[Chimera-users] help

Eric Pettersen pett at cgl.ucsf.edu
Mon Dec 15 13:59:30 PST 2003

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 at 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 .
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