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. --Eric On Aug 26, 2014, at 11:33 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
There isn't a Chimera command implementation of Attribute Calculator, sorry!
Elaine
On Aug 26, 2014, at 11:28 AM, Oliver Clarke <olibclarke@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@cgl.ucsf.edu> wrote:
On Aug 26, 2014, at 10:27 AM, Elaine Meng <meng@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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