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

Elaine Meng meng at cgl.ucsf.edu
Tue Aug 26 11:33:48 PDT 2014


There isn't a Chimera command implementation of Attribute Calculator, sorry! 

Elaine

On Aug 26, 2014, at 11:28 AM, Oliver Clarke <olibclarke at gmail.com> wrote:

> 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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