[phenixbb] Phenix.refine distorts geometry during rigid body refinement
iamslaymaker at gmail.com
Wed Sep 14 12:46:17 PDT 2011
Arthur, it looks like something similar may have happened. Thanks!
On Wed, Sep 14, 2011 at 11:48 AM, Arthur Glasfeld <glasfeld at reed.edu> wrote:
> 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.
>> phenixbb mailing list
>> phenixbb at phenix-online.org
> phenixbb mailing list
> phenixbb at phenix-online.org
More information about the phenixbb