Olivier,
But how do I find out specular's (or ANY variable's) value without
changing it?
I wrote a little extension called 'grepset' that does what you want and it
is great for finding out about other settings.
It is available at the pymol wiki site:
http://www.pymolwiki.org/index.
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
Andreas Henschel wrote:
Is it the only possibility to put all functions
> that share memory in the same plugin?
no. you can do the following:
from pymol import cmd,stored
stored.colorDict = {
'blue': '/1ewf//A/1-217 and not hetatm',
But, '#' doesn't work in p1m file.
Error: unrecognized keyword: #second
The # line involves an error but the script goes on.
I think indeed you found a bug with the parsing of p1m files.
I have the same behaviour on my Linux computer.
Nice choice of colors by the way.
Cheers,
Zac
'#' seems to be incorrect:
It is not incorrect.
If you post your script and how you use it we might be able to help.
Also, if you have something in you $HOME/.pymolrc or $HOME/.pymolrc.py
you should try temporarily moving these files elsewhere and trying again.
Something may have gone wrong in
I try to add comment lines in my pml scripts but I don't know how to do.
I tried #, /*, //,
I have the impression that this driver release (nvidia 7664)
fixed the need of the setting stereo_double_pump_mono.
This might effectively double the performance of Nvidia cards
configured to support quad-buffered stereo.
Can anyone confirm this?
Zac
Hello Ramesh,
> Is it possible to do the labelling using single letter codes for the
> amino acid residues rather than the three letter codes?
Yes.
1. Add this to your $HOME/.pymolrc file:
# start $HOME/.pymolrc modification
one_letter = {'VAL':'V', 'ILE':'I', 'LEU':'L', 'GLU':'E', 'GLN':'Q',
Hi,
I've installed the nvidia driver 7664 and it works very well
with PyMOL 0.98 under Linux (Centos4/rhel4) without crashes so far.
Zac
--
Ezequiel PANEPUCCI, Ph.D. - Institut Pasteur
Plate-Forme 6 - Cristallogénèse et Diffraction des Rayons X
Douglas Kojetin wrote:
Building on the two previous posts, is it necessary to use 'viewport'
before executing 'ray'?
this:
ray 2000, 2000
instead of:
viewport 700, 700
ray 2000, 2000
I didn't quite understand your post. The viewport command prior to ray
tracing is just so you have
yvonne leduc wrote:
I would like some confirmation or explanation about the differences I
see, and the way I understand it.
Hello Yvonne,
The command "ray" does not care about the size of your display, it may
even be used in batch mode on a computer that does not have a monitor
attached to it
Nat Echols wrote:
I'm trying to use Robert Campbell's draw_axes script with PyMOL 0.97 on
Linux. Is there a simple way to get stock PyMOL to recognize stock CCTBX?
I'm not having any success here. (If I have to I'll use the special
distribution on the lab's Mac, but I'd rather just get it going
Naveen,
I recommend graphics cards with the nvidia quadro4 xgl chips.
We several PNY Quadro4 700 XGL and they work great.
The caveat is that if you have it configured for quad buffered
Stereo then mono display (the usual) will be low performance.
zac
Naveen Michaud-Agrawal wrote:
Hi, this is mor
Hello There,
I noticed that my "button" command reassignments in $HOME/.pymolrc
are ignored/overruled when loading session files either from
the load command or from the command line.
These are the assignments that get reset when loading session files:
button m,None,PkAt
button m,
Hello There,
I am trying to download the CVS version from pymol but
I get a connection refused message.
Logging in to
:pserver:anonym...@cvs.pymol.sourceforge.net:2401/cvsroot/pymol
CVS password:
cvs [login aborted]: connect to
cvs.pymol.sourceforge.net(66.35.250.207):2401 failed: Connection r
Viktor,
maybe pymol is also ray tracing the lines which have a fixed
rendered radius. the fix for this is to "hide lines, (selection)"
where selection is the atoms/bonds you want represented as thin sticks.
zac
Viktor Hornak wrote:
I've noticed another minor problem with internal raytracer: w
select ligands, (byres gmp expand 5 and psd)
selects whole residues from molecule psd within 5 A from gmp
aaron.b.mil...@gsk.com wrote:
Hello,
I am somewhat new to PYMOL and was trying to create a selection of atoms.
What I need to do is select all atoms of a protein that are within 5
angstro
Hi People,
For your information, the latest Nvidia driver does not support stereo
with a dual monitor (aka TwinView) configuration.
It might work if you have 2 graphics cards though I haven't tried that.
Does any one know if this is possible with any of the ati firegl cards?
Thanks,
Zac
Oops!
I forgot to mention that this is related to the GeForce4 Ti 4400
that we have in our lab. So I am guessing it also applies to the
Ti4600.
On the other hand, the Quadro4 700 XGL works fine, except for the
annoying stereo-good mono-bad performance glitch.
Zac
DeLano, Warren wrote:
Zac,
Nathaniel Echols wrote:
By the way, has anyone else experimented with hardware antialiasing on
NVidia cards under Linux? I've had mixed results so far, and I'm not sure
what I'm doing wrong (this is with a GeForce 4 Ti 4600).
the nvidia driver (as far as 28.90) does not allow for simultan
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