Hello,
I'm looking to pass a .pml file, do some stuff, and then save it as a session.
Pymol -c My.pml looks like a good option. I'm trying to write hundreds of
sessions each with different arguments. I was wondering if its possible to pass
command line arguments that can then be seen by the
On Wednesday 26 June 2013 08:52:39 Jordan Willis wrote:
I'm looking to pass a .pml file, do some stuff, and then save it as a
session. Pymol -c My.pml looks like a good option. I'm trying to write
hundreds of sessions each with different arguments. I was wondering if its
possible to pass
Hey :)
You don't even need the python block, as the pymol interpreter is a python
interpreter with just some added extras. Single lines of python code are
never a problem. This works nicely for me
File test-argv.pml:
print sys.argv
for i in sys.argv[1:]: print i
Run pymol:
Hi Paul,
I have the same problem. I am using Fedora 18 and PyMOL v.1.5 (from
the repository).
It is annoying. Right now I have to use another computer if I want to
use the more 'advanced' functions of PyMOL.
I found one other person with the same problem who posted to the
Fedora forum, and got
It seems the difference I was looking for was
pymol something.pml -- arg1 arg2 arg3
I was missing the --
Thanks
Jordan
On Jun 26, 2013, at 4:21 AM, lievb...@vub.ac.be wrote:
On Wednesday 26 June 2013 08:52:39 Jordan Willis wrote:
I'm looking to pass a .pml file, do some stuff, and then
Thanks for the reply.
Of course you are correct that anaglyph in Pymol is 'optimised' for
red/cyan glasses, despite the fact that the Pymol wiki says stereo mode 10
is for green/magenta ones (which is where I got the idea when it all went
wrong for me).
I have a learned a few things not to do in
Hi Gary,
1) do not use a black background
Agreed. Something like gray works well in my experience. Don't forget in
techniques like anaglyph and chromadepth color takes on another meaning–it
encodes depth or separation. It's useful to keep this in mind.
2) do not use setting rendering
Dear all,
I'm trying to write a script to perform mutagenesis on a pdb
coordinate file via the command line. When I run the script, it
produces the expected output on the terminal and even creates the
desired output PDB file, but the output file is exactly identical to
the input file other than
Warm regards,
R. Marshall Pope
www.medicine.uiowa.edu/proteomics
Notice: This UI Health Care e-mail (including attachments) is covered by the
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