[Chimera-users] circular permuation

[Elaine Meng]

On Wednesday, May 4, 2005, at 01:12 PM, Bryan W. Lepore wrote:
> by the way, is the sequence alignment widget inacessible when doing 
> e.g.
>
> chimera --nogui cmd:input.dat
>
> (contents of input.dat):
>
> mmaker #0:.b #1:.a alg sw pair bb show true
>                                   ^^^^^^^^^
>                                   |||||||||
>                                    N.B.
>
> in other words, does mmaker have a keyword to specify an alignment 
> output?
>
> -bryan

Hi Bryan,
The "show" keyword specifies that the alignment should be shown
with Multalign Viewer, but there is no keyword that says a file should
be written out.  When you are doing things interactively, you can then 
use
File...Save As (in the Multalign Viewer menu) to save a file.  However,
in your case it is the python script from Eric that tells chimera to
save a file.

You probably saw this already, but here is the mmaker man page listing
the keywords:
http://www.cgl.ucsf.edu/chimera/1.2065/docs/UsersGuide/midas/mmaker.html

Not sure I'm answering your question, though...
Elaine