On Thu, Aug 12, 2010 at 8:11 AM, Lionel Costenaro <span dir="ltr">&lt;<a href="mailto:lcocri@ibmb.csic.es">lcocri@ibmb.csic.es</a>&gt;</span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">

Indeed some bond length or angle restraint outliers are from the ligand when refining with phenix.<br>However I don&#39;t think this is the problem, I give to refmac and phenix the same ligand dictionary (cif file from ProDRG with link definition added with JLigand). Refmac / phenix give me the following outliers &gt;4 sigma : bond length 0 / 6, bond angle 0 / 23, dihedral 23 / 13, chiral 0 / 0, plan 3 /13. Clearly phenix is not doing a good job (R decrease, but not Rfree). <br>


For refmac I&#39;m using an x-ray weighting term (matrix) of 0.8, which is more or less expected for 1.3A resolution. <br>I don&#39;t really know how to fix the weights in phenix as I never used it before and did not find any hint in the manual or bb.<br>

</blockquote><div><br></div><div>ProDRG&#39;s CIF files can be problematic, because they often have ESDs that are inappropriately low and this confuses the minimizer.  I&#39;d recommend running phenix.elbow or phenix.ready_set to generate a new CIF file.</div>

<div><br></div><div>Other comments:</div><div>- Are you adding hydrogen atoms?  This can help with the geometry (and at this resolution, it will certainly help with the R-factors).</div><div>- As pavel mentioned, you should turn on the weight optimization, but I would also recommend setting the max allowable RMS(bonds) and RMS(angles) to something more reasonable than the defaults - say, 0.02 and 2.0, if not less.  (I forget the parameter names but if you are using the GUI they are all in the same dialog window.)</div>

<div>- You should also update to version 1.6.4.</div><div><br></div><div>-Nat</div></div>