On Tue, Apr 14, 2015 at 8:01 PM, Whitwell, George <gwhitw...@ncwc.edu>
wrote:
> Greetings,
>
>
>
> The first two items developed while working with Tinker 6 output.
>
>
>
> *boundbox*
>
> I am loading Tinker 6 molecular dynamics arc files (which are catenated
> Tinker xyz files) that were the result of an NPT dynamics run with periodic
> boundary conditions. Subsequently, I read the log file for the run,
> extract the unit cell parameters, define boundbox corners for each frame,
> select the given frame and:
>
>
>
> draw boundbox modelbased mesh nofill
>
>
>
> As a drawn object, I expected that I could get different boxes for each
> frame, but only the last one is present for all frames. Is there another
> way to get a unique box for each frame?
>
> You could create a function that is run for the "animFrameCallback" and
that would allow you to customize what happens when the frame is changed.
Use
show _?
to see the various variables set by Jmol. Some of these are relevant to
frame changes.
>
>
> *unitcell*
>
> When using the unitcell command on the same output, I find that Jmol
> translates any atoms that have strayed into an adjacent cell back inside
> and then draws bonds that traverse the cell. Is there an override to this
> recelling process?
>
What load command are you using? I think Jmol is reading the atom and bond
positions as given in your Tinker file. You sure they are being
repositioned? Jmol should only be doing that if you specify that it should.
>
>
> *Tinker 7 arc files*
>
> The Tinker xyz and arc formats have a first line (for each model in an arc
> file) that is not actually a header, but gives the number of atoms in the
> model with an optional comment following. The latest version of Tinker has
> added a second line that lists the unit cell parameters from a periodic
> boundary calculation. Jmol throws an error reading this file, with or
> without a "Tinker::" identifier (in the case below, when it hits line
> 12002). I can provide a complete example if desired. Here are a few lines:
>
We should be able to work with that. I guess these are not fractional
coordinates. Please send me a couple of files, especially if they have
bond anomalies.
Bob
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