[Chimera-users] Constrainted fitting

[Christoph Wigge]

Hi Elaine,

Thanks for the quick reply. I will definitely try out your advice. I have another question because a colleague told me that it might also be possible to use the truncated part of the dimer that formed the binding site in the crystal and then to superimpose the very homologue full protein on that. Then to write out out the superimposed full molecule as one pdb file and do a rigid body fitting. What do you think of that solution?

Bests 

Christoph 


Am 23.10.2013 um 00:46 schrieb Elaine Meng:

> Hi Christoph,
> If you have the monomers already in the desired positions relative to one another, you could combine them into a single model (for example using the "copy/combine" function in the Model Panel), and then fit the single model as a rigid body into the map.
> 
> However, if you meant you only wanted to constrain the distance between the monomers but not fully fix (freeze) their relative positions, you may need to use some program other than Chimera.  Chimera doesn't do flexible fitting with constraints.  Besides simple rigid-body fitting, the options in Chimera are: sequential fitting of multiple structures (find good position for one rigid body, then find nonoverlapping good position for next rigid body, ...) and symmetric fitting of rigid-body copies of the same structure.
> 
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/fitmap.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multifit/multifit.html>
> 
> I'm not qualified to make recommendations in this area, and can only mention a few programs that might be relevant:
> 
> PyRy3D (Monte Carlo fitting with restraints) has a plugin to use Chimera as the graphical interface:
> <http://genesilico.pl/pyry3d/>
> <http://genesilico.pl/pyry3d/pyryextension/>
> 
> IMP:
> <http://salilab.org/imp/>
> 
> Molecular Dynamics Flexible Fitting (MDFF):
> <http://www.ks.uiuc.edu/Research/mdff/>
> 
> Best,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> On Oct 22, 2013, at 4:37 AM, Christoph Wigge <wigge.christoph at gmail.com> wrote:
> 
>> Dear all,
>> I would like to fit two protein monomers that form a dimer into an em density map. I know from previous mutagenesis studies that the binding takes place with two tryptophan residues and the counterpart binding pocket. How can I set this interaction as fixed so that chimera fits the rest of the molecule according to the density map without continuously changing this part of the essential protein protein interaction? I would like to fit that interaction manually and then exclude it from the automatic procedure. Thank you very much in advance.
>> Bests 
>> Christoph Wigge
>