Structural biology is continuously oriented towards understanding more and more complex structures of proteins, nucleic acids and their complexes. In structure refinement, parameters of tens to hundreds of thousands atoms are modified. Challenging data are frequently recorded at low resolution and low-resolution structure refinement can easily become unstable. The program PDBCOP is designed to reveal instabilities in coordinates and ADPs (Atomic Displacement Parameters).
The program PDBCOP performs quick calculations for common 'Table 1', reports extremes in ADPs, extreme occupancies, generates a sequence of structure model for validation against the original sequence, and compares two PDB files (most likely input and output from structure refinement models). The new version also accepts input in the CIF format.
The original version of PDBCOP by Karla Fejfarová [2] is also still available on the original url https://crysa.fzu.cz/pdbcop/. The new version written in Python3 and also compiled binaries for MS Windows are available on the new address http://kmlinux.fjfi.cvut.cz/~kolenpe1/pdbcop/.
Support by the Czech Ministry of Education, Youth and Sports to the Faculty of Nuclear Sciences and Physical Engineering (RVO14000) and by the Czech Academy of Sciences to the Institute of Biotechnology (no. 86652036) is acknowledged.