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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 On Aug 14, 2014, at 11:53 AM, Robert Nicholls <[log in to unmask]> wrote: > 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 >> >> 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/ >>> >>> >>> >> >