It depends on what is in the restraints file(s). In refmac, I believe only the bond lengths are restrained, but only if you identify specific metal-lagand links. Otherwise, there are no bond length or angle restraints.
Roger Rowlett On May 12, 2012 8:48 AM, "Dave Roberts" <drobe...@depauw.edu> wrote: > Hello > > I have a protein structure I've been working on (seemingly forever), which > includes a bound metal. In fact, I have the same structure with different > metals bound (that's it's job, so it's not a surprise). > > My question is this - the metals I'm talking about now are Ni+2, Cd+2, and > either Zn+2 or Mg+2. If I look at the electron density, the environment > around the metal is truly tetrahedral geometry (in all cases actually). > I'm fine with that, it's highly likely based on other systems that that is > correct. However, I just want to make sure the metal environment is not > due to the fact that I did something wrong in my refinement script - thus > making it tetrahedral because it was refined as tetrahedral. For example, > my nickel structure could potentially be octahedral (with waters filling in > for the other 2 ligands, or perhaps a side chain moving not too far). If > my refinement program is doing something to make it tetrahedral, would it > also change the appearance of the maps? > > Is that possible? Should I worry about this, or can I trust the electron > density to tell me what I think it's telling me. I don't use CCP4 for > refinement, I use CNS, but I'm hoping somebody will be able to guide me > here. > > Thanks > > Dave Roberts >
