Hi James,
You can put Jared's commands (below the load command is replaced with the fetch
command)
in a bash script called cntRei.sh and pass the PDB-ID from the command line.
The $1 is a place holder for the first argument on the command line, the PDB-ID
in this case.
This will enable easy reu
Hi James -
The PyMOL version you are using is quite old, and doesn't support the
'polymer.protein' selector. Try using just 'polymer' instead.
Hope that helps.
Jared
On June 24, 2019 at 11:58:54 AM, James Starlight (jmsstarli...@gmail.com) wrote:
hi Jared,
I have tried to use your script
hi Jared,
I have tried to use your script putting it into my test.sh script
I only changed the selection statement in sel = 'tmp and
polymer.protein' instead of sel = 'tmp and chain A and
polymer.protein'
since in my protein there is no chains assigned
pdb="./NpXynWT_apo_340K_MD_multi_0434.pdb"
py
Hi James -
You can give multiple commands by leaving the quote open as you did on the
first line (see Thomas' post from a day or two ago), but the `print` statement,
even though it is valid Python 2, will not work across line breaks as written
unless inside a `python` / `python end` block (als
i also tried more simple sollution directly from terminal but it
doesn't work also
pymol -c -d "
from pymol import cmd
cmd.load('my.pdb')
cmd.count_atoms('n. CA')
"
actually what I do need is to compute number of residues and store it
in a variable (inside of my shell script)
пн, 24 июн.
Thank you, Jared!
how do you think would it be possible to run this command from no-gui pymol?
pymol -c -d "
from pymol import cmd
print len( set( [(i.chain,i.resi,i.resn) for i in
cmd.get_model(selection).atom] ) )
"
?
пн, 24 июн. 2019 г. в 16:17, Jared Sampson :
>
> Hi James -
>
> Do a
Hi James -
Do any of the options from this previous BB discussion help?
https://sourceforge.net/p/pymol/mailman/message/28466955/
Cheers,
Jared
On June 24, 2019 at 8:13:47 AM, James Starlight (jmsstarli...@gmail.com) wrote:
Dear Pymol Users,
that is not very related to pymol question but
Dear Pymol Users,
that is not very related to pymol question but however probably it can
be solved via pymol as well ;-)
I am looking for some script (e.g. via running in pymol no-gui), which
will count the number of standard amino acid residues in the given
PDB. E.g. for particular pdb consisted
