Hello Albert,
On Tue, 20 Jul 2010 16:15:17 +0800 (CST) albert leuven@yeah.net wrote:
> Hello: > I am trying to use my own mutiple alignment to generate model, but it > faild, it is said : > > ---------------log---------------------------------------- > Protein specified in ALIGN_CODES(i) was not found > in the alignment file; ALIGN_CODES( 4) = protein > > > Here is parameter in my model-changeopt.py: > ---------------model-changeopt.py---------------------- > a = automodel(env, alnfile='man.ali', > knowns=('1A','2A','3A'), > sequence='protein', > assess_methods=(assess.DOPE, assess.GA341)) > a.starting_model =1 > a.ending_model = 4 > ....... > > > Here is my alignment file, man.ali: > ------------------------man.ali------------------------------- > >P1; protein
I think the problem is that you have a space before "protein" in the above line, but not in your "sequence='protein'" line in your script.
Cheers, Rob