Hi Tsutomu, If there are lots of changes (if it would require an inconvenient number of setattr commands) you could create a "define attribute" file and read it in with the "defattr" command or the Define Attribute tool. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ defineattrib/defineattrib.html#attrfile> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ defineattrib/defineattrib.html> Notice you can create your own new attributes named whatever you want, show them with colors, worms, etc., and save them to files in that same "define attribute" format. At least if you will be working with Chimera, there is no need to use bfactor and occupancy for things that aren't really bfactor and occupancy. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/ render.html#render> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html> However, if you really want them written out in a PDB file, it is necessary to put the values in bfactor or occupancy. It might cause you to lose digits on the values because those columns are not very wide. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Apr 8, 2009, at 5:13 PM, Tom Goddard wrote:

Tsutomu Matsui wrote:

...

Hi Tom,

Is it possible to change b-factor or occupancy of selected atoms, and then output the coordinates including those changes?

Tsutomu

Hi Tsutomu,

Here are Chimera commands to set bfactor and occupancy of an atom (model #0, residue 13, chain B, atom CA) and write out the PDB:

setattr a bfactor 12.3 #0:13.B@CA setattr a occupancy 0.123 #0:13.B@CA write 0 /tmp/test.pdb

If you really mean you want change the "selected" atoms use a command like:

setattr a bfactor 12.3 sel

See the setattr and write documentation for more details.

http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html

Tom