3D-viewer: NGL
Input PDBID Test Data Statistics Limitations
 Low resolution adjustment
Upload your own coordinate file in PDB format
Files Acceptable format
PDB file:
*.cif, *.pdb
Structure factors file:
*-sf.cif, *.mtz (optional, obligatory for for refinement)
Accetptable column names for refinement: F,FP; SIGF,SIGFP; FREE,FreeR_flag
CMM can now generate maps from mtz file, acceptable column names to generate maps: More 2fo-fc map: F1=[FWT, F_l, 2FOFCWT], SIG1=[SIGF, SIGFP, SIGF-obs], PHI=[PHWT, PHI_l, PH2FOFCWT], FOM(optional)=[FOM_l, FOM]
fo-fc map: F1=[DELFWT, FOFCWT], SIG1=[SIGF, SIGFP, SIGF-obs], PHI=[PHDELWT, PHFOFCWT], FOM(optional)=[FOM_l, FOM]
anomalous map: DANO=[DANO], SIG1=[SIGDANO], PHI=[PHWT, PHI_l, PH2FOFCWT]
New columns can be reported to support in the bottom of the page.
2fo-fc / cryo-EM_map file:
*.dsn6, *.map, *.mrc (optional)
fo-fc file:
*.dsn6, *.map (optional)
Anomalous signal map file:
*.dsn6, *.map (optional)
--> <--

CMM has validated 45211 PDB structures and 184679 uploaded structures submitted by 9919 users from 130 countries since June, 2012

The CMM server is developed in Wladek Minor's lab.
Citing CheckMyMetal (CMM):
1. CMM—An enhanced platform for interactive validation of metal binding sites. Gucwa M, Lenkiewicz J, Zheng H, Cymborowski M, Cooper DR, Murzyn K, Minor W (2022) Protein Sci., 32(1)

2. Characterizing metal-binding sites in proteins with X-ray crystallography. Handing KB, Niedzialkowska E, Shabalin IG, Kuhn ML, Zheng H, Minor W (2018) Nat Protocols, 13, 1062-1090

3. CheckMyMetal: a macromolecular metal-binding validation tool. Zheng,H., Cooper,D.R., Porebski,P.J., Shabalin,I.G., Handing,K.B., Minor,W. (2017) Acta crystallographica. Section D, Structural biology, 73, 223-233.

4. Validation of metal-binding sites in macromolecular structures with the CheckMyMetal web server. Zheng,H., Chordia,M.D., Cooper,D.R., Chruszcz,M., Müller,P., Sheldrick,G.M., Minor,W. (2014) Nature Protocols, 9(1), 156-70.
The service is based on several well-established concepts reported previously: bond valence (1), VECSUM (2), metal binding sites (3), coordination geometries (4), assignment of sodium versus water (5), metal binding environment (6) in protein structures. We thankfully acknowledge their important contributions. The list presented here may not be complete and suggestion for any additional references are appreicated.
1 Brown,I.D. (2009) Chem. Rev., 109, 6858-6919.
Recent developments in the methods and applications of the bond valence model.
2 Müller,P. et al. (2003) Acta Crystallogr. D Biol. Crystallogr., 59, 32-37.
Is the bond-valence method able to identify metal atoms in protein structures?
3 Harding,M.M. et al. (2010) Cryst. Rev., 16, 247-302.
Metals in protein structures: a review of their principal features.
4 Kuppuraj,G. et al. (2009) J. Phys. Chem. B, 113, 2952-2960.
Factors governing metal-ligand distances and coordination geometries of metal complexes.
5 Nayal,M. and Di Cera,E. (1996) J. Mol. Biol., 256, 228-234.
Valence screening of water in protein crystals reveals potential Na+ binding sites.
6 Zheng,H. et al. (2008) J. Inorg. Biochem., 102, 1765-1776.
Data mining of metal ion environments present in protein structures.

Reporting bugs: REPORT_A_BUG