Joe Ivanic - Contractor & Foreign National/bioanalysis wrote: > Hi, > > I am a quantum chemistry theory and program developer (mainly GAMESS), > plenty of experience with Fortran and C, but none really with Java. My > questions may be very simple but I have to ask them. > > Jmol is fantastic for visualizing almost everything. However, I still > have not found a way to translate a molecule with the mouse. There are > the move, moveto, and translate Jmol commands, however, being able to > move the molecule sideways with the mouse, rather than only rotation and > zoom, helps to accurately focus in on very specific parts of a system. > Is there a way to translate with the mouse?
The mouse manual for Jmol can be found in the Jmol Wiki at "http://wiki.jmol.org/index.php/MouseManual";. > > The above question is asked mainly because I am also using Jmol to > visualize very large networks. So I trick Jmol (with a .gpr file) into > thinking I have lots of atoms (difference for each type of node) and > then specify their connections (with bonds). This has proven very > useful. Being able to translate, though, would make network > visualization and "navigation" that much better. Being able to select a > node (atom) with the mouse, or script, and then recentering the network > (molecule) about this node would also be extremely useful, very similar > to the free translation. You can center around the currently selected atoms (nodes) by using this command: center selected; Or center around a specific atom by this one: center atomno=10; A detailed description can be found in the Jmol scripting manual at "http://chemapps.stolaf.edu/jmol/docs/";. > > My last query is about the labeling of the nodes (atoms). There is the > script command "label" which can do this very efficiently. However, > being able to have the pointer on top of a node (or atom) and then > automatically include showing of the label (not the atom, e.g. H, Li, > rather a string label) would be nice. I'm not sure how to do this within > Jmol. It seems to have the flexiblity to have an "atom name" shown, > rather than an "atom label" but I am not able to figure out just how to > accomplish this. Certainly not within the .gpr format anyway. Typing an > atom label (node label) into the script window, with the relevant > command, and this being highlighted would also be extremely useful. I > guess I am asking if we can input other types of nodes, rather than just > atoms, into Jmol. > I guess what you mean is something that is called "hover" in Jmol: a label that appears if the mouse rests a while on top of an atom (node). You can activate this and determine what is shown (but only globally, not individually) by the following command: hover "Node=%a" This would display the text "Node=" plus the individual atom name of the atom. The command is described also in the Jmol scripting manual at "http://chemapps.stolaf.edu/jmol/docs/?ver=11.2#hover";. It accepts the same label definitions as the label command ("http://www.stolaf.edu/academics/chemapps/jmol/docs/?ver=11.2#label";). Regards, Rolf ------------------------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
