[Jmol-users] Model Kit Mode

[Otis R. <osr...@ch...>]

Bob,

Paul, this is just a summary of our conversation for Bob. I’m kind of curious about what’s going on re your calculate partial charge issue, and I’d like Bob’s thoughts.

Years ago when we were first working on model kit mode, I thought I was seeing some issues that seemed to indicate that Jmol did not “know” the molfile of the edited model. I wish I could be more specific, but that’s all I have in my notes. What I did back then, and ever since, was get the current molfile from Jmol by extract and reload the model before I took Jmol script actions on the new model.

Years went by and I started having problems with partial charge calculation and display on an edited model. I noticed your addition of partial charge to the extracted molfile. So, I stripped the charge data from these files before before I reloaded them. This was done prior to the calculate partial charge command. That fixed the problem.

I suggested to Paul that this might fix his partial charge problem, and evidently it did. BUT I subsequently noticed that these partial charges are no longer in the extracted molfile!

So I guess there is a question here even if I have to express it poorly. Does it make sense that there can be edited model action issues hampered by Jmol not “knowing” the current formula?

Otis 

—
Otis Rothenberger
http://CheMagic.ORG