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