Phenix.refine distorts geometry during rigid body refinement
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
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 Arthur Glasfeld Department of Chemistry Reed College 3203 SE Woodstock Blvd. Portland, OR 97202 USA 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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Arthur, it looks like something similar may have happened. Thanks!
On Wed, Sep 14, 2011 at 11:48 AM, Arthur Glasfeld
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
Arthur Glasfeld Department of Chemistry Reed College 3203 SE Woodstock Blvd. Portland, OR 97202 USA
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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi Ian, can you send me a PDB file (and any parameter files, if any) so I can reproduce the problem? Pavel On 9/14/11 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
On Wed, Sep 14, 2011 at 11:35 AM, Ian Slaymaker
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.
The problem is with your rigid body group definitions: only residues 1-7 are included, which means they will move independently of the rest of the chains. Since the rigid-body refinement ignores geometry restraints, it will pull these residues as far apart as necessary, leaving you with bond deviations up to 16A. We probably need to check for this during refinement and alert the user; even if you are running restrained refinement afterwards, huge deviations from ideal restraint values can screw up the automatic weighting. All that aside, I wouldn't run rigid-body refinement here anyway - if Refmac and Phenix disagree on the optimal positions of the atoms, it will be much more subtle than domain-level movements, which is what the rigid-body refinement is for. -Nat
participants (4)
-
Arthur Glasfeld -
Ian Slaymaker -
Nathaniel Echols -
Pavel Afonine