Re: [PyMOL] Custom menus and shortcuts?
Hi Boris, Boris Kheyfets wrote, On 10/23/12 19:28: [...] But I want bk_hides_W to be a toggler. So I need a way to set a state of my defun. If I do def bk_toggles_W (): Hides W molecules. if cmd.get(bk_toggles_W): cmd.hide(all) cmd.show(spheres, not (resn W)) cmd.set(bk_toggles_W, 0) else: cmd.show(spheres, resn W) cmd.set(bk_toggles_W, 1) pymol is upset -- I think it is because it doesn't know bk_toggles_W setting: If you need a global variable, use pymol.stored: from pymol import stored stored.bk_toggles_W = 0 def bk_toggles_W (): Hides W molecules. if stored.bk_toggles_W: cmd.hide(all) cmd.show(spheres, not (resn W)) stored.bk_toggles_W = 0 else: cmd.show(spheres, resn W) stored.bk_toggles_W = 1 Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] How to rotate entire section of structure relative to rest
Hi Alex, sculpting is not the right tool for your task. PyMOL has all the basic editing features like rotating around a bond etc. Enter Editing mode, pick a bond with the mouse and rotate around the bond by pressing CTRL and click-dragging a second atom. You can enter Editing Mouse Mode by clicking on the lower-right panel. Hope that helps. Cheers, Thomas On 22.10.2012 22:27, Alex Truong wrote: Hi All, I'm relatively new to this software, and even though I've been using it for a few months, I haven't really had to use some of the more advanced options yet. This would be my first foray into actual manipulation. That being said, I'm trying to figure out how to move a small section at the N-terminus of my protein while keeping the rest static. That is, I'd just like to be able to rotate one bond and fix the relative positions and structures of the entire rest of the protein. I did some googling, and there was something about a Sculpting feature, but when I tried it, sections lit up that I was not interested in, and I was basically moving tiny sections at a time without preserving the structures I wanted. Is there a way to just manipulate the angle so I can swing that section out and away from its current position? I'll deal with the positions of those individual residues if this cannot method cannot resolve my problem. Thanks, Alex -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Custom menus and shortcuts?
If you need a global variable, use pymol.stored
Thank You Thomas -- that solves it.
Boris.
On Tue, Oct 23, 2012 at 9:28 PM, Boris Kheyfets kheyfbo...@gmail.comwrote:
Found a solution.
Basically it is to add
pmg_tk/startup/newmenu.py
file with the following content:
from Tkinter import *
from pymol import cmd
def __init__(self):
self.menuBar.addmenu('NewMenu', 'Sample Menu')
self.menuBar.addmenuitem('NewMenu', 'command',
'White background',
label='White Background',
command = lambda : cmd.set(bg_rgb,[1,1,1]))
self.menuBar.addmenuitem('NewMenu', 'command',
'Black background',
label='Black Background',
command = lambda : cmd.set(bg_rgb,[0,0,0]))
This adds the menu.
I got what I wanted with:
- .pymolrc:
# custom scripts:
import imp
imp.load_source('bk_pymols', os.path.expanduser('~/.pymolrc.py'))
- .pymolrc.py
from pymol import cmd
def bk_notW ():
Makes notW selection.
cmd.select(notW, not (resn W))
def bk_hides_W ():
Hides W molecules.
cmd.hide(all)
cmd.show(spheres, not (resn W))
cmd.set_key('ALT-N', bk_notW)
cmd.set_key('ALT-W', bk_hides_W)
- and finally -- pmg_tk/startup/BK.py:
from Tkinter import *
from pymol import cmd
# custom scripts:
import imp, os
imp.load_source('bk_pymols', os.path.expanduser('~/.pymolrc.py'))
from bk_pymols import bk_notW, bk_hides_W
def __init__(self):
self.menuBar.addmenu('BK', 'My menus!')
self.menuBar.addmenuitem('BK', 'command',
'Makes notW [Alt-n]',
label='Makes notW [Alt-n]',
command = bk_notW)
self.menuBar.addmenuitem('BK', 'command',
'Hides W mols [Alt-w]',
label='Hides W mols [Alt-w]',
command = bk_hides_W)
Works like a charm: I have custom menus and I can bind any of its entries
to a key.
