[PyMOL] Test - please ignore

_ Joel Tyndall, PhD Lecturer National School of Pharmacy University of Otago PO Box 913 Dunedin 9054 New Zealand Pukenga Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 913 Otepoti 9054 Aotearoa Ph / Waea

Re: [PyMOL] place atom at coordinates/screen center?

pseudoatom myobj, pos=[1.4,3.5,2.4] PyMOL>pseudoatom ? Usage: pseudoatom object [, selection [, name [, resn [, resi [, chain [, segi [, elem [, vdw [, hetatm [, b [, q [, color [, label [, pos [, state [, mode [, quiet ] _ From: pymol-users-boun...@lists.sourcefor

[PyMOL] place atom at coordinates/screen center?

I feel like I should already know this one, but is there a command line way to add an atom at specified coordinates? or at screen center? I thought there was a new-ish pseudoatom functionality but I can't seem to find or recall details. Can one specificy atom type as well? I was looking to annotat

Re: [PyMOL] Problems importing pymol functionality under a pythonscript.

David, Not sure, but you may need a vanilla "import pymol" before "from pymol import cmd". -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info "Not yet a PyMOL Subscriber, but want to support the project? Email sa...@delsci.com to quote your lab, school, or employe

Re: [PyMOL] APBS-electrostatics

Gianluigi, The API changed in PyMOL 1.0 in order to accomodate multiple PyMOL instances in a single Python interpreter -- your wizard needs to be updated so that the init method takes a "_self" keyword argument: def __init__(, _self=cmd): ... -- DeLano Scientific LLC Subscriber Support

Re: [PyMOL] moving objects freely

The "drag" action provides an easier to use solution. Right click on the atom, select molecule/chain/object then drag. >From that point on, shift-left, shift-middle, and shift-right click can be used to move those atoms. -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.i

Re: [PyMOL] identification of residue names

het_dict = {} cmd.iterate('het', 'het_dict[resn]=None') print het_dict.keys() -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info "Not yet a PyMOL Subscriber, but want to support the project? Email sa...@delsci.com to quote your lab, school, or employer. Thank you fo

[PyMOL] identification of residue names

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 multiple ligands have the same name. When I iterate over 'het', lots of identifiers are added to my list - one for each atom. list =[] cmd.iterate('het',

Re: [PyMOL] moving objects freely

Hi Tom, On Thu, 04 Oct 2007 11:20:35 -0700, Tom wrote: > From time to time, I have a need to manually move objects relative to > one another. For example, manual docking of a ligand requires that it the > translated and rotated relative to its binding pocket. It there a simple, > intuitive

[PyMOL] moving objects freely

From time to time, I have a need to manually move objects relative to one another. For example, manual docking of a ligand requires that it the translated and rotated relative to its binding pocket. It there a simple, intuitive way to do this? Thank a lot, Tom Leyh Professor of Bi

[PyMOL] APBS-electrostatics

Hi everybody, I am trying to use the "electrostatic" wizard to read some .dx file I made. It always worked..since I up-graded to pymol 1.0. Now it doesn't work ( I have already checked the "modification" in __init__.py file, it's fine). The message it give to me is: Traceback (most r

[PyMOL] Problems importing pymol functionality under a python script.

Dear PyMol Users, I am developing some programs in python. In one of them, I would need to use some PyMol funcionalities. However, I keep getting errors that I'm not able to solve. I've checked the __main__.py file instructions on the header, it doesn't work either. I'm using the following : D