PDBCat 1.3 review

PDBCat can be used to manipulate and process PDB files using commonly available tools such as Perl, awk, etc. Written by Andrew Da

License: Freely Distributable File size: 12K Developer: Andrew Dalke

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PDBCat can be used to manipulate and process PDB files using commonly available tools such as Perl, awk, etc.

Written by Andrew Dalke of the Theoretical Biophysics Group, Beckman Institute, University of Illinois. None of us are liable for any bugs, errors, or misconceptions. You may use this program freely and for free for non-comercial use. You may redistribute and modify the code as long as I am given credit for my part of the work.

Installation

1) uncompress and untar the source

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

2) change to the pdbcat directory and run make

% cd pdbcat; make

3) If it complains about not finding CC, then you'll have to edit the Makefile and set CC equal to your local C++ compilier, for instance, for gcc:

CC=gcc

4) If there is a problem with strcasecmp, uncomment the following line in the Makefile:

#DEF = -DNOSTRCASECMP

update the time stamp on the file Common.C

% touch Common.C

and run make again

Usage

pdbcat {-fields | -columns} [[-f] files]

Read any pdb file from stdin or list of files and convert the data to either a column based or field based pdb file. A '#' represents an empty field. This is useful for field based tools like awk. The default output is 'columns'.