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

[Oliver Clarke]

That works well, thanks Eric. Is there any way to reassign the ramaProbs to the bfactor column on the command line, without using the attribute calculator? That way I can set the whole sequence of commands as an alias.

Cheers,
Oliver.
On Aug 26, 2014, at 1:45 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> 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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