Hi Tofayel,

Is it possible using phenix.real_space_refine to locally refine a protein or RNA chain (against a cryo-EM map) which is part of a big complex.

no, sorry. Options:

1) Create PDB file that contains only parts of the model that you want to refine and supply that to phenix.real_space_refine. This may work just fine but dangers are that refined part of the model may clash with the one that is not refined

2) Refine entire model restraining positions of selected atoms to their initial coordinates.

During the run, I would like to keep most of my complex constant in space except neighboring one or two protein/RNA molecules which I would like to see getting adjusted to remove clashes. I am using the program through command-line.

I can see how this may be useful and I will add this functionality to phenix.real_space_refine.

Just out of curiosity: why you want to keep some parts of the model fixed?

Pavel