[PyMOL] Starting PyMol in interactive IPython Session

Hi! I stumbled upon some odd behavior when starting PyMol in an interactive IPython Session. PyMol can be launched from interactive IPython like this: In [1]: import pymol In [2]: from pymol import cmd In [3]: pymol.finish_launching() In [4]: cmd.fetch("1xyz")So far, everything is normal. Howeve

Re: [PyMOL] Starting PyMol in interactive IPython Session

I guess formatting didn't work out as i expected. So once again and hopefully formatted: Hi! I stumbled upon some odd behavior when starting PyMol in an interactive IPython Session. PyMol can be launched from interactive IPython like this: In [1]: import pymol In [2]: from pymol import cmd In [

Re: [PyMOL] Starting PyMol in interactive IPython Session

Hi Tsjerk, thanks for your reply! this was also my first guess. However it isn't a formatting issue: In [5]: print(cmd.get_coords("1xyz")[0,0]) 41.0 Also fetched structures look "teared" in cartoon representation, supposedly because of the wrong coordinates. Calling the internal function from

[PyMOL] Execution time of color command

Hi, coloring a certain residue in an object takes about 4 ms when only one object is loaded in PyMol: %time cmd.color("blue", "obj1of1 and resi 1") CPU times: user 3.33 ms, sys: 0 ns, total: 3.33 ms Wall time: 4.13 ms Performing the same operation when a lot of other objects (~300) are load

Re: [PyMOL] Execution time of color command

ad of a dictionary lookup, you may also use a callback function. > > Check out these examples for alter with space argument: > https://pymolwiki.org/index.php/Iterate#.22space.22_argument > > Cheers, > Thomas > > On 28 Feb 2017, at 09:34, Leonhard Heizinger wrote: > >&g