But I want bk_hides_W to be a toggler. So I need a way to set a state of
my defun.
If I do
def bk_toggles_W ():
Hides W molecules.
if cmd.get(bk_toggles_W):
cmd.hide(all)
cmd.show(spheres, not (resn W))
cmd.set(bk_toggles_W, 0)
else:
cmd.show(spheres, resn W)
cmd.set(bk_toggles_W, 1)
pymol is upset -- I think it is because it doesn't know bk_toggles_Wsetting:
Error: 1
QuietException Exception in Tk callback
Function: function bk_toggles_W at 0x7ff02d90cb90 (type: type
'function')
Args: ()
Traceback (innermost last):
File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py, line
1747, in __call__
return apply(self.func, args)
File /home/boris/.pymolrc.py, line 67, in bk_toggles_W
if cmd.get(bk_toggles_W):
File /home/boris/.local/lib/python2.7/site-packages/pymol/setting.py,
line 1300, in get
raise QuietException
QuietException: pymol.parsing.QuietException instance at 0x7ff018698518
How can I add the setting to pymol?
--
Boris.
On Tue, Oct 23, 2012 at 5:17 PM, Jason Vertrees
jason.vertr...@schrodinger.com wrote:
Hi Boris,
David Hall's suggestions are perfect.
Let me offer one more. If you can put up with programming a little
Python, check out pymol/modules/pymol/menu.py and
pymol/modules/pymol/preset.py. In menu.py you could add a No W menu
option (or similar) to the A Preset
Cheers,
-- Jason
On Tue, Oct 23, 2012 at 6:02 AM, Boris Kheyfets kheyfbo...@gmail.com
wrote:
Hello PyMOL users,
Menus
=
Is there a way I can add custom menu in PyMOL?
Ideally I'd like to be able to call both
* pml scripts, as well as
* full python pymol scrpts
Shortcuts
=
Similarly -- is there a way I can bind exectution of given
* pml script, or
* full python pymol script
to a given key?
The problem
===
The basic problem
-
The basic problem is to automate tasks one repeats frequenlty. For
example I
had to type::
select notW, not (resn W)
hide all
show spheres, notW
frequently.
The problem which leads to the need of menu
---
So I make a pml or full-python pymol script and load it.
But then I have to remember the name of the script. Which is terrible --
because I have custom scripts in each and every program that I use.
The problem which leads to the need of custom shortcuts
---
Having custom menu us great as a reminder of what scripts have You
written.
But it's terrible to click through the menus. One is much better with
shorcuts (hotkeys).
--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
Re: [PyMOL] wire-mesh spheres?
Hi Matt, There's currently no easy way to do this. Can you please send us some screenshots of what you'd like to see implemented? Cheers, -- Jason On Tue, Oct 23, 2012 at 4:16 PM, Matthew Baumgartner mp...@pitt.edu wrote: Hi, Is it now possible to have wire mesh cgo object spheres in pymol? I found this thread from a while ago (2004) but googleing, I didn't find anything more recent. The one sort of work around that I though of was to create pseudo-atoms and somehow modify their radius and then show them as mesh. But I would like to use CGO objects if possible. Does anyone have any suggestions? Thanks, Matt Baumgartner Sphere transparency example included below... ALPHA must preceed COLOR to be effective. PyMOL does not yet do a global sort of tranparent triangles, so there will be artifacts in OpenGL. Raytracing should look fine however. # from within a .py OR .pym file... from pymol.cgo import * from pymol import cmd obj = [ ALPHA, 1.0, COLOR, 1.0, 1.0, 1.0, SPHERE, 0.0, 0.0, 0.0, 0.5, ALPHA, 0.66, COLOR, 1.0, 0.0, 0.0, SPHERE, 1.0, 0.0, 0.0, 0.5, ALPHA, 0.33, COLOR, 0.0, 1.0, 0.0, SPHERE, 0.0, 1.0, 0.0, 0.5, ALPHA, 0.11, COLOR, 0.0, 0.0, 1.0, SPHERE, 0.0, 0.0, 1.0, 0.5, ] cmd.load_cgo(obj,'cgo01') Cheers,war...@delanoscientific.com Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Michael George Lerner Sent: Wednesday, November 17, 2004 9:43 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] wire-mesh spheres? Hi, I want to draw a bunch of spheres of various sizes and colors. I'm currently using cgos for this. No problem. Now, I also want to draw wire-mesh spheres. Does anyone have a script for making these? While I'm at it, is there a way to make cgos transparent? Thanks, -Michael -- This isn't a democracy;|_ |Michael Lerner it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan -Torrence, Bring It On| - against HTML email X | Biophysics | / \ | mler...@umich --- This SF.Net email is sponsored by: InterSystems CACHE FREE OODBMS DOWNLOAD - A multidimensional database that combines robust object and relational technologies, making it a perfect match for Java, C++,COM, XML, ODBC and JDBC. www.intersystems.com/match8 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] wire-mesh spheres?
