Hi Suhaila,
Correct me if I'm wrong but you want create *new* GUI elements for
pymol to enhance your application, right?
To my knowledge, there is not a great tutorial on this, but I can give
you some pointers to plugins that do this currently and hopefully you
can backfill some knowledge.
The f
gt; From: tlin...@gmail.com
> Date: Thu, 22 Mar 2012 22:14:39 +0100
> CC: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] GUI to improve interaction between user and PyMOL
>
>
> That is seriously the strangest thing I ever heard about...
>
> The GUI is for the sm
in...@gmail.com
Date: Thu, 22 Mar 2012 22:14:39 +0100
CC: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] GUI to improve interaction between user and PyMOL
That is seriously the strangest thing I ever heard about...
The GUI is for the small fast thing to do.Why just don't press all button
Hi Sajeewa,
paste this into a python script (script.py):
from pymol import cmd
for i in range(1, 240+1):
cmd.reinitialize()
cmd.load('%d.pse' % i)
cmd.do('@%d.pml' % i)
cmd.sync()
cmd.save('%dnew.pse' % i)
Run it with PyMOL in batch mode:
pymol -cqr script.py
See also
Hi everyone,
I have a set of (240 files) of pse files like
1.pse
2.pse
.
.
.
240.pse
I also have a set of(240 files) pml files like
1.pml
2.pml
.
.
.
240.pml
I want execute the pml files iteratively on the corresponding pse files and
save the new pse files as 1new.pse,2new.pse, so on. from the
Hi Spyros,
> Thank you for the links, this documentation is helpful! I am not actually
> creating alignments, I just choose the "Display => Sequence" option from the
> external GUI menu to get the protein sequence of my PDB structure. I was
> meaning to ask - for a couple of PDB structures when Py
Hi Spyros,
> Because I wish to determine if I can
> correlate the database motifs with ligand-binding residues, what I would
> like is some way of superimposing (if possible) one selection onto the
> other. I would color-code the selections (if possible, again) so that I
> could see if one was "on
Hi Spyros,
> Creating selections the default way places pixel-size pink dots on
> the structure, so I was wondering if there is some way to control
> this for more complex visualization tasks?
set active_selections, off
set auto_show_selections, off
both seem to hide the pixels, but I'm not sure
Hi Spyros,
In cases like these, I think it's usually best to use colours for the
selections and for the overlap:
color cyan, selection1
color yellow, selection2
color hotpink, selection1 and selection2
Hope it helps,
Tsjerk
On Tue, Jul 12, 2011 at 1:14 AM, Spyros Charonis wrote:
> Hello PyMOL
Hello PyMOLers,
A visualization query:
I have a PDB structure of a GPCR to which I have added two selections, one
where I highlight certain motif sequences extracted from a database, and the
second where I highlight a set
of residues that bind ligands. Because I wish to determine if I can
correla
; RSMD for aligning 1cll to 1ggz is: 3.85577607155
>
> as the last line of output.
>
> Cheers,
>
> -- Jason
>
>
> On Sun, Sep 12, 2010 at 6:09 PM, Li Xue wrote:
> > Hello all,
> >
> > Does someone happen to know how call the pymol commands (for example,
>
w how call the pymol commands (for example,
> align) without opening Pymol GUI window?
>
> Thanks.
>
> --
> Xue, Li
> Bioinformatics and Computational Biology program
> Computer Science
>
Hello all,
Does someone happen to know how call the pymol commands (for example,
align) without opening Pymol GUI window?
Thanks.
--
Xue, Li
Bioinformatics and Computational Biology program
Computer Science
Iowa State University
Ames, IA 50010 - USA
Tel: 1-515-450-7183
Email: me.li
rs,
Warren
From: Bala subramanian [mailto:bala.biophys...@gmail.com]
Sent: Friday, March 13, 2009 5:01 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] not getting pymol gui
Hai all,
Hai all,
Few days back, i wrote a mail regarding the problem of not getting pymol gui
while starting pymol. The folllowing are the errors it throws when i give
pymol in command line.
freeglut (pymol): Unable to create direct context rendering for window
'PyMOL Viewer'
This may hurt p
hello,
is it possible to define the gui and viewer positions on startup separately?
thanks,
marc
radiovar.get() seems to work fine for me with the code you provided.
You mention .get() but you never say radiovar.get(), so is that what
you meant? Also, radiovar.set(2) works as well for changing the
selection.
- Charlie
On 2/13/06, Martin Weisel wrote:
> Hi folks,
>
> I figured out how to p
Hi folks,
I figured out how to preselect a Radiobutton in a Tkinter-GUI. One ought to
use .select() instead of .set().
But now I've come up with another problem: How do I get the actual value of
that Radiobutton? For some reason .get() is returning 0 all the times.
from Tkinter import *
radio =
Hi everybody.
I'm currently trying to create a pop-up GUI with Radiobuttons (e.g.
checkboxes). I don't know why initial highlighting of a specific Checkbox
won't work. Attribute .set() fails at this point (see below), although
the GUI looks nice.
from Tkinter import *
root = Tk()
def
y 20, 2006 3:01 PM
To: Pymol
Subject: [PyMOL] GUI
Hi Warren,
Why can't we have little check marks in the main menu that indicate the
current setting?
For example, Setting>Rendering>Antialias gets a check, but
selecting Setting>Rendering>Shadows>None doesn't give a
Hi Warren,
Why can't we have little check marks in the main menu that indicate
the current setting?
For example, Setting>Rendering>Antialias gets a check, but
selecting Setting>Rendering>Shadows>None doesn't give a check (as do
any of the other rendering options).
Mark
_
--Original Message-
> From: pymol-users-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> Björn Kauppi
> Sent: Thursday, January 19, 2006 5:02 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] GUI output font size too small
>
Hi,
How do I control the GUI output window font size? It is too small for my eyes
on a 1600x1200 screen. I can change it manually to 12 points in the GUI window
Setting/Output size, but I can not find a command to do it for my .pymolrc!
Preferably to more than 12 points as well...
I use 0.99be
Hello everybody
At home, I run pymol on Debian/Linux without any problems. However, at
university, we only have windows machines. So I downloaded and installed
Python2.2.1, ActiveTCL 8.3.4.3 and, of course, Pymol 0.82.
So far, I can run (and use) pymol giving commands in the OpenGL window, but
the
24 matches
Mail list logo
