[Chimera-users] Setting bfactors
meng at cgl.ucsf.edu
Wed Mar 16 10:02:23 PDT 2011
Just to clarify, while each use of the "setattr" command only sets *to* a single value, it can set multiple atoms' bfactors to that value. For example,
setattr a bfactor 12.0 :8-15
would set bfactor = 12.0 for all atoms in residues 8-15.
On Mar 16, 2011, at 9:44 AM, Elaine Meng wrote:
> Hi Austin,
> The bfactor is an atom attribute, and you can change attribute values (or create new attributes) with the command "settatr" for one value at a time, or by creating an attribute definition file for setting multiple values at a time. The attribute definition file is in a simple column-separated text format:
> and is loaded with the Define Attribute tool or the command "defattr". If you were just going to use this attribute in Chimera, you could create a new one with an arbitrary name rather than naming it "bfactor" and overwriting the existing values. However, if you need it to be in the bfactor column when saving the PDB, using the name "bfactor" would be the way to go.
> Attribute values can be used in many ways such as to define an atom selection (e.g. only atoms with bfactor less than some cutoff, only residues with a certain hydrophobicity), and can be shown with colors, radii, etc.
> I hope this helps,
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Mar 16, 2011, at 9:01 AM, Austin B. Yongye wrote:
>> Hello chimera users/developers,
>> Can someone change the bfactors for a group of selected residues and save a pdb file with the new bfactors in chimera?
>> I would like to use these values as constraints for simulations in NAMD. I could use VMD, but it selects only atoms and not entire residues.
>> Any suggestions will be greatly appreciated.
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