1) How can I make a mask as mentioned above? Am I doing it the
wrong way?
You can run NCSMASK with your first placed domain and generate a
suitable mask file for DM.
2) Is there any other method to improve the density of the
missing structure? I tried several MR probes of the second barrel
fixing the first one but all failed.
GraphENT ?
Other suggestion:
since you think you know the second domain has some movements, can you
try to idetify which secondary structure elements disobey the other
models and remove them from your second domain search, then rerun phaser
or whatever MR program you used. It might also just be a small loop
which needs to be trimmed which flaggs a solution then as wrong because
of clashes, make sure to get reid of anything that is not the core of
your domain.
Jürgen
Sorry for the naive question, but this has bothered me for quite some
time. Any suggestions will be greatly appreciated.
Thanks in advance!
Tiancen Hu
Shanghai Institute of Materia Medica
Chinese Academy of Sciences
--
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone: +1-206-616-4510
FAX: +1-206-685-7002
Web: http://faculty.washington.edu/jbosch
