hi Doug & others who deal with bundles,
Many thanks for the suggestion. I worked something up using CNS/
python scripts -- but if anyone comes up with an all PyMOL
alternative, please share with the list!
Doug
i've written a quick-n-dirty python module to have pymol deal w/
multiple conformers of the same protein (NMR bundles, MD ensembles, etc)
by calculating the average structure and two types of residue-specific
RMSDs -- (i) RMSDs w/ respect to the average structure and (ii) a
pairwise RMSD that's averaged over all unique pairs (it's my
understanding that the first measure (which is <= the second measure for
a given residue) is more frequently used in the NMR world?). You can
find the "average3d.py" module (and samples of its usage) on my pymol
page by scrolling down to the "Averaging Structures!" row of the table
in the "PyMOL Examples" section (http://mccammon.ucsd.edu/~cmura/PyMOL ;
i should put it on pymolwiki soon).
details), load that into pymol, and voila. If the effect isn't enough,
you could always multiply your RMS values by some value (eg. 10). Good
luck!
JP Cartailler
This type of pre-processing of B-factors shouldn't be necessary -- you
should be able to get the desired effect by tweaking putty cartoon
settings (particularly 'cartoon_putty_scale_power'). you can see the
relevant settings (and their default vals) via Zaq Panepucci's nifty
grepset:
PyMOL>import grepset
PyMOL>grepset putty
cartoon_putty_quality 11.00000
cartoon_putty_radius 0.40000
cartoon_putty_range 2.00000
cartoon_putty_scale_max 4.00000
cartoon_putty_scale_min 0.60000
cartoon_putty_scale_power 1.50000
good luck,
cameron
=== pymol-users-requ...@lists.sourceforge.net wrote (on 07/21/2005 08:13
PM): ===
Subject:
Re: [PyMOL] putty/sausage NMR figure
From:
Douglas Kojetin <djkoj...@unity.ncsu.edu>
Date:
Thu, 21 Jul 2005 10:49:21 -0400
To:
pymol <pymol-users@lists.sourceforge.net>
To:
pymol <pymol-users@lists.sourceforge.net>
CC:
"Cartailler, Jean-Philippe" <jp.cartail...@vanderbilt.edu>
Many thanks for the suggestion. I worked something up using CNS/
python scripts -- but if anyone comes up with an all PyMOL
alternative, please share with the list!
Doug
On Jul 20, 2005, at 1:18 PM, Cartailler, Jean-Philippe wrote:
One way to do this would be to calculate RMSD between your models
(using
whatever package) and replace the B-factor column with those values
(make sure you respect the PDB format (B-factors are in columns 61 -
66,
with first column as "1" - see
http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_62.html for
details), load that into pymol, and voila. If the effect isn't enough,
you could always multiply your RMS values by some value (eg. 10). Good
luck!
JP Cartailler
-----Original Message-----
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Douglas
Kojetin
Sent: Tuesday, July 19, 2005 3:48 PM
To: pymol
Subject: [PyMOL] putty/sausage NMR figure
Hello All-
From what I've read, the 'cartoon putty' command uses the PDB B-
factor
value to determine the appearance of the sausage diagram. How can I
use
the 'cartoon putty' command with NMR structures in a way that
represents
the structure ensemble, similar to that as the MOLMOL sausage diagram?
Thanks,
Doug
--
Cameron Mura
UCSD
