Re: [PyMOL] FW: Query of running script of Contact Map Visualizer Plugin

Hi Suhaila, I uploaded a modified version (2.1) of the contact map visualizer plugin. It now provides a command so it can be called from command line. This will also work if you "run" the script instead of installing it as a plugin. USAGE contact_map_visualizer [ image_file [, selection

Re: [PyMOL] problem with running py script in pymol

> But I get the following errors. Could anyone please help me in > overcoming this error? > > Traceback (most recent call last): >File "C:\Program Files (x86)\PyMOL\PyMOL/modules\pymol\parser.py", > line 338, in parse > parsing.run_file(path,self.pymol_names,self.pymol_names) >File "C:

Re: [PyMOL] FW: Query of running script of Contact Map Visualizer Plugin

Hello Thomas. Where exactly did you upload the modified script? I can't see any attachment here. Cheers,Suhaila. > Date: Thu, 22 Mar 2012 09:46:05 +0100 > From: spel...@users.sourceforge.net > To: bell_beaut...@hotmail.com > CC: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] FW: Query

Re: [PyMOL] FW: Query of running script of Contact Map Visualizer Plugin

Oh I see what you mean now. It's on the website. I'll have a try with it right away. Many thanks Thomas!Suhaila > Date: Thu, 22 Mar 2012 09:46:05 +0100 > From: spel...@users.sourceforge.net > To: bell_beaut...@hotmail.com > CC: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] FW: Query o

[PyMOL] clicking to select cgo objects

Hi, Is there a way to select a CGO object by clicking on it in the display? Is it possible to add python handler for a mouse-click event? The scenario is this: I draw some CGO objects to the display. When the user clicks on one, I want to hide that object and display another one. -Peter ---

Re: [PyMOL] FW: Query of running script of Contact Map Visualizer Plugin

Hello Thomas. I tried running the following: contact_map_visualizer [ contact-map.xpm [, contact-map.jpg]] on Linux terminal command line or is it supposed to be contact_map_visualizer [ contact-map.xpm [, jpg]] Or is it supposed to be running on PyMOL command line? Cheers, Suhaila > Date: Th

[PyMOL] FW: FW: Query of running script of Contact Map Visualizer Plugin

And also I checked via PyMOL command line that it doesn't contain g_mdmat but my Linux terminal does have it. How should I connect so that g_mdmat is found in PATH from a running PyMOL session? Just move the Gromacs file directory under PyMOL? Many thanks, Suhaila. From: bell_beaut...@hotmail

Re: [PyMOL] FW: FW: Query of running script of Contact Map Visualizer Plugin

Hi Suhaila, "contact_map_visualizer" is a PyMOL command, so you need to type it in the PyMOL command line. You must not type the square brackets, these denote optional arguments. Example: PyMOL> load structure.pdb PyMOL> contact_map_visualizer contact-map.xpm "g_mdmat" is not a PyMOL command,

[PyMOL] Maximum number of objects/menu items in internal GUI ? machine has lots of RAM and big GPU- Solved

Hello All, I managed to solve the problem where many objects were not getting included into a script created session "all" meta object  with help from Jason . Once I got rid of duplicate object names either using python or the setting "auto_rename_duplicates"..I could load around 250 objects witho

[PyMOL] old-school stereo and Lion

The imminent replacement of Mobile-Me by iCloud provides an impetus for me to upgrade to Lion; but I'm currently happily using old-school stereo (i.e., a CRT monitor + Crystal-Eyes LCD glasses) under Snow Leopard. Can anyone attest to being able to use such equipment with Coot/PyMol under LIon?

Re: [PyMOL] clicking to select cgo objects

Hi Peter, > Is there a way to select a CGO object by clicking on it in the display? > > Is it possible to add python handler for a mouse-click event? > > The scenario is this: I draw some CGO objects to the display. When the > user clicks on one, I want to hide that object and display another one.

[PyMOL] Hide lines for certain states, combine states

Hello, I was wondering if anyone could help me with some state mapping for movies. I have 1000 states or so that are output from a dynamics simulation automatically to pymol. I was wondering two things: 1. Can I hide the lines for state 500-1000 and show the lines for 1-500? I have all the sta

Re: [PyMOL] GUI to improve interaction between user and PyMOL

OK. It does sound pretty weird prolly because the way I asked isn't precise. We plot predicted contacts that can be viewed in various ways. So it'd be better to create a GUI select menu or something like that for user's ease of interacting with our project. Suhaila. From: tlin...@gmail.com Dat

Re: [PyMOL] Hide lines for certain states, combine states

Jordan, The 'hide' and 'show' commands to not take a state parameter. You could use the "multiplex" option when loading the trajectories and then use 'mdo' in the movie to control which states are shown/hidden. This will slow down moviemaking and be a pain, but will get you where you need to be.