Check My Metal
3D-viewer: NGL

Input PDBID Test Data
 Low resolution adjustment

Upload your own coordinate file in PDB format
Files Acceptable Format And Information
PDB file:
*.cif, *.pdb (obligatory)
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 map file:
*.dsn6, *.map (optional)
fo-fc map file:
*.dsn6, *.map (optional)
Anomalous signal map file:
*.dsn6, *.map (optional)
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CMM has validated 42875 PDB structures and 90576 uploaded structures submitted by 6935 users from 54 countries since June, 2012

The CMM server is developed in Wladek Minor's lab.
Citing CheckMyMetal (CMM):
1. 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

2. 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.

3. 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.



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