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 ca
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
wrote:
> Dear Vinod,
>
>
> One option is to call PyMOL function from Python script.
>
> import __main__
> __main__.pymol_argv = ['pymol','-q
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 fil
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 suggestions
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
the
I will try this
thank you for your input
Sent from my iPhone
> On Sep 9, 2014, at 12:00, David Hall wrote:
>
> 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
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 tr
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
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 o
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 wr
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
gl
Hi guys
I know that this is a list for questions about pymol but I need help in
calculating energies from breaking and/or creating bonds. I'm new at
this crystallography stuff so I don't even know where to start looking
for a program that could calculate these energies. I don't know if pymol
is
Hi Aaron,
> I am somewhat new to PYMOL and was trying to create a selection of atoms.
> What I need to do is select all atoms of a protein that are within 5
> angstroms of an inhibitor (the protein and inhibitor are separate
> molecules). I cannot figure out how to do this from the examples in t
..@gsk.com]
> Sent: Friday, October 11, 2002 12:36 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Need help with selections
>
>
> Hello,
>
> I am somewhat new to PYMOL and was trying to create a
> selection of atoms.
> What I need to do is select all atoms of
Hello Aaron,
* aaron.b.mil...@gsk.com [2002-10-11 15:36] wrote:
> Hello,
>
> I am somewhat new to PYMOL and was trying to create a selection of atoms.
> What I need to do is select all atoms of a protein that are within 5
> angstroms of an inhibitor (the protein and inhibitor are separate
> mole
select ligands, (byres gmp expand 5 and psd)
selects whole residues from molecule psd within 5 A from gmp
aaron.b.mil...@gsk.com wrote:
Hello,
I am somewhat new to PYMOL and was trying to create a selection of atoms.
What I need to do is select all atoms of a protein that are within 5
angstro
Hello,
I am somewhat new to PYMOL and was trying to create a selection of atoms.
What I need to do is select all atoms of a protein that are within 5
angstroms of an inhibitor (the protein and inhibitor are separate
molecules). I cannot figure out how to do this from the examples in the
manual. I
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