Re: [modeller_usage] Problem modelling protein dimer close to DNA ...

[Modeller Caretaker <>]

On 1/21/11 4:11 AM, Sergio Garay wrote:
> I'm trying to model a protein dimer interacting with a small DNA
> molecule. Following the manual instructions I was able to build my dimer
> using:
...
> But I have some problems to add my DNA molecule as an additional restraint:

It's difficult to tell what your problem is without seeing a "real" 
alignment file. But note that you need to put the '.' residues for each 
DNA residue in *both* your template and your target - it looks from your 
post as if you only have them in the template.

Note that Modeller does know the topology of RNA and DNA, so you can use 
one-letter codes to get these residues in your model. However, it 
doesn't know anything about the secondary structure of nucleic acids, so 
they will probably not be modeled correctly. You are usually better off 
using the '.' residue, since that will force Modeller to preserve the 
structure from the template (and the interaction between RNA/DNA and 
your protein).

	Ben Webb, Modeller Caretaker
--
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