Right, thank you! just tested it with the recent Pymol version.
one question - is there any way to plot the name of the loaded pdb on
the image (produced by PNG command) in some automatic fashion (it
could be useful when I use it directly from terminal, without GUI)?
вт, 20 окт. 2020 г. в 14:46, T
Dear Pymol Users,
I am dealing with the analysis of protein-ligand binding predicted by
Auto-Dock, mainly focusing on the visualization of ligand clusters on
the surface of the receptor.
Assuming that I have in current pymol session several distinct
clusters of ligand, would it be possible to col
See last question here ("Ray tracing does not work"):
https://pymol.org/edu/faq.php
Cheers,
Thomas
On Tue, Oct 20, 2020 at 1:18 PM Mooers, Blaine H.M. (HSC)
wrote:
>
> Hi Jeff,
>
> I have the incentive version of PyMOL.
> It too is saving draw images with ray tracing when using the batch mode
PyMOL from macports has been rock solid for several years.
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 1
Hi Jeff,
I have the incentive version of PyMOL.
It too is saving draw images with ray tracing when using the batch mode and
also when using the pymol api in Jupyter.
As you report, saving a draw image from inside PyMOL works.
This is a very annoying bug.
You should report it as an issue on the P
hey Michel,
I always use homebrew without sudo, since
Error: Running Homebrew as root is extremely dangerous and no longer supported.
As Homebrew does not drop privileges on installation you would be giving all
build scripts full access to your system.
вт, 20 окт. 2020 г. в 12:55, Michel Rickh
Hello,
I am trying to install Open source version of Pymol on my mac using
recommended method. Although I've never had problems with brew, here I
got the following error message:
brew install brewsci/bio/pymol
touch: /usr/local/Homebrew/.git/FETCH_HEAD: Permission denied
touch: /usr/local/Home
Hi Blaine,
I've just checked on trial 26 day version of Pymol it use always RAY=1
while I run pymol from script regardless of ray flag (tested with
ray=1, ray=0, without ray as in you case etc :-)
I am going to try open source pymol!
Cheers,
J
вт, 20 окт. 2020 г. в 12:39, Mooers, Blaine H.M. (HSC)
Hi Jeff,
I do not know the answer to your question. This is a work around.
Try dropping ray=0 and adding the draw command with the dimensions in pixels
(width, height).
cmd.draw(1600,1600);cmd.png('test1600.png')
I would not use the Educational PyMOL for the kind of serious work that you are
t
hello,
I am using educational version of Pymol to generate png image of
protein-ligand complex
First, there are no problems in the case of PNG command from pymol's
GUI. However if I run the same from script from terminal:
MacPyMOL -c -d "
from pymol import cmd
cmd.load('${pdb}')
cmd.png('
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