[Chimera-users] matchmaker output

Eric Pettersen pett at cgl.ucsf.edu
Fri Mar 18 10:34:40 PDT 2011

On Mar 18, 2011, at 9:39 AM, Tiziano Tuccinardi wrote:

> Thanks Eric!!
> It works very well!! Is it also possible to save the alignment file  
> without omitting the all-gap columns?

Hi Tiziano,
	I guess your question confuses me in two ways:

1) AFAIK, MatchMaker-generated alignments never have all-gap columns.

2) Although the MAV save dialog defaults to "omit all-gap columns",  
the script I sent doesn't.  I would have to add few more lines of code  
to the script to get it to omit all-gap columns.

	Maybe you were assuming it was omitting them when it wasn't?


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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