Hi Thomas,
I'm not sure I get it. Does that mean that `cmd.sync()` is actually not
doing anything at all if called outside of `cmd.do()`?
Cheers,
Lorenzo
Il giorno mer 18 dic 2019 alle ore 10:49 Thomas Holder <
thomas.hol...@schrodinger.com> ha scritto:
> Hi Lorenzo,
>
> Thanks for the script, and great that you could identify cmd.sync() as the
> culprit. I looked at the code, cmd.do("cmd.sync()") literally blocks itself
> until it times out after 1 second. cmd.do() puts commands in a queue, and
> cmd.sync() tries to ensure that all queued commands 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
>
>
> > On Dec 17, 2019, at 11:42 AM, Lorenzo Gaifas <bris...@gmail.com> wrote:
> >
> > After playing around with it a bit longer, it's clear that I
> misunderstood. The issue was not with `cmd.alter` nor with `cmd.show_as`,
> but with `cmd.sync`.
> >
> > I was calling many times a smaller function that contained `cmd.sync()`,
> which resulted - it seems - in all these calls piling up.
> >
> > Still, I don't know if it's intended behaviour for `sync` to be so much
> slower if it's called as a pymol function. Attached you will find a minimal
> working example to show the difference.
> >
> >
> > Il giorno lun 16 dic 2019 alle ore 17:52 Thomas Holder <
> thomas.hol...@schrodinger.com> ha scritto:
> > OK 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 <bris...@gmail.com> wrote:
> > >
> > > Yes, it does. Both cases are with the GUI and ewual graphical
> representation.
> > >
> > > On Mon, Dec 16, 2019, 17:37 Thomas Holder <
> thomas.hol...@schrodinger.com> wrote:
> > > Hi Lorenzo,
> > >
> > > When you say "run from a python script", is that with the graphical
> GUI? That "instant update", does that include instant update of visual
> representations?
> > >
> > > Thanks,
> > > Thomas
> > >
> > >
> > > > On Dec 13, 2019, at 12:55 PM, Lorenzo Gaifas <bris...@gmail.com>
> wrote:
> > > >
> > > > 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 system to change the
> properties and representation.
> > > >
> > > > If I run it calling func() from a python script, its effects are
> almost instant. If I call it with cmd.do('func') (or directly from within
> pymol with func), it’s extremely slow (up to 10 seconds) and Pymol freezes
> completely during this time.
> > > >
> > > > I expected this to be due to an overhead of the api itself, but when
> I do the same thing with a simpler function, I see no noticeable difference.
> > > >
> > > > Why exactly is this happening? And more importantly, how can I get
> the performance of func even when I call it from within pymol?
> > > >
> > > > Thank you,
> > > > Lorenzo
> > > >
> > > > _______________________________________________
> > > > PyMOL-users mailing list
> > > > Archives:
> http://www.mail-archive.com/pymol-users@lists.sourceforge.net
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> > >
> > > --
> > > Thomas Holder
> > > PyMOL Principal Developer
> > > Schrödinger, Inc.
> > >
> >
> > --
> > Thomas Holder
> > PyMOL Principal Developer
> > Schrödinger, Inc.
> >
> > <slow.py>
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>
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