Subject: Re: [modeller_usage] model generate error
From: Robert Campbell <>
Date: Tue, 20 Jul 2010 10:31:04 -0400
Hello Albert,
On Tue, 20 Jul 2010 16:15:17 +0800 (CST) albert <> 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
<> http://pldserver1.biochem.queensu.ca/~rlc