Hi all, I used Modeller in the past to create small loops from scratch. Now I have a protein-DNA complex, and I have to build and model 4 loops of my protein. My first problem is that MODELLER does not support DNA, so I have to strip the DNA from the PDB and use the protein alone. Considering the problem that I have to "paste" the DNA to the modelled structure, I use the options *a.md_level= None* to keep the rest of the protein fixed and the option * a.loop.md_level* to model the loops. Now, these two commands work on three of the 4 loops, but I have another problem now: I have a very long loop to build (35 aa) and using these two commands, MODELLER create a very strange hairpin loop to connect these two positions. I know which will be the correct structure of this loop because I have a similar protein that present this loop, and the modelling is wrong. Finally, if I don't usage a.md_level=None, MODELLER builds a very good loop, but all the protein is in a complete different position with respect of the starting one. Any suggestion? Best regards Rubben
On 11/17/11 1:23 AM, Rubben Torella wrote: > My first problem is that MODELLER does not support DNA
Sure it does - you can use the '.' residue type just like a ligand to copy the DNA from the template directly into the model. Modeller will automatically add restraints on it to keep it rigid.
> I use the options _a.md_level= None_ to keep the rest of the protein > fixed
md_level only controls the level of MD refinement, not all of the optimization. If you set it to None, the model will still be optimized with CG. If you don't want it to move at all, see http://salilab.org/modeller/9.10/manual/node23.html
> I have another problem now: I have a very long loop to build (35 aa) > and using these two commands, MODELLER create a very strange hairpin > loop to connect these two positions. I know which will be the correct > structure of this loop because I have a similar protein that present > this loop
In that case you should probably align that other protein with your model in the loop region. Modeller is unlikely to successfully model a 35aa loop without a template - the conformational space is just too large.
Ben Webb, Modeller Caretaker
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Modeller Caretaker -
Rubben Torella