Hi Blaine,
I confirm, this is a regression bug in PyMOL 1.6.
This will only happen when using PyMOL commands, not when doing the same thing
with a Python script. Here is an equivalent replacement for your alias:
python
from pymol import cmd, preset
@cmd.extend
def q1():
cmd.reinitialize()
cmd.fetch('3v6d', 'HIVrt', type='pdb')
preset.ball_and_stick("c. P and i. 822")
cmd.zoom('c. P and i. 822')
cmd.rock()
python end
Cheers,
Thomas
On 11 Feb 2016, at 09:55, Mooers, Blaine H.M. (HSC) <blaine-moo...@ouhsc.edu>
wrote:
> Dear PyMOLers,
>
> I am using incentive version 1.8.0.5. I made the following python script
> with an alias
>
> from pymol import *
> cmd.alias('q1', 'delete all;fetch 3v6d, HIVrt, type=pdb,
> async=0;preset.ball_and_stick("c. P and i. 822");zoom c. P and i. 822;rock')
>
> Repeated entry of the alias name changes the color scheme of the atoms and
> toggles on and off the rocking motion.
> Apparently, the settings are not reset with "delete all".
>
> If I replace "delete all" with "remove all" or 'reinitialize", the command
> history windows shows thepdb file haveing been fetched but no molecular
> object show ups in the internal gui. In version 1.55, reinitialize works as
> expected.
>
> It seems that the reinitialize needs a "pause until completed signal" like
> "async=0 " in fetch or theunix "&&".
>
> Best regards,
>
> Blaine
>
> Blaine Mooers, Ph.D.
> Assistant Professor
> Director of the Laboratory of Biomolecular Structure and Function
> Department of Biochemistry and Molecular Biology
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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