[Chimera-users] Assigning pre-calculated attribute to B-factor column of pdb

Conrad Huang conrad at cgl.ucsf.edu
Tue Aug 26 12:04:05 PDT 2014


I've changed the Attribute Calculator so that assigning non-numeric 
values to bfactor (and occupancy) no longer generates an error.  They 
are counted as "unable to calculate" errors and the atom attribute value 
left unchanged.  This means you need to use the setattr command to set a 
default value for all atom bfactor (or occupancy) attributes before 
using the Attribute Calculator, or else you might get a mixture of old 
bfactor values and the newly computed attribute values.

Conrad

On 8/26/2014 10:45 AM, Eric Pettersen wrote:
> On Aug 26, 2014, at 10:27 AM, Elaine Meng <meng at cgl.ucsf.edu
> <mailto:meng at cgl.ucsf.edu>> wrote:
>
>> Hi Oliver,
>> The more direct way I tried used Attribute Calculator (in menu under
>> Tools.. Structure Analysis) to calculate attribute "bfactor" for
>> "atoms" using the formula:
>>
>> residue.ramaProb
>>
>> (after assignment using Ramachandran).  It currently generates an
>> error, which seems buglike.  I could create a new atom attribute with
>> that formula, but not overwrite "bfactor". We'll look into that .
>
> The problem here is that bfactors /must/ be numeric, but some residues
> have a ramaProb of "None" (e.g. they are terminal residues or
> non-peptides and lack either a phi or a psi).  You can assign such
> residues a ramaProb of -1.0 with this command:
>
> setattr r ramaProb -1.0 :/^ramaProb
>
> You could then use the Attribute Calculator to assign the ramaProbs to
> the bfactors.
>
> --Eric
>
> Eric Pettersen
>
> UCSF Computer Graphics Lab
>
> http://www.cgl.ucsf.edu
>
>
>
>
>
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