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