Thank you Dr. Murshudov for the information. But please I still need help.

In restrained refinement, I could not find where to enter the residues I want to restrict from moving much. I was only able to find that in rigid body refinement, so I tried it and got a higher R factor than the initial file (before refinement). 

Is it normal to get a higher R factor when doing rigid body refinement?  if not, any suggestion regarding what could be wrong?

Is there a way to restrict one chain or part of a chain from moving much while doing restrained refinement? 

Thank you for any input,

Remie

On Aug 13, 2014, at 10:48 AM, Garib Murshudov <[log in to unmask]> wrote:

Hi Remie,

You can add harmonic restraints for parts you do not want to move too much. Instructions could be found here:
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/refmac_keywords.html#Harmonic


Regards
Garib


On 13 Aug 2014, at 15:44, Remie Fawaz-Touma <[log in to unmask]> wrote:

Hi everyone,

Does anyone know of a way to refine with CCP4 - Refmac5 (restrained refinement is what I do) fixing a part of the the ligand?

Thank you very much for your input,

Remie

Dr Garib N Murshudov
MRC-LMB
Francis Crick Avenue
Cambridge 
CB2 0QH UK
Web http://www.mrc-lmb.cam.ac.uk, 
http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/