Great! Thanks for the help Thomas. It works fine!
2017-07-05 12:34 GMT+02:00 Thomas Holder <thomas.hol...@schrodinger.com>:
> 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 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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