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 sincerely amutha 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) --------------------------------- Do you Yahoo!? New Yahoo! Photos - easier uploading and sharing
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 .
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 regards amutha Eric Pettersen <pett@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@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 .
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) --------------------------------- Do you Yahoo!? New Yahoo! Photos - easier uploading and sharing
participants (2)
-
amutha ramaswamy -
Eric Pettersen