On 23/08/13 20:57, Tim wrote:
Hi,
I'm running into trouble when trying to add an alternative conformation to a
non-standard residue type and subsequently trying to do real-space refinement.
I am working on the structure of a fluorescent protein that cyclizes three
residues in the middle of an alpha-helix. So the chromophore is connected to
the protein still, but I have to list it as a separate residue type with a .cif
dictionary. I have managed to get it all working, except for real space
refinement of a chromophore with alternative conformations in Coot. I can
real-space refine in Coot when I only have one conformation with no problem. I
can run refinement in Phenix with no problem on the alternative conformations.
But when I try to real-space refine a zone (the alpha helix containing the
chromophore) in Coot with the alternative conformations of the chromophore
present, Coot seems to forget that there is a chromophore and refines the
surrounding residues but not the chromophore (it even wants to move the
surrounding alpha helical residues down into the density filled by the
chromophore!).
I'd appreciate any help and can provide cif dictionaries and all of that if it
would be of help.
When you say "Real Space Refinement" which function are you activating?
The one "under" the button on the toolbar on the right? (That has a
primitive "by-sequence-number only" neighbour search (sphere refine is
more sophisticated)).
Paul.
