have been executed.
> PyMOL calls cmd.sync() in a few places right before capturing an image for
> example.
>
> Not sure how this could be improved. Maybe cmd.sync() should print a
> warning if it times out, that would help to notice a self-lock.
>
> Cheers,
> Thomas
&
thanks. I haven't seen such performance differences before and couldn't
> reproduce it so far. Could you share your script (and data files if
> possible) with me?
>
> Thanks,
> Thomas
>
>
> > On Dec 16, 2019, at 5:42 PM, Lorenzo Gaifas wrote:
> >
> > Yes
include instant update of visual
> representations?
>
> Thanks,
> Thomas
>
>
> > On Dec 13, 2019, at 12:55 PM, Lorenzo Gaifas wrote:
> >
> > Dear Pymol users,
> >
> > I just discovered something I did not expect: the same python function
> can have extrem
Dear Pymol users,
I just discovered something I did not expect: the same python function can
have extremely different performance when called as a python function or
using the pymol api.
To be more specific: I have a function func that (among other things) uses
cmd.alter several times over a big
t; Best regards,
>
> Blaine
>
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Str
Dear pymol users,
I'm trying to properly represent a coarse-grained protein model that has an
elastic network.
I would like to show the bonds that are part of the elastic network with a
different color (and possibly representation) from the normal bonds between
atoms. However, as far as I know,
Hi James,
not sure if it's relevant in this case, but you might also want to use
retain_order, to avoid messing up your pdbs.
https://pymolwiki.org/index.php/Retain_order
Cheers,
Lorenzo
Il giorno mar 25 giu 2019 alle ore 16:04 Thomas Holder <
thomas.hol...@schrodinger.com> ha scritto:
> >
ealth Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
>
>
> From: Lorenzo Gaifas [bris...@gmail.com]
> Sent: Saturday, May 25, 2019 5:48 AM
> To: pymol
Dear pymol users,
I'm working on a script, using the python API, that needs to add a very
large number of bonds to the loaded structure.
I thought simply using cmd.bond() in a for loop would do the trick, but
-even though it works- it is extremely slow. I figured something was fishy,
since pymol