Hi Doug,
Please see the batch mode option:
http://www.pymolwiki.org/index.php/Command_Line_Options
I ran into some issues under Win
(http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg12855.html),
but it works fine on my Ubuntu.
Vitaly
On Tue, Nov 11, 2014 at 1:56 PM, Douglas Houst
Hi Pymolers,
I have some Python script that I would like to run on Pymol in the
batch mode. To do this, I have written a "startup.py" script which I
call from Python. The script is supposed to launch Pymol and run it in
the batch mode with the "work.py" script. However, once I execute it,
Pymol qu
Hi,
After installing Dynoplot I was able to start it via the plugins menu
(which works fine), but when I try starting it via the command line it
throws an error (please see the log file).
Eventually I'd like to use Dynoplot in combination with "Monitor file
continuously" one to visualize the outp
ular light
>
> set edit_light, 2
>
> Now, in 3-button Lights mode, the mouse will move light 2.
>
> The default light is ambient which cannot be moved. If you have 3 lights on
> (ambient and two specular), then you can move the two specular two lights by
> setting edit_l
Occasionally I need to play around with the number of lights and their
vectors to get nice rendering. It's not something I do often, so every
time I need to scour through the mailing list to recall Pymol
definitions of light sources (the page on "light" badly needs
updating). So... Can someone writ
Hello,
Is there a quick way to delete the objects that do not contain any atoms?
Thank you in advance,
Vitaly
--
LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
Remotely access PCs and mobile devices a
ate to a pdb:
>
> save ~/state5.pdb, my_object, 5
>
> Why are you deleting objects instead of hiding them (using scenes)?
> Name collisions? Something else?
>
> Cheers,
>
> -- Jason
>
> On Mon, Jun 18, 2012 at 2:40 PM, V.V. wrote:
>> Hello,
>>
>>
Hello,
I have a 60-state session file that contains three objects: one of
them has a single state, while other two have several. In the first
state of the session objects #1 and #2 are loaded, and halfway through
object #2 is deleted and object #3 is loaded.
Is it possible to save the individual s
t;
>> mview store, scene=001
>>
>>
>> Add various scenes at various frames and PyMOL will interpolate
>> movement and representations for you.
>>
>> Cheers,
>>
>> -- Jason
>>
>>
>> On Wed, May 16, 2012 at 7:41 AM, V.V. wro
Hello,
Is there a way in Pymol to combine the trajectory with the camera
movement? I load the trajectory, which is a pdb file where each
conformation is represented as a model entry, and call pml script with
the view adjustment commands. If I call the following snippet, the
view is set to "YYY" th
Hello,
I have an old session file, and I would like to extract the color
information of certain objects in it. I use print
cmd.get_session()['names'] to get the scene information, but which
values in the output arrays contain the information about the color?
Thank you,
Vitaly
On Tue, Feb 21, 201
There may be a better way of doing this, but I would put the "hide
all" and "show spheres" commands you mention in a script file and call
it after loading the structure.
Vitaly
On Tue, Feb 15, 2011 at 21:29, John Russo wrote:
> Hi to all,
> I have a simple question but I've googled extensively
12 matches
Mail list logo
