[Chimera-users] coloring of nearly identical protein sequences in multialign viewer

[Elaine Meng]

> Thanks for mentioning the SCF file. I can create a script to create  
> the file from the alignment. Does the SCF parser in the multialign  
> viewer read the new format or the old format (I guess newer)?
>
> Thanks,
> Sabuj Pattanayek

Hi Sabuj,
You can use whichever you prefer.  The file reader automatically  
figures out which format is being used.   The rows/columns will be  
colored as specified in the alignment, and the corresponding residues  
in any associated structures will be colored the same way.  The part of  
the Multalign Viewer man page about this is:

http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ 
multalignviewer/multalignviewer.html#seqsel

Best,
Elaine