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.
Andras
--
,
Andras Fiser, PhD # phone: (212) 327 7206
The Rockefeller University # fax: (212) 327 7540
Box 270, 1230 York Avenue # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras