[Chimera-users] color by RMSD

[Elaine Meng]

Oh, I thought Thomas meant he wanted to use more atoms than CA.  If not, and CA-CA only values are OK (the main issue was doing the calculation for different chains than used for superposition), what Eric suggests is much simpler.
Elaine

On Apr 4, 2012, at 11:00 AM, Eric Pettersen wrote:

> In addition to the methods Elaine describes, you could alternatively do the following.
> 
> 1) match the B chains
> 2) open the Sequence tool for one of the A chains
> 3) use the Structure->Associations menu item to also associate the other chain A with the sequence
> 4) show the RMSD header
> 5) proceed as Elaine described in yesterday's mail
> 
> Note that in order to do this you will have to download the 1.7 daily build since a bug got fixed yesterday that prevented RMSD attributes from being assigned when only a single sequence is shown in an "alignment".  Also, I hope you aren't using Linux since the daily build didn't successfully build last night for Linux, so you would have to wait until tomorrow's build for a Linux version...
> 
> --Eric
> 
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu
>