Hi Boaz, Yes, you can save any alignment from Multalign Viewer (the tool that shows the alignment by default) in the same formats that can be read: aligned FASTA, aligned NBRF/PIR, Clustal, MSF, RSF, and Stockholm. This is done with File... Save As in the Multalign Viewer menu. You can also save an encapsulated PostScript image to use in a paper or presentation (File... Save EPS in the Multalign Viewer menu). To see the full manual page for Multalign Viewer, which includes many other features, click the Help button on the Multalign Viewer window (the window showing the sequence alignment). Here it is in our "development" documentation: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ multalignviewer/framemav.html I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Oct 11, 2005, at 9:15 AM, Boaz Shaanan wrote:

Hi,

Is it possible to save as a file (or print) the alignment that is produced by matchmaker between two structures that are read in ?

Thanks,

Boaz

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