Hi, So some brief background, I am writing a pymol plugin for displaying pharmacophores queries from ZincPharmer ( http://zincpharmer.csb.pitt.edu/), which is developed in my lab. Version 1 of my plugin is available here: http://sourceforge.net/projects/pharmer/files/ under the name load_query. Sorry if that quickly turned into an advertisement, but what I would like to be able to reproduce in pymol is something like this: http://i.imgur.com/hiX2i.png . Where the wire mesh sphere's represent the pharamacophores. Currently, I am using the cgo sphere's but they do not do well when there are overlapping pharmacophores (a common case). Thanks, Matt On 10/24/2012 03:06 PM, Jason Vertrees wrote: Hi Matt, There's currently no easy way to do this. Can you please send us some screenshots of what you'd like to see implemented? Cheers, -- Jason On Tue, Oct 23, 2012 at 4:16 PM, Matthew Baumgartner mp...@pitt.edu wrote: Hi, Is it now possible to have wire mesh cgo object spheres in pymol? I found this thread from a while ago (2004) but googleing, I didn't find anything more recent. The one sort of work around that I though of was to create pseudo-atoms and somehow modify their radius and then show them as mesh. But I would like to use CGO objects if possible. Does anyone have any suggestions? Thanks, Matt Baumgartner Sphere transparency example included below... ALPHA must preceed COLOR to be effective. PyMOL does not yet do a global sort of tranparent triangles, so there will be artifacts in OpenGL. Raytracing should look fine however. # from within a .py OR .pym file... from pymol.cgo import * from pymol import cmd obj = [ ALPHA, 1.0, COLOR, 1.0, 1.0, 1.0, SPHERE, 0.0, 0.0, 0.0, 0.5, ALPHA, 0.66, COLOR, 1.0, 0.0, 0.0, SPHERE, 1.0, 0.0, 0.0, 0.5, ALPHA, 0.33, COLOR, 0.0, 1.0, 0.0, SPHERE, 0.0, 1.0, 0.0, 0.5, ALPHA, 0.11, COLOR, 0.0, 0.0, 1.0, SPHERE, 0.0, 0.0, 1.0, 0.5, ] cmd.load_cgo(obj,'cgo01') Cheers,war...@delanoscientific.com Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Michael George Lerner Sent: Wednesday, November 17, 2004 9:43 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] wire-mesh spheres? Hi, I want to draw a bunch of spheres of various sizes and colors. I'm currently using cgos for this. No problem. Now, I also want to draw wire-mesh spheres. Does anyone have a script for making these? While I'm at it, is there a way to make cgos transparent? Thanks, -Michael -- This isn't a democracy;|_ |Michael Lerner it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan -Torrence, Bring It On| - against HTML email X | Biophysics | / \ | mler...@umich --- This SF.Net email is sponsored by: InterSystems CACHE FREE OODBMS DOWNLOAD - A multidimensional database that combines robust object and relational technologies, making it a perfect match for Java, C++,COM, XML, ODBC and JDBC. www.intersystems.com/match8 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_sfd2d_oct___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
