Hi all and thanks for your input.
I am trying to fix a sugar chain that has consecutive glucoses and I need the angle C-O-C to be as close to 104 degrees as possible keeping alpha bonds between the sugars, so when I do a Real Space Refinement in Coot, the structure gives angles close enough to 104, and the C-O bonds are at acceptable lengths.
Running refmac 5 afterwards always deviates the angles by a great amount to 145 degrees or more for most of the angles. So when I run a Real Space Refinement in Coot for the Refmac5 product, the angles readjust to what is “normal” close to 104.
I have tried restrained and rigid body refinement. And I did external harmonic restraints according to suggestions below by creating a pdb file having only the sentence: "external harmonic residues from 843 E to 850 E sigma 0.02”,
but I still get very wide angles, any suggestion?
Thanks for your help,
Remie
Hi Remie,
You could always generate self-restraints using one chain or a specific part of a chain using prosmart. These will ensure that the model does not move too far from its current conformation. Let me know if you want help to do this.
Regards,
Rob
On 14 Aug 2014, at 16:11, Remie Fawaz-Touma wrote:
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
Hi Remie,
You can add harmonic restraints for parts you do not want to move too much. Instructions could be found here:
Regards
Garib
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
