On Monday, December 15, 2003, at 08:57 AM, amutha ramaswamy wrote:
Dear sir I am using the Chimera molecular visualising software. I am not able to color the PDB structure according to the B-factors. could you plase let me know how do i color accroding to the bfactor. i would greatly apprecuate your help in this regard
Dear Amutha, We just got a question very similar to yours on the list a few days ago. I should say that we are working on an interface to allow coloring of ribbons/atoms/surfaces by any attribute, using any number colors in either a continuous spectrum, or as discrete "color bars". The interface isn't ready yet and will not be ready for the snapshot release that will be out in a few days. We hope it will be ready for the release after that. Until then, you can use typed-in commands to color by B-factor in discrete ranges, as described in the part of the previous mail that I've quoted below. Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu
To color a structure so that B factors less than 10 are shown as green, between 10 and 20 as yellow, and over 20 as red, do:
color green color yellow @/bfactor>10 color red @/bfactor>20
Obviously, use whatever numerical cutoffs and colors you want. There is a discussion of the the atom/residue/model attributes you can use in commands at http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ atom_spec.html#descriptors .