Re: [modeller_usage] Question about a protein structure

[Modeller Caretaker <>]

Ester Fusté Domínguez wrote:
> I have a problem with modeller and probably you can help me.
> I want to do protein  structure  modelling.
> I have the sequence of a bacterium protein, and it's known that it has
> tree identical chains like this:
> MQMKKLFPIL IGLGLTGFSA MSQAENLLQV YQQARISNPD LRKSAADRDA
...

It would be more helpful if you could show the actual Modeller inputs 
(i.e. Python script, and alignment file) you're using. I'm assuming this 
sequence isn't the actual alignment file you're passing to Modeller - 
for one thing, Modeller sequences must not have spaces in them. And what 
are the templates you're using? Do they also have three identical 
chains, or are you trying to build a trimer from a monomer template?

> I don't really know what can I do to avoid the chains overlap.
> I have tried to copy the sequence three times but it doesn't work.

I'm not sure what you mean by "chains overlap". But what you are 
certainly missing in your sequence are chain breaks - '/' characters - 
which will prevent the termini in adjacent chains from being bonded. See 
also http://salilab.org/modeller/9v1/manual/node27.html

When you say "doesn't work" what is the error message you receive?

	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage