On Fri, Nov 25, 2011 at 1:52 PM, Ian Kirker <[email protected]> wrote: > On Fri, 25 Nov 2011 18:09:03 -0000, David Lonie <[email protected]> wrote: >> On Fri, Nov 25, 2011 at 8:46 AM, Victor Eduardo Bahamonde Padilla >> <[email protected]> wrote: >>> Hello >>> Is there any way to see the value of the atomic charges on each atom of the >>> molecule displayed as gaussview? >> >> Click "Display Settings" and check "Label", then open the label >> configuration dialog. In Atom Labels --> Text there are Formal Charge >> and Partial Charge options. However, I don't see an way to set the >> formal charges, other than to read them in from a calculation or enter >> them manually under View --> Properties --> Atom Properties. >> >> Does anyone know of a way to perceive them? This sounds like something >> OpenBabel should be able do. > > As far as I can tell from the OpenBabel source, it should read (Mulliken) > charges from .log files but not from formatted checkpoint files. Charge > information *is* contained in both, but the fchk format reader doesn't seem > to contain any code to read it in from fchks as far as I saw.
I think OpenBabel has an algorithm somewhere (OBAtomTyper maybe?) that should be able to perceive formal charges from new molecules built by hand, too. But I'm not sure if this is exposed in Avogadro or not. I can't find anything after a quick check. > So, I guess the answer for now is: open the .log file instead of the .fchk > file, if you haven't already. I gave it a quick try using Avogadro 1.1.0 and > it seems to work, though as an additional note, Victor, you may have to add > the Label display if it's not already in the list of display types, by > clicking "Add" (the one next to "Duplicate" and "Remove"), then selecting > "Label", "OK", then following the procedure above to set it to show partial > charge labels. Yes -- thanks for pointing this out :-) > (I can't help thinking this is a thing that could stand to be a bit > easier/more intuitive to do. Maybe some sort of "Add Labels..." option under > the View menu?) The current design is aimed at modularity so that new display types can be added easily, and I agree, the interface ends up being rather opaque from a new user's viewpoint. Your suggestion is a good one, however, the current library design doesn't allow for display engines to provide menu actions. I think that improving menu/action/feature customizability should be a focus for 2.0 -- after all, that is the major benefit of the modular approach ;-) Dave ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d _______________________________________________ Avogadro-Discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
