Hi João
Thanks! it worked fine!
>>Just make sure not to have 0.0 bfactors in there!
true :) I normalized them by adding 1 to all.
Cheers
Afonso
On Thu, Jul 4, 2013 at 1:13 PM, João Rodrigues <anar...@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!
>
> Cheers,
>
> João
>
>
> 2013/7/4 Afonso Duarte <afonsomdua...@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?
>>
>>
>> Best
>>
>>
>> Afonso
>>
>>
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