On Fri, Oct 29, 2010 at 5:46 PM, Tom Huxford <thuxf...@sciences.sdsu.edu>wrote:
> I'm working with good quality relatively complete x-ray diffraction data > collected to a resolution limit 2.6 Å from a crystal of a protein with a > small molecule ligand bound. I ran MR from 10-4 Å and then did maximum > likelihood rigid body refinement in Refmac5 against data from 50-3.5 Å. Now > I would like to run restrained refinement from 50-3 Å. The reason for doing > this is that, in order to minimize the divergence between R-cryst and R-free > during refinement my advisor who, by the way, is forwarding this e-mail for > me (and editing it so please don't bash him too mercilessly) suggested I > first build in the ligand and newly positioned polypeptide loops and refine > against data at a lower resolution limit before opening it up to all the > available data. Apparently this has worked well for him in the past (and it > has!). The problem is that I'm to the point where I'd like to extend the > resolution down to 3 Å during restrained refinement but even if I set the > range from 50-3 Å in the ccp4i window refinement only happens from 50-3.5 > Å. If I take a step back and do the rigid body refinement from 50-3 Å and > then carry out restrained refinement from 50-3 Å it works fine. Why would > the limits imposed by rigid body refinement cause the subsequent restrained > refinement to be stuck at the rigid body refinement's resolution limits? > Did you refine against the file output by Refmac after rigid-body refinement, instead of using the original reflections? -Nat
