[PyMOL] Re: putty/sausage NMR figure (Douglas Kojetin)

[Cameron M. <cm...@uc...>]

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


=== pym...@li... wrote (on 07/21/2005 08:13 
PM): ===

> Subject:
> Re: [PyMOL] putty/sausage NMR figure
> From:
> Douglas Kojetin <djk...@un...>
> Date:
> Thu, 21 Jul 2005 10:49:21 -0400
> To:
> pymol <pym...@li...>
>
> To:
> pymol <pym...@li...>
> CC:
> "Cartailler, Jean-Philippe" <jp....@Va...>
>
>
> 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: pym...@li...
>> [mailto:pym...@li...] 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