Dear PyMOL List
It comes up once in a while, is it possible to use PyMOL features from
outside of PyMOL? An example, the below is a script (inspired by Thomas
Holder) which saves down to disk all amino acids of a protein structure
into separate PDB files.
# *
Hi Martin,
the recommended way is to use PyMOL as your python interpreter, so
instead of:
python file.py
do this:
pymol -cqr file.py
However, launching a PyMOL process from a python terminal as you
suggested is also possible. Have a look at Example 2 of
http://pymolwiki.org/index.php
By the way also I've tried use super_all script wich can do multiple
alignment via Super command
pldserver1.biochem.queensu.ca/~rlc/work/*pymol*/*super_all*.py
but as the consequense the resulted sequence alignment in CGO in pair-wise
manner. How could I make something like this super all but for
Hi James,
paste the following piece of code into the PyMOL command line. It does
more or less the same as "A > align > all to this" but with "super"
instead of "align".
names = cmd.get_object_list()
for name in names[1:]: cmd.super(name, names[0], object='aln')
The first object in the list wil
Hi Martin,
I don't have a Mac so I can't test this, sorry.
I suspect that the _cmd module is built into the MacPyMOL executable.
This would imply that you cannot use MacPyMOL like in the
"Launching_From_a_Script" examples. Maybe someone of the MacPyMOL users
knows more?
Cheers,
Thomas
Mar
Martin,
The _cmd module is indeed statically linked into MacPyMOL. But, if you
built from open-source it's dumped into site-packages/pymol. Also,
view the files inside pymol/examples/launching. There are plenty of
examples. If you're using a pre-built package from elsewhere, then
please contact th
On Mon, Nov 21, 2011 at 8:55 PM, Donnie Berkholz wrote:
> I always wonder, are there actually people who feel they gain some sort
> of competitive advantage by having access to PyMOL features first?
> Doesn't seem to make sense because anyone else can pay for the same
> level of access. Plus it's
Thanks for the answers. I'll be trying to get it compile on a linux box,
if I could access some of the PyMOL features there, that's fine as well.
A friend tried to compile PyMOL on Mac and had quite some trouble, so
I'll be first trying the Linux option.
Martin
Am 22.11.11 15:56, schrieb
Hello,
I would like to know how to create these pictures. I have looked
at all available pymol tutorials online but am not able to find anything
that would help me create these pictures. Thank you very much for your
help. Here are the links to the pictures:
https://lh3.googleuserco
Hello,
I would like to know how to create these pictures. I have looked
at all available pymol tutorials online but am not able to find anything
that would help me create these pictures. Thank you very much for your
help. Here are the links to the pictures:
https://lh3.googleuserco
Hi,
Can anyone guide me how to use the pymol script to calculate the angle
between two helices?
Where and how to edit the script? I have 2 helices in a pdb file as follows:
protein.pdb
hel1 is chain A: 6-20
hel2 is chain A: 26-39
Thanking you in advance...
Hena
--
Hi Hena,
you don't need to edit the script. If you paste the script to a file
named script.py, then you can continue by typing into the PyMOL command
line:
run script.py
angle_between_helices chain A and resi 6-20, chain A and resi 26-39
Cheers,
Thomas
Hena Dutta wrote, On 11/22/11 20:50:
Hi Anjana,
> https://lh3.googleusercontent.com/-0TJhgxEIAIM/TsvUewyNAoI/Aic/kFcIE2shs8A/s830/pi%2Bstacking.jpg
This isn't difficult. You need the structure, then you have to select
the ladder and show it as ball-and-stick. Next, show the bases as
sticks and you're set. Start here, http://
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