Hi Elo
The formula for cmputing the putty radius is found in layer1/ Extrude.c in the source:
        switch(source_field) {
        default: /* b*/
          scale = (range+(at->b - mean)/stdev)/range;
            scale = 0.0F;
          *sf = scale;
From this I can see:
* The "cartoon_putty_scale_max" and "cartoon_putty_scale_min" settings are not scaling factors, but rather cut-off values to avoid extremely thin or thick tubes.
* "cartoon_putty_scale_power" is a kind of "gamma correction" which allows to enhanche areas with extreme b-factors. Set it to 1 if you want linear scaling to b-factor.
* "cartoon_putty_range" is the only user-adjustable parameter that affects the actual scaling. 
* The mean value and standard deviation of the b-factors is used for the scaling. This seems very strange to me - is this a bug or a feature? :-)
It is quite hard to make a workaround (without changing the source).  The best I could find was to combine all the (aligned) structures into one object, but with different chainid, eg
alter obj01, chain='A'
alter obj02, chain='B'
create comb, obj01+obj02
Then make the putty cartoon
show cartoon, comb    # Notice that the complete object must be selected, the putty scaling works only on the displayed atoms!
cartoon putty, comb
But then your putty cartoons of the different structures are - at least partly - covering each other. Then translate the different chains to create the view you want, eg:
translate [20, 0 0 ], comb and chain A
You can use this view directly, or just translate the "unwanted" chains far enough to be off the screen
Hope this helps :-)  
But I I would really like an option to do manual scaling on the putty cartoon, eg by changing the source line to.
scale = at->b * cartoon_putty_myscaling; 
Where cartoon_putty_myscaling is a new setting.
 ----Original Message-----
From: pymol-users-bounces@lists.sourceforge.net [mailto:pymol-users-bounces@lists.sourceforge.net] On Behalf Of Caspar Elo Christensen
Sent: 24. juli 2006 22:24
To: PyMOL-users@lists.sourceforge.net
Subject: [PyMOL] Putty

I'm using cartoon putty to display rmsd between an enzyme with and without ligand. I've got two enzymes (that is four structures all in all) and have prepared two figures. The problem is that the extreme rmsd values vary; in one figure it goes from 0.1 to 1.66 while in the other it goes from 0.1 to 2.33. It seems that the rmsd values are normalized by putty, so that the figures only allow me to compare the distribution of rmsd values in each set of structures, not the actual values.How do I put the two figures on the same scale, so that I can compare them quantitatively?
I've tried to play around with the scale range parameters with little luck.
Any help will be much appreciated,