Great! Thanks for the help Thomas. It works fine!
2017-07-05 12:34 GMT+02:00 Thomas Holder :
> Hi Gianluca,
>
> I can reproduce the problem and found the bug. This is already fixed in
> Incentive PyMOL. For Open-Source PyMOL, you can apply the attached patch.
>
> Cheers,
> Thomas
>
>
>
>
> > On
Hi Thomas,
the script below reproduce the behavior for me. I don't use pymolrc file or
k flag.
I loaded the script like this and two different behaviors were detected on
the renderised image.
1) pymol script.py
2) pymol -c scritp.py
from pymol import cmd
cmd.fetch("1c0k","a",async=0)
cmd
Hi Gianluca,
I can reproduce the problem and found the bug. This is already fixed in
Incentive PyMOL. For Open-Source PyMOL, you can apply the attached patch.
Cheers,
Thomas
stick_ball-valence-ray.patch
Description: Binary data
> On Jul 4, 2017, at 3:39 PM, Gianluca Tomasello wrote:
>
>
Hi Gianluca,
You get the sphere with stick_ball=on. It's unexpected that batch mode and GUI
mode give different results. Could it be that you have the stick_ball setting
in a (directory specific) pymolrc file, and/or do you pass -k flag (ignores
pymolrc files) in batch mode?
Cheers,
Thomas
Hi, I am trying to execute a script that sets valence bonding on sticks and
then it gives me back a rendered image. There seems there is a difference
when i try to run the script normally or in batch mode (pymol -cq
script.py). If i run it in batch mode, each atom with a double bond is
rendered wi
