Hi! I am trying to differentiate two protein chains in simulation with each other by changing the color of one of them in VMD. However, I am not able to find out how to select the entire chain to recolor, only certain residues. Please advise on how I could accomplish this. Thanks!
Please check this out:
Without knowing how the topology is arranged, a safe option would be to use a range of residues chosen by you to define the chain selection.
If you’re trying to color chains from a GRO file or trajectory, you can’t use VMD’s chain selection command to color different chains. Unfortunately, the chain information is lost in the GRO file (you’ll see they are all marked as “X” when opened in VMD). However, you can specify a residue or atom index range to select separate chains in VMD. Hope it helps!
Hi Cathrine,
Thank you so much for your response, that is what I would like to do. What word inputs what I write to color the two proteins by atom index? I want atoms 1-1326 to be one color and atoms 1327-3395 to be another, representing the two proteins. Thanks again!
Indices are zero-based. So index 0 to 1325 covers atoms 1-1326. See the VMD documentation and tutorials for more information.