[PyMOL] can we show ligand in 2D?

[Albert]

Hello:

I've got a 3D coordinate in 3D.  I am just wondering is it possible to 
show it in 2D diagram in Pymol for a ligand so that we can get more 
clear idea how exactly the ligand looks like?

thanks a lot

Albert

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Re: [PyMOL] can we show ligand in 2D?

[Osvaldo Martin]

Hi Albert,

Probably you should check Pose_View


Cheers,
Osvaldo.


On Mon, Sep 14, 2015 at 11:52 AM, Albert  wrote:

Hello:
>
> I've got a 3D coordinate in 3D.  I am just wondering is it possible to
> show it in 2D diagram in Pymol for a ligand so that we can get more
> clear idea how exactly the ligand looks like?
>
> thanks a lot
>
> Albert
>
>
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Re: [PyMOL] loop through many pdb files and show their centre of masses

[Osvaldo Martin]

Hi Zakir,

The following script computes the Center Of Mass (or alternative the
geometric center) and then draws a pseudoatom
. I think you could adapt
the script to your needs if you find difficulties, don’t hesitate to
contact the list again (your question is not silly).


import pymol
from pymol import cmd
pymol.finish_launching()
import numpy as np

def center(selection, com=True):
model = cmd.get_model(selection)
xyz = np.array(model.get_coord_list())
mass = [i.get_mass() for i in model.atom]
xyz_m = xyz * np.array([mass]).T
if com:
return tuple(np.sum(xyz_m, 0)/model.get_mass())
else:
return tuple(np.average(xyz, 0))


cmd.load('some_file.pdb')
COM = center('all')
cmd.pseudoatom('center', pos=COM)

Alternatively, you can use this script
 to compute the center
of mass.

Cheers,
Osvaldo


On Mon, Sep 14, 2015 at 4:29 PM, Zakir Tnimov 
wrote:

Hi there,
>
> I have no experience in scripting what so ever thus this simple task
> drives me nuts.
> I was using ZDOCK to dock my protein on the complex. It spits me out 2000
> pdb files that each contain a ligand and receptor. Receptor position is
> fixed, ligand is not. What I want to show is just centre of mass of the
> ligand and a receptor. I understand that I should be doing something like
> this:
>
> from pymol import cmd
> from glob import glob
>
> for file in glob("*.pdb"):
> print file
> cmd.load(file,'prot')
> for a in cmd.index("CYS/SG"):
> identify COM
> print its location as a dot or sphere
> delete loaded file
> go to another one until list is exhousted
>
> cmd.delete("all”)
>
> Thank you a lot and sorry for bothering you with such a silly question!
>
>
> zakir.tni...@gmail.com
>
>
>
>
>
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[PyMOL] pymol crashes when try opening a file created by gromacs

[Raag Saluja]

Hi!
I am running a simulation using Gromacs. I was able to visualise the .pdb
file using pymol. But when I tried to visuals the files created by Gromacs,
pymol crashed. Can you please help? Thank you in advance!

-- 
Regards,
Raag
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[PyMOL] loop through many pdb files and show their centre of masses

[Zakir Tnimov]

Hi there,

I have no experience in scripting what so ever thus this simple task drives me 
nuts.
I was using ZDOCK to dock my protein on the complex. It spits me out 2000 pdb 
files that each contain a ligand and receptor. Receptor position is fixed, 
ligand is not. What I want to show is just centre of mass of the ligand and a 
receptor. I understand that I should be doing something like this:

from pymol import cmd
from glob import glob
 
for file in glob("*.pdb"):
print file
cmd.load(file,'prot')
for a in cmd.index("CYS/SG"):
identify COM
print its location as a dot or sphere
delete loaded file 
go to another one until list is exhousted

cmd.delete("all”)

Thank you a lot and sorry for bothering you with such a silly question!


zakir.tni...@gmail.com




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[PyMOL] on surface function in the setting

[Smith Liu]

Dear All，


For my windows version of pymol, I cannot locate the surface function under the 
setting button. Will you please tell me how can I make my surface cavity pocket 
function workable?


Best regards.


Smith--
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