[Chimera-users] Assigning pre-calculated attribute to B-factor column of pdb
olibclarke at gmail.com
Tue Aug 26 11:28:03 PDT 2014
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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