Hi Joćo

Thanks! it worked fine!

>>Just make sure not to have 0.0 bfactors in there!

true :) I normalized them by adding 1 to all.



On Thu, Jul 4, 2013 at 1:13 PM, Joćo Rodrigues <anaryin@gmail.com> wrote:
Hi Afonso,

PyMOL allows for Python scripting so in principle you could do something like:

import math
alter structure, b=math.log(b, 10)

Just make sure not to have 0.0 bfactors in there!



2013/7/4 Afonso Duarte <afonsomduarte@gmail.com>

Dear All,

I have a pdb file composed by several chains where the b-factor column was replaced by a physical property of the proteins. I am now trying to color according to b-factor and to obtain a better representation of the properties described. i.e. I am interested in calculating the log of the b-factor and place that value in the b-factor column.

I tried to export this column form the pdb, process it and then import it back, but due to the presence of different chains the b-factors got messed up.

Would it be possible to do this kind of math  operation directly in Pymol? 



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