Hi, i am Yang here..
I try to build a model by using basic tutorial, that begin with only protein sequence, to look for potential templates. However, i have encountered a problem during build_profile.py loading, it generate problem as below: Protein specified in ALIGN_CODES<i>, was not found in the alignment file;ALIGN_CODES< 1>= ALL The alignment file i saved in plain text format, with suffix .ali (bleg1_2439.ali), is that affected the reading by modeller? I don't specified the templates are used, so just follow the python file from basic example, the only thing i change, is only the align file that attached above..
Your feedback is important and appreciated..
Thank you
On 11/17/11 1:38 AM, si yang wrote: > Protein specified in ALIGN_CODES<i>, was not found in the alignment > file;ALIGN_CODES< 1>= ALL > The alignment file i saved in plain text format, with suffix .ali > (bleg1_2439.ali), is that affected the reading by modeller?
Plain text is fine (almost all Modeller files need to be plain text) but it sounds like your alignment file is not valid PIR format. See http://salilab.org/modeller/9.10/manual/node473.html
Ben Webb, Modeller Caretaker
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si yang