Fwd: [Chimera-users] writing alignment

Elaine Meng meng at cgl.ucsf.edu
Wed May 4 13:57:48 PDT 2005

Begin forwarded message:

> From: Elaine Meng <meng at cgl.ucsf.edu>
> Date: Wed May 4, 2005  1:56:54 PM US/Pacific
> To: "Bryan W. Lepore" <lepore at 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

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