Begin forwarded message:

From: Elaine Meng <meng@cgl.ucsf.edu> Date: Wed May 4, 2005 1:56:54 PM US/Pacific To: "Bryan W. Lepore" <lepore@brandeis.edu> Subject: Re: [Chimera-users] writing alignment

On Wednesday, May 4, 2005, at 01:41 PM, Bryan W. Lepore wrote:

...

however i'd like to ask if mmaker is in fact not written to handle specific stretches of a model - e.g you can do #1:.a at the least? e.g., not something like #1:.a1-10,a15-20... to prune out areas to ignore.

-bryan

Hi Brian, You can specify which chains (like in that example you included in a previous mail) to construct an alignment with, but not subparts of those chains.

However, remember that the structure matching will only use residues that are actually aligned in the initial sequence alignment. So, it doesn't matter if the sequences have other parts that are essentially unalignable. Elaine