Hi,
I am loading a pdb file in a python script for pymol.
The script has the following structure:
def script
do something
cmd.load(file.pdb)
do lot more
cmd.extend(script, script)
When the python script is completed, the molecule file.pdb is shown
in the openGL display, but not before. How
Hi Matthias,
use spawn instead of run.
http://pymolwiki.org/index.php/Fork
Cheers,
Thomas
On 09/14/2011 02:30 PM, Matthias Schmidt wrote:
Hi,
I am loading a pdb file in a python script for pymol.
The script has the following structure:
def script
do something
cmd.load(file.pdb)
do
Try to do the following:
in your script.py
from pymol import cmd
cmd.load(file.pdb)
def script():
do something...
cmd.extend(script, script)
In this case your pdb will be loaded before the script completes.
2011/9/14 Thomas Holder spel...@users.sourceforge.net:
Hi Matthias,
use spawn
So what exactly do you want your script to do?
1. Show loaded file
2. Modify file
3. Show modified file
Is it right?
2011/9/14 Matthias Schmidt matthias.rene.schm...@gmail.com:
Hi,
This approach does not work, because file.pdb is written in do something...
Also, if I say spawn script.py
Hello PyMOLers,
I have a GPCR protein molecule (pdb file) whose structure I would like to
visualize, but instead of seeing the entire structure as one entity, I would
like to separate it, somehow as if I was using an imaginary plane to chop
the protein into two entities (extracellular interface,
Hello Tim,
It sounds like a combination of mview store (saving your scenes) and
mview reinterpolate (interpolating between them) is what you are looking
for.
http://www.pymolwiki.org/index.php/MovieSchool_4
Unless you mean interpolating between different representations of your
structure. Could
Hi Tim,
I love pymol for creating high quality figures and analysing my
structures. But creating movies in pymol is rather tedious... CCP4mg
seems to be much easier to use for creating movies, you just have to
save a scene and CCP4mg interpolates between the created scenes.
Is there a plan
Yes, that is exactly what I wanted.
Perfect. Thank you very much.
Am 9/14/11 5:59 PM, schrieb Jason Vertrees:
Hi Tim,
I love pymol for creating high quality figures and analysing my
structures. But creating movies in pymol is rather tedious... CCP4mg
seems to be much easier to use for
Hi Spyros,
This can be done pretty easily in PyMOL. Please check out the following:
Plane Wizard:
* -- http://www.pymolwiki.org/index.php/Plane_Wizard;
BNI-tools Plane Wizard
* -- http://sourceforge.net/projects/bni-tools/
Section 2.6 of the supplemental information to our PLoS paper
* --
Hello everyone,
Speaking of movies, is there a way to control the fade-in and fade-out rate of
objects between scenes (eg. by changing the value of the transparency variable
over a series of frames perhaps) using the native pymol movie features?
Kristian Rother wrote a great movie script a
Hi Brian,
Speaking of movies, is there a way to control the fade-in and fade-out rate
of objects between scenes (eg. by changing the value of the transparency
variable over a series of frames perhaps) using the native pymol movie
features? Kristian Rother wrote a great movie script a
So I've tryed to use cmd.refresh() and it has worked!
So your script must include the following:
cmd.load
cmd.refresh
[some actions]
cmd.load
cmd.refresh
[some actions]
etc.
2011/9/14 Matthias Schmidt matthias.rene.schm...@gmail.com:
Hi, not quite the script does the following:
1: load a file
Hi,
when I tried to set something,
let's say
set stick_radius, 0.5
found not ideal, and I wanna be back to default setting,
how do I check the default settings very quickly.
above just an example, not real case,
Thanks for any suggestions,
--
Best Regards,
lina
Hi Lina,
In most cases, you can set it back to default by setting it to -1.
To know what the default value is, you can use 'get setting_name', before
you start fiddling with the setting.
Hope it helps,
Tsjerk
On Sep 15, 2011 4:12 AM, lina lina.lastn...@gmail.com wrote:
Hi,
when I tried to
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