Mark,
 
Sorry, but the current C code appears to be broken.  For future reference, you should be able to do the following:
 
load $TUT/1hpv.pdb
 
# absolute linear scaling from the B factor
 
set cartoon_putty_transform, 7
 
# set a base radius of 1.0 (will be scaled based on B factors)
 
set cartoon_putty_radius, 1.0
 
# no limits on the scaling
 
set cartoon_putty_scale_min, -1
 
set cartoon_putty_scale_max, -1
 
# set the B factors
 
alter all, b=0.2
 
# display the cartoons appropriately
 
unset cartoon_smooth_loops
 
unset cartoon_flat_sheets
 
as cartoon
 
cartoon putty
 
# unfortunately, the above does not in fact work because there is a bug in the code when all B factors are the same...you get a radius of 1 instead.
 
# regardless, setting non-identical B factors should currently work:
 
alter chain A, b=0.2
 
alter chain B, b=0.4
 
rebuild
 
Cheers,
Warren
 
--
DeLano Scientific LLC
Subscriber Support Services
mailto:support@delsci.com
 


From: Mark A. White [mailto:mawhite@utmb.edu]
Sent: Monday, December 15, 2008 3:34 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] B-factor putty tube representation

Hi,

I would like to define the radius of the cartoon putty on absolute, rather than a relative scale.  Is there any way to do this?  If I am comparing rmsd, for example, I would like every image to be representative of the true RMSD differences, rather than being a unique relative scale for each comparison.

I notice that others have also asked about this in the past, but I did not see a response on the Pymol-Users Email Archive.  Maybe there are new features in 1.1 that address this?

[PyMOL] putty tube representation From: Evan Kantrowitz <evan.kantrowitz@bc...> - 2007-08-09 21:37
Attachments: HTML-Email.html      I am making tube representations as a comparison between two
structures. I have the rmsd in the b-factor field.
1) If I do a putty representation it works. How does the program
decide on the width variation of the tube?
2) How can this be reset?
I want to do this so when I compare two different rmsd plots the
width of lets say 1 rms is the same in both figures.

Any help would be apprecipated.
-------------------------------------------------------------------
Evan R. Kantrowitz,
Ph.D
evan.kantrowitz
Boston
College



Yours sincerely,

Mark A. White, Ph.D.
Assistant Professor, Dept. Biochemistry and Molecular Biology,
Manager, Sealy Center for Structural Biology and Molecular Biophysics X-ray Crystallography Laboratory,
Basic Science Building, Room 6.660 C
University of Texas Medical Branch
Galveston, TX 77555-0647
Tel. (409) 747-4747
Cell. (409) 539-9138
Fax. (409) 747-4745
mailto://white@xray.utmb.edu
http://xray.utmb.edu
http://xray.utmb.edu/~white