Hi Terry, I am guessing this is to use as input to some other program? There are much better ways to save attribute values (charge, hydrophobicity, etc.) if you are going to be using them in Chimera. You can tell Chimera to change the bfactor to equal the charge, then save a PDB file (File... Save PDB or command "write"). However, the bfactor column only has 2 digits after the decimal and you lose a lot of the actual charge data. First add charge, then reset bfactor to equal them: - open Attribute Calculator (under Tools... Structure Analysis) http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/calculator/ calculator.html - in that tool, Calculate attribute bfactor for atoms with the Formula: atom.charge This is really twisting the intent of PDB saving in Chimera. We generate only standard PDB format, so you can't write the bfactor column with more digits. If you were saving the attribute values for later use in Chimera, you would instead save an attribute assignment file, which would preserve the entire values. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/ defineattrib.html#attrfile Names of several atom attributes are listed here: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ atom_spec.html#atprops Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Mar 6, 2008, at 12:17 PM, Terry Lang wrote:
Hey Everyone,
I would like to use Chimera to write charges for a pdb file in the b-factor column. I feel like this is possible but couldn't quite figure out how to do it.
Sincerely, Terry
-- P. Therese Lang Post Doc Alber Lab, UC Berkeley
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