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Hello all, I apologize for my first posting sounding confusing. The cofactors I am referring to in my structure do not occupy the same density. The cofactors are stacking against one another for a hydride transfer reaction, and the electron density supports them being about 3.3 A apart from one another. Refinement in Refmac pushes one of the cofactors back slightly, changing the distance between the two from 3.3 to ~3.5 A, and as a result the cofactor is moved out of the middle of the density. In CNS this was a quick fix in that all I had to do was define an "igroup" definition to make the cofactors ignore one another with respect to van der waals interactions, and they both stayed in their respective densities. However, my structure is refining much better in Refmac, and I'm looking for a way to make the cofactors ignore van der waals interactions (with respect to each other) during refinement. Is there a way to make the two cofactors ignore one another with respect to VDW? One suggestion I have received is to name each cofactor as "A" and "B", and give them partial occupancy. Jamie Wallen [EMAIL PROTECTED] wrote: >*** For details on how to be removed from this list visit the *** >*** CCP4 home page http://www.ccp4.ac.uk *** > > >Hello all, > >I am currently trying refine a structure that contains two cofactors. When >I run refinement in Refmac, one of the cofactors is pushed out of the >electron density, and I believe this is due to a Van der Waals clash >between the two cofactors. Does anyone know of a way that I can keep the >cofactor in the electron density during refinement? I think it may involve >turning off van der waals between the two cofactors, but I am not sure how >to do this. I tried setting both cofactors to partial occupancy, but got >the same result. > >Any help will be grately appreciated! > >Jamie Wallen
