Re: [PyMOL] cartoon range transparency help

Hi Paul, check out https://pymolwiki.org/index.php/Cartoon#Breaking_Up_a_Visualization_with_Cartoon_Skip You'll want to skip the residues you want to make transparent in the original (opaque) object, and include some more residues on both ends in the copy you want to make transparent. Skip the ad

Re: [PyMOL] Help for saving movie in png

Hi Pranab, Am 13.11.2015 um 17:00 schrieb Pranab Jyoti Bhuyan: > Can you please tell me how to save a movie as a series of *.png files > from terminal in linux? This can be done with the mpng command. See http://pymolwiki.org/index.php/Mpng Cheers, Christian ---

Re: [PyMOL] scripting: pymol.session

id(): print id(pymol.session) > > @cmd.extend def set_foo(value): pymol.session.foo = value > > @cmd.extend def print_foo(): print pymol.session.foo --- end > script.py --- > > Cheers, Thomas > > On 29 Jan 2015, at 20:20, Christian Becke > wrote: > >> Dear pymol experts, &g

[PyMOL] scripting: pymol.session

Dear pymol experts, I found some odd behaviour when trying to use pymol.session in my script. I'm using open source pymol 1.7.4.0 (built from svn) on linux. Here comes a minimal example: 1) Create a directory, containing the following 2 files: --- script.py --- from pymol import cmd, session

Re: [PyMOL] REGARDING_PyMOL_3D_Movie_in_FFMPEG

used with. > I humbly seek your assistance for running the python script(mpng.py) for > saving my movie into right-left png images. > Looking forward to your reply... > > -- > Sincerely, > Tarun JaiRaj Narwani.. > Protein Evolution Lab- Dr. S.Srikrishna > IMTECH, Chand

Re: [PyMOL] pymol 3D movies

[1] http://ffmpeg.org [2] http://bino3d.org [3] http://ffmpeg.org/ffmpeg-filters.html#stereo3d [4] http://www.imagemagick.org -- Christian Becke Freie Universität Berlin Fachbereich Biologie, Chemie, Pharmazie Institut für Chemie und Biochemie AG Strukturbiochemie Takustr. 6 14195 Berlin Ger

Re: [PyMOL] pymol 3D movies

Hi Xevi, I have prepared side-by-side 3D movies that I could play on a 3D TV using pymol and ffmpeg. I ray-traced the movie, one frame for each eye, and used ffmpeg to compile the resulting png files to an h264 movie file. With side-by-side stereo, you of course lose resolution, but ffmpeg can

Re: [PyMOL] movie, ~1700 residues, out of memory

s_mode > > Cheers, > Thomas > > On 09 Nov 2013, at 13:58, Christian Becke > wrote: > >> Dear pymol users, >> >> I'm trying to create a movie, using lsqman and pymol, of a molecule of >> ~1700 residues (HETATMs deleted, no hydrogens, alternativ

[PyMOL] movie, ~1700 residues, out of memory

Dear pymol users, I'm trying to create a movie, using lsqman and pymol, of a molecule of ~1700 residues (HETATMs deleted, no hydrogens, alternative conformations removed). I created 60 pdb files with lsqman and loaded them (as different states of the molecule) into pymol. In the default "lines"