Re: [modeller_usage] model generate error

[Robert Campbell <robert.campbell AT queensu.ca>]

Hello Albert,

On Tue, 20 Jul 2010 16:15:17 +0800 (CST) albert <leuven AT 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
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821            Fax: 613-533-2497
<robert.campbell AT queensu.ca>    http://pldserver1.biochem.queensu.ca/~rlc