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
---
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
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 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 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
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 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
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
