[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [modeller_usage] Please help me with tutorial error



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
--
             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage