From: Brenton H. <bre...@gm...> - 2013-04-08 12:56:13
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I have installed Jmol from the sh file, but for some reason the implicit hydrogens are hidden in my models. I have "Show Hydrogens" enabled (i.e. the box ticked) under Style->Atoms menu that appears on right clicking the molecule. How do I overcome this problem? I am running Ubuntu 12.10 32 bit, with OpenJDK Java 6 as my Java platform. |
From: Robert H. <ha...@st...> - 2013-04-08 14:32:39
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Brenton, "showHydrogens" are for *explicit* hydrogens. If you want Jmol to attempt to calculate implicit hydrogens you can try from the console: calculate hydrogen A better alternative, if this is a PDB file is: set pdbAddHydrogens TRUE which will automatically add hydrogen atoms and multiple bonding when a PDB file is loaded, fetching the necessary ligand files to determine bonding in ligands. Bob Hanson On Mon, Apr 8, 2013 at 7:56 AM, Brenton Horne <bre...@gm...>wrote: > I have installed Jmol from the sh file, but for some reason the implicit > hydrogens are hidden in my models. I have "Show Hydrogens" enabled (i.e. > the box ticked) under Style->Atoms menu that appears on right clicking the > molecule. How do I overcome this problem? I am running Ubuntu 12.10 32 bit, > with OpenJDK Java 6 as my Java platform. > > > ------------------------------------------------------------------------------ > Minimize network downtime and maximize team effectiveness. > Reduce network management and security costs.Learn how to hire > the most talented Cisco Certified professionals. Visit the > Employer Resources Portal > http://www.cisco.com/web/learning/employer_resources/index.html > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > 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 |
From: Brenton H. <bre...@gm...> - 2013-04-08 21:04:42
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How do I place these commands into the console? I opened the console via going to the help menu but when I type what you have said and click "Enter" nothing happens. On Tue, Apr 9, 2013 at 12:32 AM, Robert Hanson <ha...@st...> wrote: > Brenton, > > "showHydrogens" are for *explicit* hydrogens. If you want Jmol to attempt > to calculate implicit hydrogens you can try from the console: > > calculate hydrogen > > A better alternative, if this is a PDB file is: > > set pdbAddHydrogens TRUE > > which will automatically add hydrogen atoms and multiple bonding when a > PDB file is loaded, fetching the necessary ligand files to determine > bonding in ligands. > > Bob Hanson > > > > > > > On Mon, Apr 8, 2013 at 7:56 AM, Brenton Horne <bre...@gm...>wrote: > >> I have installed Jmol from the sh file, but for some reason the implicit >> hydrogens are hidden in my models. I have "Show Hydrogens" enabled (i.e. >> the box ticked) under Style->Atoms menu that appears on right clicking the >> molecule. How do I overcome this problem? I am running Ubuntu 12.10 32 bit, >> with OpenJDK Java 6 as my Java platform. >> >> >> ------------------------------------------------------------------------------ >> Minimize network downtime and maximize team effectiveness. >> Reduce network management and security costs.Learn how to hire >> the most talented Cisco Certified professionals. Visit the >> Employer Resources Portal >> http://www.cisco.com/web/learning/employer_resources/index.html >> _______________________________________________ >> Jmol-users mailing list >> Jmo...@li... >> 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 > > > > ------------------------------------------------------------------------------ > Minimize network downtime and maximize team effectiveness. > Reduce network management and security costs.Learn how to hire > the most talented Cisco Certified professionals. Visit the > Employer Resources Portal > http://www.cisco.com/web/learning/employer_resources/index.html > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > |
From: A. H. <ang...@ua...> - 2013-04-08 21:48:08
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Hi Brenton You need the script console, not the Java console (that's only for seeing errors and such). It's on the File menu (top bar), or in the popup meny (right-click) > How do I place these commands into the console? See e.g. http://wiki.jmol.org/index.php/The_Toolbar |
From: Michael P. <mpa...@wi...> - 2013-04-08 22:51:22
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Is there a way to selectively show implicit hydrogens in just one or a few amino acids? Michael Patrick UW-Madison >Brenton, > >"showHydrogens" are for explicit hydrogens. If you want Jmol to >attempt to calculate implicit hydrogens you can try from the console: > >calculate hydrogen > >A better alternative, if this is a PDB file is: > >set pdbAddHydrogens TRUE > >which will automatically add hydrogen atoms and multiple bonding >when a PDB file is loaded, fetching the necessary ligand files to >determine bonding in ligands. > >Bob Hanson > > > > > > >On Mon, Apr 8, 2013 at 7:56 AM, Brenton Horne ><<mailto:bre...@gm...>bre...@gm...> wrote: > >I have installed Jmol from the sh file, but for some reason the >implicit hydrogens are hidden in my models. I have "Show Hydrogens" >enabled (i.e. the box ticked) under Style->Atoms menu that appears >on right clicking the molecule. How do I overcome this problem? I am >running Ubuntu 12.10 32 bit, with OpenJDK Java 6 as my Java platform. > >------------------------------------------------------------------------------ >Minimize network downtime and maximize team effectiveness. >Reduce network management and security costs.Learn how to hire >the most talented Cisco Certified professionals. Visit the >Employer Resources Portal ><http://www.cisco.com/web/learning/employer_resources/index.html>http://www.cisco.com/web/learning/employer_resources/index.html >_______________________________________________ >Jmol-users mailing list ><mailto:Jmo...@li...>Jmo...@li... ><https://lists.sourceforge.net/lists/listinfo/jmol-users>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>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 > > >------------------------------------------------------------------------------ >Minimize network downtime and maximize team effectiveness. >Reduce network management and security costs.Learn how to hire >the most talented Cisco Certified professionals. Visit the >Employer Resources Portal >http://www.cisco.com/web/learning/employer_resources/index.html > >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users |
From: A. H. <ang...@ua...> - 2013-04-08 22:58:34
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Michael, it's in the doc: http://chemapps.stolaf.edu/jmol/docs/#calculate calculate HYDROGENS [atom-expression]{default: *} Adds hydrogens at calculated positions based on bonding patterns at the designated atoms or, if no atoms are specified, at all atoms. Note that this command is not intended to be used for the assignment of hydrogen atoms in proteins. In order to work, all atoms must have any formal charges already designated, and all multiple bonds must be in place. |