[Chimera-users] Assigning pre-calculated attribute to B-factor column of pdb
pett at cgl.ucsf.edu
Tue Aug 26 11:39:34 PDT 2014
As Elaine says, there is no command equivalent. However, a tiny Python script will do it:
from chimera import openModels, Molecule
for m in openModels.list(modelTypes=[Molecule]):
for a in m.atoms:
a.bfactor = a.residue.ramaProb
If you put the above in a file ending in '.py', you can open it in Chimera with the "open" command to run it and therefore can just put that open command in your script/alias. Indentation is important in Python, so preserve the indentation when you create the .py file.
On Aug 26, 2014, at 11:33 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 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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