PDBCat

PDBCat is a software that allows users to manipulate and process PDB files with ease. The software is designed to be used with commonly available tools like Perl and awk, among others. Andrew Dalke, a member of the Theoretical Biophysics Group at Beckman Institute, University of Illinois, created the software.

It is important to note that none of the team involved in PDBCat is responsible for any bugs, errors or misconceptions that may arise while using the software. This software is free for non-commercial use, and users are allowed to modify and redistribute the code as long as Andrew Dalke is given credit for his part of the work.

To install PDBCat, users will need to decompress and untar the source of the software. They can do this by running the following command:

% cat pdbcat_1.tar.Z | uncompress | tar -xf -

While changing to the pdbcat directory and running the Makefile, users may need to set the CC equal to their local C++ compiler. If there is a problem with strcasecmp, then the user can simply uncomment a line in the Makefile and run make again. To update the time stamp on the file Common.C, users can run the command % touch Common.C.

PDBCat can be used for reading any pdb file from stdin or a list of files, and converting data to either a column-based or field-based pdb file. Users are also provided with a useful feature where a "#" represents an empty field. This is very helpful for field-based tools like awk. The default output is 'columns'.