Evangelos,
Maybe you could write a wizard instead of a script, look at
C:\..\pymol\modules\pymol\wizard\renaming.py
Zac
evangelos papadopoulos wrote:
Hello all,
I am using the windows binaries for PyMol. Whereas in Python it is
easy to do a:
a=raw_input()
When I use PyMol under windo
Sebastien,
I cannot
change the color for rendering modes I defined.
I do not understand what you mean by this.
Cheers,
Warren
I mean that the color, for cartoon view, is unchangeable when 'set
cartoon_color' is defined in the $HOME/.pymolrc file.
Thus, when I define 'set cartoon_color' in
Hi,
I'm trying to apply the command 'set_dihedral' to residue from a
molecule object which contains only three non-consecutive residues from
the original protein. The program complains with the following error
message:
GetDihedral-Error: Selection 1 doesn't contain a single atom/vertex.
GetD
Esben,
Fantastic! I wasn't aware that nVidia quadro cards could do this. That
provides a compelling reason to purchase nVidia Quadro cards for passive
stereo under Linux.
For the record: to configure passive stereo using the quadbuffer API
with a Quadro card under Linux, XF86Config needs to be
Ah...
That make things a bit clearer :-) We do have a geowall, but the Linux driver
supplied by Nvidia directly supports sending the left and right images of the
quad-buffered stereo to the two separate video heads on the card, which are
then connected to the two projectors. This elimina
Andrew,
It's either-or for now. Either you can render pharmacophores using CGOs
or you can represent them as molecules and thus align them.
Cheers,
Warren
--
Warren L. DeLano, Ph.D.
Principal Scientist
. DeLano Scientific LLC
. 400 Oyster Point Blvd., Suite 213
I'll try it when I get back to work tomorrow - but I'm a bit confused :-) The
features you mention, haven't they been part of PyMOL for some time already? We
have active stereo glasses for our workstations, and use the same PyMOL version
(0.99beta14) for those and the Geowall.
Cheers,
Esben
The best way to approach this is simply to build a small molecular object on
the fly.
See examples/devel/chempy_model*.py
Cheers,
Warren
--
Warren L. DeLano, Ph.D.
Principal Scientist
. DeLano Scientific LLC
. 400 Oyster Point Blvd., Suite 213
. South San Fran
Evangelos,
This is architecturally impossible in PyMOL due to clash between the
asychronous nature of GUI event handling and the synchronous nature of
script execution using the main thread.
Right now, the best thing you can do is add a new command into the
language which calls your function foll
Michael
d/l a recent build http://delsci.com/beta
and use the "find"->"polar contacts" option under the objects Action "A"
menu in the viewer window.
Cheers,
Warren
--
Warren L. DeLano, Ph.D.
Principal Scientist
. DeLano Scientific LLC
. 400 Oyster Point Blvd., Suite 21
Sebastien,
* Sebastien Moretti [2005-10-17 08:41]
wrote:
> >Sebastien,
> >
> >>I cannot
> >>change the color for rendering modes I defined.
> >
> >I do not understand what you mean by this.
> >
> >Cheers,
> >Warren
>
> I mean that the color, for cartoon view, is unchangeable when 'set
> carto
PyMOL Users:
Regarding "geowalls" [also known as dual-projector passive stereo setups
that use polarized lenses & glasses to deliver low-cost stereo 3D to
large audiences]...
Does anyone have one set up right now who might be able to test a new
PyMOL build with improved geowall stereo support?
C
Hello everybody,
I am new to PyMOL and I have a short question: In pyMOL - is it possible to
automatically compute and visualize H-bonds in .PDB files as it is e.g.
possible in SWISS-PDB-VIEWER? Maybe there is a pyMOL script for this purpose? I
need such a function for my work with catalytically
Hello all,
I am using the windows binaries for PyMol. Whereas in Python it is
easy to do a:
a=raw_input()
When I use PyMol under windows it either gets crashed or halted while I
am unable to input from keybord. I searched in this email list and I
found some similar questions but no answer.
Hi all!
I'm trying to pick a discrete coordinate outside of the loaded protein
structure (something like "create name, coord[x,y,z]") to which I can
apply the "around" command. Creating an additional atom as a probe
would be a makeshift solution. Is there a way to use the Fragment Builder
Michael Morbious wrote:
> Dear All,
> I am a new pymol user. Does anyone know if it is
> possible to merge four units (all units are same) of a
> tetrameric assembly by using pymol? Each unit has the
> same Id and when I load each of them, they overlap.
> If you please help me, I will be really
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