X-dVal: X-ray Data Validation

phenix.xtriage / Matthew's Coefficient / Twinning Detection / CRYST Record analysis

This server uses software developed by the Phenix project, specifically the phenix.xtriage program, and software developed in our lab.

SAVES | [XdVal] | MTZdump | Ramachandran Plot | pdbU | pdbSNAFU (Check for ADIT compliance) | PROCHECK | Verify3D | ERRAT

1. We run phenix.xtriage which "is a program that performs a number of basic 'sanity' checks on an Xray data set. It provides a quick way of determining certain idiosynchrasies of the data."
2. We run a program to report the Matthew's coeffient, solvent percents, and the number of molecules in the asu.
3. We use the Padilla-Yeates algorithm to detect any twinning.
4. Finally, using the cell dimensions, we search the entire PDB for matches and report these as possibly similar structures.

See an example of the output

• We expect users to acknowledge they have a license for Phenix when using this server •

New Job. Upload MTZ or CNS file here:

Please indicate the file type:
Molecular Weight (Not required)

CRYST1 % Distortion Cutoff: % (Only show those, up to 50, that have % unit cell distortion within this range)

Help Contact: holton at mbi.ucla.ucla


Padilla-Yeates algorithm:
J. Padilla & T. O. Yeates. Acta Crystallogr. D59, 1124-30 (2003) "A statistic for local intensity differences: robustness to anisotropy and pseudo-centering and utility for detecting twinning. "

P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010) "PHENIX: a comprehensive Python-based system for macromolecular structure solution."