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
10 matches
Mail list logo
