[Chimera-users] Setting bfactors

[Austin B. Yongye]

Hi Elaine,
Thanks a lot for the responses. This command worked:
setattr a bfactor 12.0 :8-15
Thanks!
Austin-

--- On Wed, 3/16/11, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> From: Elaine Meng <meng at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Setting bfactors
> To: "Austin B. Yongye" <ybausty at yahoo.com>
> Cc: "UCSF Chimera Mailing List" <chimera-users at cgl.ucsf.edu>
> Date: Wednesday, March 16, 2011, 10:02 AM
> 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.
> 
> Elaine
> 
> 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:
> > 
> > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attrfile>
> > <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>
> > 
> > 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.
> > 
> > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attribdef>
> > 
> > I hope this helps,
> > Elaine
> > -----
> > 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.
> >> Thanks,
> >> Austin-
> 
>