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