[Chimera-users] Assigning pre-calculated attribute to B-factor column of pdb
meng at cgl.ucsf.edu
Tue Aug 26 11:33:48 PDT 2014
There isn't a Chimera command implementation of Attribute Calculator, sorry!
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.
> 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:
>>> (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 Pettersen
>> UCSF Computer Graphics Lab
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