[phenixbb] Phenix.refine distorts geometry during rigid body refinement

Arthur Glasfeld glasfeld at reed.edu
Wed Sep 14 11:48:43 PDT 2011

This may not be helpful - but I had a similar thing happen at low resolution a few months ago.  It turned out that a couple of residues just "blew out" of the structure for some reason.  Their crappy geometries skewed everything else (though I had bad bond angles to go with the bad distances).  It took me a while to see it, since everything else (99% of the structure) looked fine.  

Good luck,

Arthur Glasfeld
Department of Chemistry
Reed College
3203 SE Woodstock Blvd.
Portland, OR 97202

On Sep 14, 2011, at 11:35 AM, Ian Slaymaker wrote:

> I am bringing a PDB refined in Refmac back to phenix.refine. After an
> initial rigid body refinement to compare numbers (one chain per
> group), the geometry (specifically the bond length rmsd) had
> surprisingly increased. Phenix.validate confirmed the Refmac (initial)
> geometry numbers and then afterwards confirmed the distorted geometry.
> What is strange is that when opened in COOT, the initial and final
> models are completely super imposed.
> REMARK Start: r_work = 0.3375 r_free = 0.3624 bonds = 0.006 angles = 0.768
> REMARK Final: r_work = 0.3379 r_free = 0.3626 bonds = 0.145 angles = 1.019
> can you help me figure out what is going on here? These are the final
> few refinements of a 4.1 A structure.
> Thanks,
> Ian
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