Tara,
Use Python (and the run command with .py files).
from pymol import cmd
f=open('dist.txt','w')
dst=cmd.distance('tmp','mol1///25/ha','mol1///26/ha')
f.write("%8.3f\n"%dst)
f.close()
You could measure the whole protein this way by putting a loop around the
distance command:
from pymol impo
> 0. Upgrade to 10.2.3 if you have not already done so.
On a side note, did they fix NIS compatability again after breaking it in
10.2? I dropped OS X as soon as I discovered that, since that made it
nearly useless for the environment I work in. If they got it working
again, that and the new X
Hi,
I have a file which measures a bunch of distances between atoms (of the
form "distance (mol1///25/ha), (mol1///26/ha)"), and rather than having to
look at the results on the screen I'd like to have the values output
to a text file. Is it possible to do this?
Thanks,
Tara
Tara Sprules
Post-D
Oh, and if you already have installed pymol with fink, you don't need
to do anything apart from installing Apple's X-windows.
William G. Scott
Associate Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
Sinsheimer Laboratories
University of Calif
Awesome! I was hoping Apple's new release might have this impact.
In my hands the X-windows version of pymol on OS X went from unusable
to almost as fast as the native version.
Apple's GLUT driver can now bind to the hardware drivers under X11 at
the
same time as the Tcl/Tk external GUI
To get the fink 0.86 version of PyMOL running hardware accelerated on
Mac OS X using Apples newly released X11 you will need to install both
Apples X11 public beta and their X11 software development kit available
here:
http://www.apple.com/macosx/x11/
You also need to get fink up and running.
Hi Dirk
This might actually be a hardware affect rather than a software effect.
The GeForce4
is undoubtably quicker that the GeForce 2 bu there comes a time when the
actual CPU is lagging behind in the amount of data it can pass to the GPU-
this also includes other limitations such as the graphics
Awesome! I was hoping Apple's new release might have this impact.
Apple's GLUT driver can now bind to the hardware drivers under X11 at the
same time as the Tcl/Tk external GUI. It used to be an either/or
situation. Apple has finally answered our requrests to support a fast 3D
environment just l
Many thanks for the replies. I had forgotten the import statement (Doh!).
Now working fine again.
On a different note, one of the best features of 0.86, in my humble
opinion, is the new scrolling objects list. Previously I've created
sidechain objects to toggle individual sidechains on/off with o
Dear Gordon,
I assume that you changed the default "nv" driver in your XF86config(-4) file
to the Nvidia driver "nvidia". I've replaced on my private Pentium III (733
MHz) PC a GeForce2 GTS against a GeForce4 Ti4200 and I also observe less
improvement than expected. Here are my observations:
1.
> If anyone has any suggestions they'd be most appreciated. I like ScriptBox
> a lot so do you think there's any chance of incorporating this into PyMol
> either as a GUI window or as its own dropdown scripts menu that could also
> list all the scripts in a given directory??
Hello,
There is a ver
Hi
I recently upgraded from a geforce 2 to a geforce 4 ti4200, and I don't
really notice a performance improvment (running linux). I judge this
based on how smoothly large sized proteins can be rotated with spheres
on.
Just wondering why?
Thanks in advance
Gordon
--
Gordon Wells
Department of B
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