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 <giagi...@gmail.com> wrote:
>
> 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.show_as("sticks")
> cmd.set("stick_radius",0.3)
> cmd.set("stick_ball",1)
> cmd.set("stick_ball_ratio",2)
> cmd.set("valence",1)
> cmd.set("valence_mode",0)
> cmd.set_view (
> [0.922998726, -0.368575215, 0.110539697,
> -0.093491152, -0.493465245, -0.864722848,
> 0.373262018, 0.787807524, -0.489932150,
> -0.000001901, -0.000001147, -21.332012177,
> 34.310882568, 117.484252930, 39.097888947,
> 17.685882568, 24.978404999, -20.000000000] )
> cmd.png("test.png",width=1185, ray=1)
>
> 2017-07-04 14:09 GMT+02:00 Thomas Holder <thomas.hol...@schrodinger.com>:
> 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
>
> > On Jul 2, 2017, at 5:32 PM, Gianluca Tomasello <giagi...@gmail.com> wrote:
> >
> > 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 without the sphere in the atom center (only double bond is shown).
> >
> > Instead, if i try to execute the script in default mode the central atom
> > sphere is correctly rendered.
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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