Hi Pavel, Thanks so much for your reply. Following your suggestion, I could apply "reference_coordinate_restraints" section from http://www.phenix-online.org/documentation/reference/real_space_refine.html and it seems to be working perfect for me. Regarding why do I like to keep some part fixed: In my cryo-EM density some parts are not resolved due to flexibility and I had to manually build models after low pass filtering the density. Because I still don't have suitable restraints in those parts, a real space refinement is making the models go haywire. So, for the time being, I wanted to keep those difficult regions fixed. Best regards, Tofayel ________________________________ From: Pavel Afonine Sent: Tuesday, November 29, 2016 10:46:11 PM To: #AHMED TOFAYEL#; PHENIX user mailing list Cc: Pavel Afonine Subject: Re: [phenixbb] Refine only selective chains in a complex using phenix.real_space_refine 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