbital type i. (Untested past g.) Anything past f will be ignored. Assumptions here: type spherical/cartesian: G 9/15, H 11/21, I 13/28 (all ignored) http://chemapps.stolaf.edu/jmol/jmol-13.1.16_2013.05.12a.zip Bob On Sun, May 12, 2013 at 12:41 PM, Latévi Max LAWSON DAKU max.law...@unige.ch mailto:max.law...@unige.ch wrote: Dear Bob, I have been able to generate an input file, in molden format, which can be viewed with molden/gmolden-5.0 (geometry and MOs). Trying to open it with Jmol-13.0.14 fails with the following error message script ERROR: Error reading file at line 442: g 2 1.00 8 for file /tmp/molden.inp type Molden load molden.inp which may correspond to the fact that g functions are not supported. Do you have time to look at this ? If so, the file, compressed, (molden.inp.gz) can be downloaded at the following address This file (molden.inp.gz) can be found at the a http://dl.free.fr/muBvAUeyr All the best, Max On 03. 05. 13 14:47, Robert Hanson wrote: On Thu, May 2, 2013 at 2:40 PM, Latévi Max LAWSON DAKU max.law...@unige.ch mailto:max.law...@unige.ch wrote: On 02. 05. 13 19:34, Robert Hanson wrote: Max, Dear Bob, I thank you a lot for your kind reply. Well, there are a couple problems with the Malden reader -- requiring no blank line after [GTO] is an easy fix; g orbitals not implemented (easily fixed). Maybe a bigger issue (not solvable, probably). Q: Are you OK with ignoring the g orbitals? Yes. They should contribute little to the molecular orbitals, which I am interested in. Actually, if proceeding so, would it possible to ignore 'h' and 'i' functions as well ? sure. What are the number of orbitals in h/i cartesian/spherical sets? There seems to be something I'm missing. There are only 492 listed MO coefficients, but there are 711 listed atomic orbitals. 711 = 166 s + 84 p(x3) + 34 d(x5) + 15 f(x7) + 2 g(x10) Those numbers should match. (NEED to match.) Q: So what is 492? This really is the number of basis functions: the basis set is made of 492 contracted Gaussian functions, consisting each in a linear combination of some of the 711 primitive Gaussian functions. I guess that the manner in which the MOs are listen takes the contractions into account. I don't see it. Please explain this particular file set in detail. There 301 Gaussian sets listed, not 492. 301 = 166 s + 84 p + 34 d + 15 f + 2 g For example: s 22 1.00 4316265.0001.00 646342.4000.00 147089.7000.00 41661.5200.00 13590.7700.00 4905.750
[Jmol-users] [jmol-13.0] behind a corporate fire wall
He all, may someone can tell me how to use Jmol-13.0 behind a corporate firewall which needs some authentication information to reach out and load molecule data from a remote molecule database. I have added to the jmol.bat the following @echo off rem Set JMOL_HOME to the Jmol installation directory. rem set JMOL_HOME=E:\Users\C770817\SW-UMGEBUNG\jmol-13.0.15 if %JMOL_HOME%x==x set JMOL_HOME=. java -Xmx512m %ANT_OPTS% -jar %JMOL_HOME%\Jmol.jar %1 %2 %3 %4 %5 %6 %7 %8 %9 where ANT_OPTS is a Windows Vista environment var ANT_OPTS=-Dhttp.proxyHost=bcproxyserver.ch.my.com -Dhttp.proxyPort=8080 -Dhttp.proxyUser=C770817 -Dhttp.proxyPassword=mypassword -Dhttp.auth.preference=Basic If this information is not passed to our proxy server we can not reach out to remote locations. So Any hints how to make things work OR what option file I missed and have to write to make things work is very welcome. Josef -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] visualizing molecular orbitals in molden format
This version does the energy sorting so that HOMO and LUMO work properly http://chemapps.stolaf.edu/jmol/Jmol-13.zip To NOT sort by energy, add FILTER NOSORT to the load command. You can also select by symmetry using FILTER SYM=AU for example. Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department 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 -- AlienVault Unified Security Management (USM) platform delivers complete security visibility with the essential security capabilities. Easily and efficiently configure, manage, and operate all of your security controls from a single console and one unified framework. Download a free trial. http://p.sf.net/sfu/alienvault_d2d___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
