[Chimera-users] color by RMSD

Elaine Meng meng at cgl.ucsf.edu
Wed Apr 4 11:06:10 PDT 2012

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.

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

More information about the Chimera-users mailing list