Albert, I just note that JSmol reads PyMOL PSE files directly - fully
JavaScript/HTML5 - and allows interactive viewing of them in JavaScript as
well as all the functionality of Jmol; nothing to change in terms of the
PyMOL file. Just load it.
Of course, not every capability of PyMOL is reproduced
Hi Albert,
For batch processing (no GUI), run PyMOL with -c. See also
https://pymolwiki.org/index.php/Command_Line_Options
I fixed the script, it was written for an old PyMOL version.
Cheers,
Thomas
On 25 Jan 2017, at 17:01, Albert wrote:
> BTW, I try to run the example command line, but i
BTW, I try to run the example command line, but it always failed with
messages:
PyMOL>pymol2glmol 1tqn
Traceback (most recent call last):
File "/usr/lib64/python2.7/site-packages/pymol/parser.py", line 256,
in parse
self.result=apply(layer.kw[0],layer.args,layer.kw_args)
File "/home/
Hi Thomas,
Thanks a lot for your information. I know this command and that's what I
needed.
However, I don't what to open the PyMOL GUI. Is it possible that we run
PyMOL with a text mode and convert the .pse file directly to a .html file?
Thanks again.
Albert
On 01/25/2017 10:46 PM, Thomas
Hi Hena,
You're probably missing additional module requirements for these plugins. To
get a meaningful stacktrace, import the plugin modules on the PyMOL command
line. E.g.:
import pmg_tk.startup.mtsslDockGui
For 3D stereo: Have you tried "Display > Stereo" from the menu?
Cheers,
Thomas
On
Hi Albert,
What kind of HTML content do you expect? A page with a PNG image? Or an
interactive 3D model? Check out this:
https://pymolwiki.org/index.php/Pymol2glmol
Cheers,
Thomas
On 23 Jan 2017, at 16:11, Albert wrote:
> Hello,
>
> I've got a pymol .pse file and I am just wondering how c
Hi Himesh,
On the PyMOL command line, this should do the trick:
# load desmond trajectory
load sample-out.cms, mytraj
load_traj sample_trj/clickme.dtr, mytraj
# save multi-model PDB file
save multi.pdb, mytraj, state=0
See also:
https://pymolwiki.org/index.php/Load_Traj#Examples
https://py
Hello,
I would like to convert the simulation output [which was performed by using
Desmond (maestro)] into .PDB format. It will be very helpful if anyone help
me out with the same.
Thanks a lot,
Himesh
--
Thanks & Regards,
Himesh Makala
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