: [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 and see?
It can only take a little time.
Or google: pymol + name of button
That should give you
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
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 and
see?It can only
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
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
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 s.charo...@gmail.com
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,
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 top
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 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
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...@gmail.com
--
Start
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 performance
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,
Few days
hello,
is it possible to define the gui and viewer positions on startup separately?
thanks,
marc
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 =
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 martin.wei...@gmx.de wrote:
Hi folks,
I
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
Hi Warren,
Why can't we have little check marks in the main menu that indicate
the current setting?
For example, SettingRenderingAntialias gets a check, but
selecting SettingRenderingShadowsNone doesn't give a check (as do
any of the other rendering options).
Mark
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, SettingRenderingAntialias gets a check, but
selecting SettingRenderingShadowsNone doesn't give a check (as do any
of the other rendering options
: 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
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
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