Re: [PyMOL] Showing conserved residues

[Donnie Berkholz]

On 13:10 Thu 29 Jan , Abhinav Kumar wrote:
> Is there someway to select and show conserved residues when a bunch of 
> superimposed structures are loaded into Pymol?
> And if so, can identical and similar residues be selected separately?

I often use ConSurf, which will give you a PDB with a conservation index 
in the B-factor field. You can then load that into PyMol and color by B 
as usual.

Since it's unclear exactly what you intend to do with this, I can't tell 
you whether ConSurf makes sense for your use.

-- 
Thanks,
Donnie

Donnie Berkholz
Developer, Gentoo Linux
Blog: http://dberkholz.wordpress.com


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[PyMOL] Surface Residues

[QT]

Dear all,

Once again, I need some help from pymol experts.  I would like to select
surface residues via the surface calculation algorithm of Pymol.  Is this
possible?  What is the surface calculation algorithm that Pymol use and is
it scattered among many source-code files or is it contained in just one
source-code file?

Thanks in advance.
Best,
Quyen

[PyMOL] plugins for MacPyMOL?

[Matthew O'Meara]

Hi,
We have created a wizard that we would like to distribute, however a fair
number of our users will be using the MacPyMOL version.  It seems that the
Plugin menu has been disabled as well as running scripts from the
"file->run..." menu.  Also plugin scripts dropped by hand into the
modules/pmg_tk/startup folder are not executed.  Why has it been disabled?
 Is there anyway that I can allow users to install our wizard?

Thanks,

Matt

Re: [PyMOL] plugins for MacPyMOL?

[Warren DeLano]

Matt,

 

Please note that we have not taken anything away!  MacPyMOL simply is
not (and has never been a Tcl/Tk/Tkinter)-based application in its
default configuration.  

 

To run it as an X11-based Tcl/Tk:  First, make sure that X11 is
installed and launched.  Then make a copy of MacPyMOL and rename it:

 

PyMOLX11Hybrid

 

When double-clicked, this renamed build will then launch using the same
Tcl/Tk/tkinter-based interface as the Windows and Linux versions.

 

Cheers,

Warren

 



From: Matthew O'Meara [mailto:mome...@email.unc.edu] 
Sent: Friday, January 30, 2009 6:45 AM
To: pymol-users@lists.sourceforge.net
Cc: Jon Latane
Subject: [PyMOL] plugins for MacPyMOL?

 

Hi,

 

We have created a wizard that we would like to distribute, however a
fair number of our users will be using the MacPyMOL version.  It seems
that the Plugin menu has been disabled as well as running scripts from
the "file->run..." menu.  Also plugin scripts dropped by hand into the
modules/pmg_tk/startup folder are not executed.  Why has it been
disabled?  Is there anyway that I can allow users to install our wizard?


 

Thanks,

 

Matt