[Chimera-users] Color by RMSD for multi-chain structure?

Oliver Clarke olibclarke at gmail.com
Fri Jun 13 11:08:08 PDT 2014

Hi all,

Is there an easy way to color two superimposed structures by RMSD (per C-alpha pair)?

I had a quick look through the manual and the mailing list and I couldn’t find any easy way to do so for a structure that consists of more than one chain.

I think this would be a very useful addition to either render by attribute or the calculation of a morph (because presumably the paired CA-CA distances are already calculated in the process of generating the morph).

I have aligned based on one chain in a complex, and would like to color the entire complex by RMSD (to highlight the parts that move the most between two states of the same complex).

I can calculate the per CA RMSD using “rmsd #1 #2”, but I can’t see any obvious way to assign that to a residue attribute using the attribute calculator or setattr etc.

Many thanks,

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