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 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
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From: Mark A. White []
Sent: Monday, December 15, 2008 3:34 PM
Subject: [PyMOL] B-factor putty tube representation


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,

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