Hi Praz,
I use a bit of a different script than you for this (I don't use any movie
commands, just moving camera and writing the png), so I'll just cut out the
relevant part below. It may need some tweaking to work in your script.
In this case I had previously defined molname and chainid so that
Great, perfect now, completely re-done my script in this way, works as a
charm! Thanks again!
I would also like to know if it is possible to render multiple .pngs from
one .pdb? For example, in my old script I have a full circle rotation
across 450 frames:
mset 1, 450
util.mroll 1, 450, 1
set ray
Glad is working!
Since the script is a Python script (not a PyMOL script) you should be
using the PyMOL API syntax. For example:
- “set light_count,8” becomes cmd.set(“light_count”, “8”)
- “load filename” becomes cmd.load(“filename”)
I hope it helps.
Cheers,
Osvaldo.
On Mon, Jun 8, 2015 a
Thanks Osvaldo, now it works perfectly. I even managed to figured out how
to load sdf files instead of pdb.
One question - in the code where there is ### insert your code here ###, I
paste my PyMol settings, but I get an "invalid syntax" error. For example,
I put "set light_count,8" and that resul
Hi Praz,
Sorry. Please use this new version of the script.
import __main__
__main__.pymol_argv = ['pymol','-qc']
import pymol
from pymol import cmd
pymol.finish_launching()
import glob
import os
path = os.path.dirname(pymol.__script__)
cmd.delete('all')
pdb_files = glob.glob(os.path.join(path,
Thank you Osvaldo.
However, as a beginner, I am having problems with getting this to work. I
pasted your script in a file (script.txt) and placed it in the same folder
where the pdb files are. Then I ran PyMol and typed "run
c:\somefolder\script.txt", but I all get is a black screen and no .png
fi
Hi Praz,
When I want to process several files, do complex or repetitive tasks I
prefer to write a Python script and access the PyMOL functions using the
PyMOL API, as in the code below.
This example will upload all the pdb files in the folder where the script
is located, one file at a time, save
Hi all,
I'm a beginner at PyMol, but I'm wondering if a batch action like this
would be possible: If I have a bunch of .sdf and .pdb files in a folder,
and I want to apply a specific "look" to all of them (I've written the
parameters regarding light, field of view etc.), is it possible to batch
pr
