[Chimera-users] join models

[Elaine Meng]

Hi Valentina,
Some general possibilities are one or a combination of the following:

(a) manually rotate bonds (or specify different backbone angles when you join the models in the first place)
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#adjust>

(b) use “movement mouse mode” tool to generally move one domain relative to the other
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movemode/movemode.html>

(c) minimization of part (e.g. just linker) or all of the structure
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html>

(d) molecular dynamics (minimization alone is unlikely to get you far)
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html>

However, as you know the protein conformation landscape is huge and unless you do a long calculation (lots of dynamics) it may not sample the most realistic conformations. It also depends on your goal, if you are just trying to make a schenatic figure or do some kind of serious quantitative modeling.  If the latter, you may need to use some other software devoted to simulations, like AMBER or Gromacs, for more efficient calculations.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On May 8, 2018, at 1:19 AM, VALENTINA BRANDI <valentina.brandi at uniroma3.it> wrote:
> 
> Hi,
> I’m a Phd student and I need to join different domains of a protein. I have used the tool “join models” of Chimera, but unfortunately after the union there is a partial superimposition between the two models. How can I solve this problem?
> Thank you so much,
>  
> Valentina Brandi
>