firstname.lastname@example.org wrote: > > Dear Modellers: > > I got a problem when i'm modelling my protein. The situation is that: > > I found my protein (aam) has a partial similarity with 1nkl ('5:' ' 127:'), made a > ali. file, and call routine ='model' or using "build_model" . I got a PDB format > file or .ini file (for example aam.B999901 or aam.ini). Then, i try to transfer / or > modify another segment of aam from a high similarity protein (1udg, '223:' > '289:') without losing 1nkl ('5:' '127:') information in aam.ini file, but in vain. > Could you tell me which commands fit this purpose? > > Thanks for help. > > Xingxuan He, MD. > Associate > Dept. of Human Genetics > Mt. Sinai Medical Center
I do not know how long is your model sequence (aam), but visibly none of the templates can be fully aligned alone to it. In general, if you have several template structures you should prepare your alignment accordingly, with all the sequences. If you wish to force modeller, to use template from only one of the given templates at certain segments, you should have blank spaces for the other sequence in the alignment etc.
for details see FAQ 4 in the manual.