[Chimera-users] help

amutha ramaswamy amutha_ramu at yahoo.com
Tue Dec 16 08:32:51 PST 2003

Dear Sir
Thank you so much for your kind reply. Yes definitely, the chimera users would grately benifit from the option of coloring the ribbon diagram accoridng to any required parameter..
thank you so much

Eric Pettersen <pett at cgl.ucsf.edu> wrote:

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 .

Dr Amutha Ramaswamy
Postdoctoral Fellow, Department of Biomedical Informatics
3184 Graves Hall, 333 West 10th Avenue
The Ohio state University, Columbus, OHIO 43210
Phone: 614-688-3236 (Office); 614-291-0071(Residence)
Fax:    614-292-7659 (Office)

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