Re: [PyMOL] question on differential coloring of protein chains
On Tuesday, February 17, 2004, at 02:57 PM, ALEX DAJKOVIC wrote: hello- i am new to pymol and am trying to figure out how to differentially color different chains (i.e. different proteins) in the structure i am viewing. the structure i am working with is actually a structure of two proteins that were co-crystalized and i would like assign different colors to them. thanks for your help. alex dajkovic Hello Alex, I think what you want is to use the 'select' function in combination with the 'resi' function. This is documented in the reference manual. Following is a helpful summary that was sent to me by Robert L. Campbell, Ph.D. Let's say I wanted to create a single residue selection for Lysine 465 (and I choose to call the selection 'K465'), so that I could color and display it the way I wanted: (insert your particular atom coordinates file name where you see square brackets below) ___ select K465, ([filename] and chain A and resi 465) or you could shorten the selection string: select ak465, (abc & c. a and r. 465) or use the shorthand notation: select ak465, /abc//a/465 ___ ˜ Now to create multiple residue selections, just separate the start and end residue numbers by a colon, I think, following the word 'resi' Once you create your unique selections they show up in the right panel list and you can further manipulate their display properties as you see fit. Regards, --Michael
Re: [PyMOL] question on differential coloring of protein chains
Hi Alex. > hello- > i am new to pymol and am trying to figure out how to differentially > color different chains (i.e. different proteins) in the structure i am > viewing. the structure i am working with is actually a structure of two > proteins that were co-crystalized and i would like assign different > colors to them. > thanks for your help. > alex dajkovic > As long as I know you can do that by creating copies of the same molecule. Do like this: load molecule.pdb, mole create copy, (mole) Then assign different colors to each (for example): color blue, mole color red, copy Finally show each chain separately: show cartoon, (mole & c;A) show cartoon, (copy & c;B) (in the case you what a cartoon representation of chains A and B). I hope that helps you. -- Mario Sanches, PhD Student Protein Crystallography Group São Paulo University, São Carlos Physics Institute Phone: +55 (16) 273 9868 sanc...@if.sc.usp.br
[PyMOL] question on differential coloring of protein chains
hello- i am new to pymol and am trying to figure out how to differentially color different chains (i.e. different proteins) in the structure i am viewing. the structure i am working with is actually a structure of two proteins that were co-crystalized and i would like assign different colors to them. thanks for your help. alex dajkovic