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
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
Hi Tom,
On Thu, 04 Oct 2007 11:20:35 -0700, Tom tl...@optonline.net 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
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 =[]
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
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
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
pseudoatom myobj, pos=[1.4,3.5,2.4]
PyMOLpseudoatom ?
Usage: pseudoatom object [, selection [, name [, resn [, resi [, chain [,
segi [, elem [, vdw [, hetatm [, b [, q [, color [, label [, pos [, state [,
mode [, quiet ]
_
From:
_
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
