Hi Andy, To color a binding site I would select the ligand (DNA in your case) then select all the nearby atoms using Select / Zone..., then use Actions / Color to color those atoms. Tom Anindito Sen wrote:
Another question - I need to color a portion of the crystal structure differently (ribbon diagram) in order to indicate the binding sites of the DNA with the protein molecule and how do I do that.
Thanks and Best Wishes Andy
Hey Chimera-folks, I've got a nice movie with morph conformations, and then wrote a script that goes along with it that generates tranparent multiscale models (molmap) and displays a ligand with solid atom spheres for each frame in the movie. But I'd like to make a sphere that tracks along with the domain movement - it can't be transparent because the model is transparent already. The shape command looks like it can do this, make a sphere with a specified radius in mesh, but I can't figure out how to specify the origin according to a particular atom's coordinates, and then script it so that it tracks with the conformational changes in the movie. And it would be really cumbersome to write a bild file for each of the ~200 frames in the movie. I'm guessing something like "getcrd" will get the coordinates that I'd like to use for the origin but "shape sphere" doesn't allow me to specify origin. Alternatively I could render the atom I'm tracking as a radius 25 sphere, but am unable to display an atom as mesh. Can you point me in the right direction? Thanks, Ed Brignole Asturias Lab The Scripps Research Institute
Hi Ed, To make a mesh sphere centered at a specific atom, say the CA atom of residue 283 of model #0 how about molmap #0:283@CA 10 gridSpacing 1 modelId 5 volume #5 style mesh color yellow You can do this each frame of the MD trajectory and the molmap will by default replace the sphere so you don't have to worry about removing the previous sphere. This makes a map from one atom with resolution 10. Not sure what radius that produces. You could figure it out from the molmap documentation or simply adjust the resolution value until you get a radius that looks right. Tom Edward Brignole wrote:
Hey Chimera-folks,
I've got a nice movie with morph conformations, and then wrote a script that goes along with it that generates tranparent multiscale models (molmap) and displays a ligand with solid atom spheres for each frame in the movie. But I'd like to make a sphere that tracks along with the domain movement - it can't be transparent because the model is transparent already. The shape command looks like it can do this, make a sphere with a specified radius in mesh, but I can't figure out how to specify the origin according to a particular atom's coordinates, and then script it so that it tracks with the conformational changes in the movie. And it would be really cumbersome to write a bild file for each of the ~200 frames in the movie.
I'm guessing something like "getcrd" will get the coordinates that I'd like to use for the origin but "shape sphere" doesn't allow me to specify origin.
Alternatively I could render the atom I'm tracking as a radius 25 sphere, but am unable to display an atom as mesh.
Can you point me in the right direction?
Thanks, Ed Brignole Asturias Lab The Scripps Research Institute
participants (2)
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Edward Brignole -
Tom Goddard