Hello Everyone,
I am trying to find a way to calculate the buried surface area in a complex
with 2 molecules using pymol. Can anyone direct me to the correct way to do it?
I am currently trying out the following method, and I need to find out if there
is anything else I need to do to do this
Thanks Osvaldo for your suggestion .
I will work it out and let you know if any issues raises .
Regards
On Mon, Aug 24, 2015 at 5:17 PM, Osvaldo Martin aloctavo...@gmail.com
wrote:
Dear Vinod,
One option is to call PyMOL function from Python script.
import __main__
__main__.pymol_argv
Hi All
I doing one task with pymol where I need to calculate Solvent Accessible
Surface Area for individual residues numbers.
I tried with get_area command but little confused on how to put it for
individual residues .
Could any one please suggest command or script to do it ?
Any
Dear Vinod,
One option is to call PyMOL function from Python script.
import __main__
__main__.pymol_argv = ['pymol','-qc']
import pymol
from pymol import cmd, stored
pymol.finish_launching()
cmd.set('dot_solvent', 1)
cmd.set('dot_density', 3)
cmd.load('pdb.file') # use the name of your pdb
Dear all,
I need help.
I just start using Pymol in Ubuntu, this was advised to me since windows
give a lot of trouble.
I install pymol already on ubuntu, but I need an manual how to transport
the data from the pdb to ubuntu pymol.
I can enter pdb nicely but after I dowload the files I cannot
I am very unsure of your question, but I believe you're asking if you have
a PDB id, how to load that into pymol. For that, you can use the fetch
command ( http://www.pymolwiki.org/index.php/Fetch )
You type:
fetch 1acb
into the pymol interface and it will download pdb id 1acb and load it into
Hello Pymol Users
I am quite new to python and more specifically to PYTHON ,PYMOL interface
hence I urgently need a help from you.
I simple need to calculate the RMSD between two pdb files and use that rmsd
for further programming but somehow I can not figure how to do it
This is what I have
Hello,
I am quite new to python and more specifically to PYTHON ,PYMOL interface
hence I urgently need a help from you.
Welcome! This list has about 1500 people on it and is accepting of
new users. A couple hints to get you started. First, you can type
help commandName in PyMOL to help on a
Hi,
Just a small doubt
cmd.load(pdb%04d.pdb%ener1)
cmd.load(pdb%04d.pdb%ener2)
so if
ener1 =0001
ener2 =0002
The program will understand the pdb0001 and pdb0002 in
v = cmd.fit(pdb0001 and name CA, pdb0002 and name CA) or not ?
or would I need to assign them some names while loading
Folks,
We are trying to track down and hopefully resolve a problem with the
left and right images getting confused in stereo mode with PyMOL. I
think this problem is limited to nVidia Quadro cards, but need more
info. So...
If (and only if) you use PyMOL in hardware stereo mode (with shutter
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