[PyMOL] How do I select an atom in the command line

Hi. I have a xyz file in the following form: C0 0 0 O0 0 1 O0 0 2 C0 0 6 O0 0 5 O0 0 4 . . . How can I select an atom from the list? How can I measure an atom from that list? -- My other email account has a professional

Re: [PyMOL] How do I select an atom in the command line

Is this a .pdb file which can be opened with pymol? Can you provide a file that pymol accepts? Can you in some way find the id number? Check out these commands in pymol: print cmd.get_names() print cmd.get_pdbstr(chain A) print cmd.get_pdbstr(chain A).splitlines() print cmd.get_pdbstr(chain

Re: [PyMOL] How do I select an atom in the command line

The xyz http://en.wikipedia.org/wiki/XYZ_file_format file format opens easily with pymol (pymol fileName.xyz). I can find the id that pymol gives to the ``atom'' via the GUI but I don't know what to do with it. I tried select 2338 (a valid number) but I get Selector-Error: Invalid selection name

Re: [PyMOL] How do I select an atom in the command line

Check this page: http://pymol.sourceforge.net/newman/user/S0220commands.html On the middle of the page. you would probably need: select id 2338 or select index 2338 (Probably this) The id, is the id number which is provided external in the pdb file. Normally the column after ATOM. Beside the id

Re: [PyMOL] How do I select an atom in the command line

Great, thanks 2011/8/22 Troels Emtekær Linnet tlin...@gmail.com Check this page: http://pymol.sourceforge.net/newman/user/S0220commands.html On the middle of the page. you would probably need: select id 2338 or select index 2338 (Probably this) The id, is the id number which is

Re: [PyMOL] Interacting with Mutagenesis wizard in command line.

Hi Troels It's indeed possible. The wizards are available through the cmd module. # Initialize load yourProtein cmd.wizard(mutagenesis) cmd.do(refresh_wizard) # To get an overview over the wizard API: for i in dir(cmd.get_wizard(): print i # lets mutate residue 104 to GLN

Re: [PyMOL] Interacting with Mutagenesis wizard in command line.

Absolutely fantastic! :-) I got this to work with the pymol propka script. fetch 1ohr, async=0 create 1ohrB3C, 1ohr hide everything, all show cartoon, 1ohrB3C cmd.wizard(mutagenesis) cmd.do(refresh_wizard) # To get an overview over the wizard API: #for i in dir(cmd.get_wizard()): print i #

Re: [PyMOL] Interacting with Mutagenesis wizard in command line.

to close the wizard, you can also apply cmd.set_wizard(done) and you need to be carefull about the rotamer you're choosing. it happens that the first one ends up being in physically non-reasonable contact distance to other residues, so atoms become overlayed. also, the mutagenesis wizard has

Re: [PyMOL] Interacting with Mutagenesis wizard in command line.

Thanks! Your comments are gold! I put the warning on the propka page. http://pymolwiki.org/index.php/Propka#Mutagenesis_analysis Best Troels Troels Emtekær Linnet Karl-Liebknecht-Straße 53, 2 RE http://maps.google.dk/ 04107 Leipzig, Tyskland Mobil: +49 1577-8944752 2011/8/22 Martin Hediger

[PyMOL] pymol propka: Fetching and displaying the pKa of your protein - Fast and easy

Hi PyMOL'ers. I am happy to announce, that I have finished working on a script that fetches the pKa values of your protein. The script contacts, download results, processes the files, and write a pymol command that make pka atoms, labels, colors, bonds, distances and such. See more here:

[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 run

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

[PyMOL] Ray tracing - distinction between inside and outside of binding pocket

Hi, Having prepared and superimposed the binding pockets that I spoke of in my earlier email, I'm now trying to come up with a way of producing high resolution images of them. The problem I'm now facing is that I can't seem to come up with a high-res rendering that clearly distinguishes

[PyMOL] pymolrc file on Windows7

Dear all, I have quite silly question but I could not find an answer so far. I am trying to use Pymol in a Power point presentation. For that I would like to change the default setting in Pymol - set security, off I have created a file pymolrc and put it in C:/Program Files/PyMol/PyMol/. When I

Re: [PyMOL] pymolrc file on Windows7

Hi Tanya, Does it say more than syntax error? Can you send the whole output? (copy crom the grey screen). In addition, can you send the pymolrc file as attachment? There might be something to do with line endings; so don't paste it in the mail, but attach the actual file that fails. Cheers,