Re: [modeller_usage] Please help me with tutorial error

[Modeller Caretaker <modeller-care@ucsf.edu>]

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
--
modeller-care@ucsf.edu             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage