Hi Tristan,
I am trying to phenix real-space refine a structure containing AMPPNP, which I have modelled very accurately with ISOLDE.
I create inputs using the isolde write phenixRsrInput
command, including the restrainPositions true and
includeHydrogens true arguments (which normally works perfectly).
However, in this case, the Rsr output yields AMPPNPs with bond-length RMSZs > 2, although this is not the case in the input model itself.
Would you be able to advise as to how I can potentially restrain the AMPPNP heavy atoms from the ISOLDE model as well? I am not a phenix expert, so not having to create these
manually would be ideal.
Perhaps a phenix command that will automatically generate an appropriate restraints file (to append to the
isolde write phenixRsrInput command or phenix.real_space_refine itself), and/or lines that may be added to the real_space_refine.eff file created by ISOLDE?
Any help would be immensely appreciated.
Best regards,
Taha