Hi Reza,

What is the syntax for having phenix.real_space_refine refine a single chain of a multi-chain complex?

unlike phenix.refine, currently phenix.real_space_refine will refine the entire content of provided PDB or mmCIF file. You can edit the file to leave only the part you want to refine and run refinement (map does not need any change, use full map). Then paste refine part back to the full model. Not ideal and ugly, but may just work. Alternatively, you may cut out a box with piece of model and map around it and do the same as above. This is slightly nicer but still not ideal. Adding functionality to refine only select part of the model is in to-do list.

I have separated the chains into distinct files and run refinement on a single chain (file) with undesirable results.  It seems that residues adjacent to the density of a neighboring chain get pulled into the neighboring density –possibly because the neighboring density is vacant.  I hope my explanation is clear.

I see. Ok, this is sort of expected. Then use the second option above: cut out a box. When cutting out a box make sure you define mask around model with some generous buffer and set everything outside to zero.. Normally this should do the trick. Pavel