I've changed the Attribute Calculator so that assigning non-numeric values to bfactor (and occupancy) no longer generates an error. They are counted as "unable to calculate" errors and the atom attribute value left unchanged. This means you need to use the setattr command to set a default value for all atom bfactor (or occupancy) attributes before using the Attribute Calculator, or else you might get a mixture of old bfactor values and the newly computed attribute values. Conrad On 8/26/2014 10:45 AM, Eric Pettersen wrote:
On Aug 26, 2014, at 10:27 AM, Elaine Meng <meng@cgl.ucsf.edu <mailto: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
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