[PyMOL] Custom surface?

Hi everybody. Is it possible to define some surface mathematically in pymol? I can generate points for my surface but how can I plot it in pymol? For example if I want to make a toroid surface? Thanks. ___ PyMOL-users mailing list Archives: http://www.

[PyMOL] Cmd: PyMOL lagging behind API requests...

Hi. I try to run pymol via python in batch mode. It works fine if I define all variables in the python file. But it stops working when I send variables as cli arguments. With multiple messages like : Cmd: PyMOL lagging behind API requests... Any hints? Thanks. Petro. ___

Re: [PyMOL] Amber trajectories

Hi Hira. I have had similar experience. The trick is that you have to load them into the same object. load file.top, protein load file.rst, protein where protein, is the object name. Best. Petro *[PyMOL] Amber trajectories * From: Hira

[PyMOL] How to label a cartoon representation?

Hi all. I have a protein structure in cartoon representation. It has 5 helices and iconnecting loops. I have colored 3 of the helices in to different color. now i want to add text label to them. How can I do it? Thanks. Petro. ---

[PyMOL] How to disable automatic atom connection?

Hi all. How can I disable automatic atom connection in pymol. I want Pymol to make bonds only using connect field in pdb file. Thanks. Petro.

Re: [PyMOL] identification of residue names

Hi Martin May be this will help: from sets import Set list =[] cmd.iterate('het', 'list.append(resn)') residname =Set(list) print residname Best. Petro Hi there, how can I collect the identifiers contained in a pdb-file in a list, so that there is one identifier for EACH residue - even if mul

[PyMOL] is there bond ? How to check?

Hi all I want to write a script like this: if there is bond between atom1 and atom2 do something elif there is no bond between atom1 and atom2 do something else. But I don't know how to check the bond existence between atoms in Pymol. Thanks in advance for any idea how to do it. Pet

[PyMOL] How to save hydrogen bonds?

Dear all. Does anybody know the way to save hydrogen bonds in pymol (HYDBND field in pdb file). An alternative can be to list all pairs of atom ids connected by dashed lines using "find ->polar contacts" Thanks. Petro.

[PyMOL] script error? SyntaxError: invalid syntax

Hi all I have some errors if I run script: PyMOL>run c:\pict.pml Traceback (most recent call last): File "C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parser.py", line 273, in parse parsing.run_file(exp_path(args[nest][0]),pymol_names,pymol_names) File "C:\Program Files\DeLano Scie

[PyMOL] Surface atoms again

Dear all. I need to select surface atoms. Friend of mine recommended me this way: For solvent accessible surface one can try Molmol: Load your molecule, say " SelectAtom '' " in command line, say "CalcSurface" - select the solvent radius (1.4A for water by default), put "by atom" radio button on