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" wrote:
Hi,
when I tried to set something,
let's s
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
---
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 :
> Hi, not quite the script does the following:
>
> 1: load a file
> 2: modifiy this file using
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 n
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 num
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
* -- http:
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 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
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. Cou
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,
Dear users or developers,
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
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 :
> Hi,
>
> This approach does not work, because file.pdb is written in "do something..."
>
> Also, if I say "spawn script.py gloabl" instead of "run scr
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 :
> Hi Matthias,
>
> use "spawn" instead of "run".
>
> htt
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("
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. Ho
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