Re: [PyMOL] Performance of extended commands vs python function

mands 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, > Tho

Re: [PyMOL] Performance of extended commands vs python function

a 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

Re: [PyMOL] Performance of extended commands vs python function

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

[PyMOL] Performance of extended commands vs python function

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

Re: [PyMOL] [EXTERNAL] Differentiate between bond types by color and representation

only than > object so > you can have sticks of different thickness in the same scene. > > Best regards, > > Blaine > > Blaine Mooers, Ph.D. > Associate Professor > Department of Biochemistry and Molecular Biology > College of Medicine > University of Oklahoma

[PyMOL] Differentiate between bond types by color and representation

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, c

Re: [PyMOL] PDB post-processing and TER records

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: > > gene

[PyMOL] `selection` argument in load_traj

Dear pymol users, What is the purpose of the `selection` argument in the `load_traj` command? My intuition would say that it allows to somehow select which atoms to load into pymol before the actual loading happens. However, it seems to do nothing whatsoever. What am I missing? Thanks, Lorenzo _

[PyMOL] Scripting: printing progress of a slow function

Dear pymol users, I'm working on a script that often requires a long time to execute. As I wait for the underlying issue to be addressed in the upstream repository, I would like to give the user some sort of a progress bar to let them know the program did not crash. Unfortunately, pymol seems to f

Re: [PyMOL] [EXTERNAL] Absymal performance when creating large numbers of bonds

Oklahoma Health 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 >

[PyMOL] Absymal performance when creating large numbers of bonds

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