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

Eric Pettersen pett at cgl.ucsf.edu
Tue Aug 26 10:45:06 PDT 2014


On Aug 26, 2014, at 10:27 AM, Elaine Meng <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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