Re: [modeller_usage] Protein specified in ALIGN_CODES<i> was not found in the alignment file; ALIGN_CODES< 1> = 1N11

[Robert Campbell <>]

On Wed, 2013-10-30 17:04  EDT,  <> wrote:

> Hello everybody !
> I am new to modeller, so please excuse me if my question seems trivial.
> I have a problem building a model from multiple templates.
> When i try to run build model script I get an error:
> 
> "Protein specified in ALIGN_CODES<i> was not found in the alignment file;
> ALIGN_CODES<     1> = 1N11"
> 
> I followed all the previous steps from advanced modeling tutorial and all
> of them worked fine. Now I am stuck, and all solutions I`ve tried dont
> work. I attatch my script and alignment file.
> 
> Thank you for your help in advance !


Your list of known structures in your scr4.py file

  knowns=('1N11','2YVI','3UD1'), sequence='ANK1')

does not match the entries in your alignment file:
>P1;1N11A
>P1;2YVIA
>P1;3UD1A
>P1;ANK1

You should change the scr4.py file to have 

  knowns=('1N11A','2YVIA','3UD1A')

or change the alignment file to remove the "A" after each PDB code.


Cheers,
Rob

-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Dept. of Biomedical & Molecular Sciences
Botterell Hall Rm 644
Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
<>    http://pldserver1.biochem.queensu.ca/~rlc