Re: [PyMOL] Coordinates of an atom

Dear Mohsen, when I Google "pymol coordinates atom", the top hit is this: https://pymolwiki.org/index.php/Get_Coordinates_I Worth a try. All best. Andreas On Thu, Dec 1, 2016 at 2:19 PM, Mohsen Chitsaz < mohsen.chit...@flinders.edu.au> wrote: > Hi all, > > >

Re: [PyMOL] Coordinates of an atom

Hej, try this command and specify the atom selection: cmd.get_atom_coords('atom selection') see also: https://pymolwiki.org/index.php/Get_Coordinates_I Cheers, Andreas On Thu, Dec 1, 2016 at 2:19 PM, Mohsen Chitsaz < mohsen.chit...@flinders.edu.au> wrote: > Hi all, > > > > Can anyone please

[PyMOL] Coordinates of an atom

Hi all, Can anyone please help me in how to get coordinates of a selected atom or residue? Thank you Mohsen -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)

Re: [PyMOL] Coordinates of ligand-binding site

Hi James, the "get_extent" command in PyMOL will give you the corners of the selected region, from which you easily can calculate center and edge lengths. http://pymolwiki.org/index.php/Get_extent Example: box = cmd.get_extent('sele') print 'Center:', [(a+b)/2.0 for (a,b) in zip(*box)] print '

Re: [PyMOL] Coordinates of ligand-binding site

Jordan, Thank you for advise. I've tried to do the same already but 1- In Resulted pbd file ( with ligand and surrounded residues only) the coordinates of ligand and residues have been changed in comparison to the initial pdb/ How to prevent it? 2- The resulted pdb consist of coordinates of e

Re: [PyMOL] Coordinates of ligand-binding site

I'm thinking a good work around is simply this. Select the binding site of the amino acids and ligand in pymol. Then copy those selected aa's and atoms to another object: save -> model -> copied_object as output.pdb output.pdb will then contain all the x,y,z coordinates of only what was

[PyMOL] Coordinates of ligand-binding site

Dear PyMol users! Some of docking servers (e.g swiss dock) which I'm using need in explicit definition of the coordinates (in XYZ) of the docking region as well as coordinates of its COM. How I could obtain such coordinates of intrested pdb file based on the knowing protein-ligand interaction sit

Re: [PyMOL] Coordinates of a mesh

Hi Bjoern, Please do also give a more explicit account of what you want to achieve in the end and what you've tried to get there, including the commands used. Cheers, Tsjerk 2011/8/25 Troels Emtekær Linnet : > Check this, and tell if it works. > > http://pymolwiki.org/index.php/Matrix_Copy > >

Re: [PyMOL] Coordinates of a mesh

Check this, and tell if it works. http://pymolwiki.org/index.php/Matrix_Copy Troels Emtekær Linnet Karl-Liebknecht-Straße 53, 2 RE 04107 Leipzig, Tyskland Mobil: +49 1577-8944752 2011/8/25 Bjoern-oliver Gohlke < bjoern-oliver.goh...@student.uni-tuebingen.de> > The err

Re: [PyMOL] Coordinates of a mesh

The error I get is from the following command: super 1A9U, mesh ExecutiveAlign: invalid selections for alignment. I think that the problem is that I try to align the mesh points with an protein. In my understanding, I need this one to run the get_object matrix command. Or do I understand somet

Re: [PyMOL] Coordinates of a mesh

Can you provide the error message? 2011/8/25 Bjoern-oliver Gohlke < bjoern-oliver.goh...@student.uni-tuebingen.de> > Hi, > > I actual try to get the coordinates of the mesh from a protein/selection. > > At first I run the following command: > open("pymol.mesh","w").write( cmd.get_povray()[1] )

[PyMOL] Coordinates of a mesh

Hi, I actual try to get the coordinates of the mesh from a protein/selection. At first I run the following command: open("pymol.mesh","w").write( cmd.get_povray()[1] ) There I get points shifted by one axis or something like that. Then somebody here from the mailinglist tells me that I have to u

Re: [PyMOL] Coordinates of the mesh-points

Hey Björn, The mesh will be in Pymol camera coordinates, not in PDB coordinates. You'll have to take the object_matrix (cmd.get_object_matrix) and apply it to the protein to convert it to the same space if you are to use it outside of Pymol. Hope it helps, Tsjerk On Mon, Aug 22, 2011 at 8:12 PM

[PyMOL] Coordinates of the mesh-points

Hey, I have a little problem to get the points/coordinates of a mesh. I know he command: open("pymol.mesh","w").write( cmd.get_povray()[1] ) But when I run this command, the coordinates of these spheres are not equal to these of the mesh. For example, if a generate the mesh for a protein and ru

Re: [PyMOL] coordinates

But it is very doable using grep/cut, you'll just have to use the -b flag that allows you to cut columns: grep CA .pdb | cut -b 13-26,30-54 Cheers, Tsjerk On Mon, Mar 22, 2010 at 3:58 PM, Robert Campbell wrote: > Hi Jed, > > On Mon, 22 Mar 2010 10:23:34 -0400 Jed Goldstone wrote: > >> Of

Re: [PyMOL] coordinates

Of course you're all correct - Thierry Fischmann already emailed me to correct me :) I hadn't actually tested anything (mea culpa). I was just trying to point out for those of us less familiar with python that there were alternatives to doing this relatively simple thing outside of pymol. Apol

Re: [PyMOL] coordinates

Hi Jed, On Mon, 22 Mar 2010 10:23:34 -0400 Jed Goldstone wrote: > Of course, you could just use the .pdb file as a text file: > > grep CA .pdb | cut -f 2,4,7,8,9 > > will get you the amino acid number, the amino acid identity, and x,y,z > coordinates for the CA. Often this will work, but

Re: [PyMOL] coordinates

Of course, you could just use the .pdb file as a text file: grep CA .pdb | cut -f 2,4,7,8,9 will get you the amino acid number, the amino acid identity, and x,y,z coordinates for the CA. Jed Jason Vertrees wrote: > In newer PyMOLs this is as simple as: > > print cmd.get_atom_coords(oneAtom

Re: [PyMOL] coordinates

In newer PyMOLs this is as simple as: print cmd.get_atom_coords(oneAtom) where 'oneAtom' is an object or selection of one atom in PyMOL. For example, load $TUT/1hpv.pdb print cmd.get_atom_coords("A/30/CA"); -- Jason On Mon, Mar 22, 2010 at 9:04 AM, Tsjerk Wassenaar wrote: > Hi Mohan, > > You

Re: [PyMOL] coordinates

Hi Mohan, You can use iterate_state, which would be the pymol approach: coords = {} iterate_state 1,n. ca,coords[i]=(x,y,z) Or you can take a lower level approach; the python one: for i in cmd.get_model('n. ca').atom: print i.coord cmd.get_model builds you a ChemPy model from a given selecti

[PyMOL] coordinates

hi all: could any one tell me how to get the coordinates for a specific atom in a particular amino acid using pymol commands is their a commant with can list the coordinates for each aminoacid in a protein molecule?? \ kindly clarify, thanking you in advance. - mohan ---

RE: [PyMOL] Coordinates for End Groups

> From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > "Dr. Ramón Garduño-Juárez" > Sent: Tuesday, February 08, 2005 1:02 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Coordinates for End Groups >

[PyMOL] Coordinates for End Groups

Dear Pymol-users: We are working on an interface between PYMOL and ECEPP/3 inorder to perform a conformational search in small peptides. We have done most of the dirty work, but still can not figure out how to include coordinates for End Groups other than the ones given in the modules/chempy s