Claire Wei wrote: > I am pretty new using MODELLER. I met some problem with the tutorials. > http://www.salilab.org/modeller/7v7/tutorial/basic.html > I am using MODELLER 8v2. Thanks a lot if someone could tell me what > might be wrong.
Don't use the Modeller 7v7 tutorial; use the most recent version, which works with 8v2, at http://salilab.org/modeller/tutorial/
> Here is the seq_search.top file: > SET SEARCH_RANDOMIZATIONS = 100 > SET FILE = 'TvLDH.ali' > READ_SEQUENCE_DB > SEQUENCE_SEARCH ALIGN_CODES = 'TvLDH', DATA_FILE = ON
If you want to use that TOP file, you should change it to:
SET SEARCH_RANDOMIZATIONS = 100 SET FILE = 'TvLDH.ali' READ_SEQUENCE_DB READ_ALIGNMENT ALIGN_CODES = 'TvLDH' SEQUENCE_SEARCH DATA_FILE = ON
SEQUENCE_SEARCH was changed in Modeller 8v0 to take a previously-read alignment file (READ_ALIGNMENT) as input, rather than reading the sequence itself. See the last entry in the 8v0 changelog at http://salilab.org/modeller/manual/node20.html
Ben Webb, Modeller Caretaker