mse

[battaile at post.its.mcw.edu]

I am trying to use mse like I would use lineup in gcg. I want to create a
manual alignment, that I can reload at later dates to make adjustments/add
new sequences/etc... Lineup in gcg allows this by saving the alignment to a
file. I have tried this in mse and can't seem to get anything to work. The
only thing I can figure is that I could write out each sequence individually
to a separate file. Personally, I would rather not have to write out 15
sequences separately every time I end a session. 

I have tried...

write: this works fine, but as I said above, I would rather not have to
write out each individual sequence every time I quit.

hardcopy: this also seems to work, but I can't read the multisequence
alignment back in (mse -msf sequence-file gives a can't read error). 

exit [filename]: this doesn't work at all. If I am inserting gaps (which is
99% of the job) the sequences aren't recognized as being changed. If I type
in, then delete some residues, I get the message 'Sequences modified do you
wish to continue exiting [N]'. If I choose the default [N], I get dumped
back into the editor. If I choose 'Y', the program exits. Either way, no
file gets written.

Am I doing something completely backwards? Any suggestions?

Thanks,

Kevin Battaile