Dear Jacob and Andreas,
The PyMOL launching procedure occurs IMO in three
steps:
1) Start main PyMOL window and command processor
2) Start floating Tk window
3) Start plugins
(it should be similar when you use PyMOL in batch
mode).
Thus, it may occur that commands from your .pml
scripts are executed while the rtools plugin has not
been initialized yet.
A simple solution would be to issue a delay of 2-5 sec
at the start of the script to make sure rtools is up
and running.
You could do this using:
time.sleep(5)
This is actually pure Python, but it works from the
PyMOL cmd line as well.
Yours,
Kristian Rother
Humboldt Universität Berlin
--- Jacob Corn <jc...@uclink.berkeley.edu> wrote:
> This is, unfortunately, not the case. For our
> installation, rtools
> already starts automatically (it's in the
> pmg_tk/startup directory).
> Adding "run <path>/rtools.py" to the .pymolrc does
> not allow rtools to
> be used from within the script.
>
> Jacob
>
> andr...@biochem.utah.edu wrote:
> > Jacob,
> >
> > I believe rtool will always be usable if you put
> > run <path>/rtools.py
> > into your .pymolrc file.
> >
> >
> > Andreas
> >
> >
> >
> >
> >
> >>This is an odd concidence, since I was just about
> to post about
> >>something very similar.
> >>I would like to use rtools commands from a .pml
> that is read from the
> >>command line (eg - with the -qc flag, instead of
> using the graphical
> >>interface).
> >>When starting pymol normally, rtools loads and
> everything is hunky dory.
> >>However, even if I add a "run <path>/rtools.py"
> command to the .pml
> >>script, none of the rtools commands are
> recognized. Manually running
> >>rtools.py from within the .pml produces no errors.
> >>Is there a way to use rtools from within a script
> that never sees the
> >>graphical front end?
> >>
> >>Jacob
> >>
> >
> >
> >
> >
> >
> >
>
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> --
> Jacob Corn
> UC Berkeley - Berger Lab
> Lab: 510-643-8893
> Fax: 510-643-9290
> jc...@uclink.berkeley.edu
>
>
>
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