Author: Veselin Kolev [email protected]
1. Introduction
When writing the content of PDB files, the old versions of MOLARIS simulation package do shift with one position left the atom name records. That is not a major error, but sometimes it might cause problems, especially when reading the PDB for sake of analysis by using tools like VMD and USCF Chimera.
The Python 3 scripts provided here help to identify and convert those PDB files.
2. How to download the source code of the project.
The preferable method for obtaining the code is to use the tool git and clone the source tree locally to your file system:
git clone https://github.com/vessokolev/molaris_pdb_convert_tools.git
You may download the source as a ZIP-archive by pressing the button "Clone or download" in the web-interface on GitHub, or by using wget:
wget https://github.com/vessokolev/molaris_pdb_convert_tools/archive/master.zip
3. Identifying if the PDB matches the old format.
To check if a PDB file is created by an old MOLARIS version, invoke the script check_if_pdb_is_in_old_molaris_format.py:
check_if_pdb_is_in_old_molaris_format.py input.pdb
If input.pdb matches the old format, the following message will appear on the screen:
The supplied PDB file matches the old MOLARIS format! Do convert it!
When finishing, the script returns a value to the invoking shell. If the return value is 0, then the PDB file should not be converted. If the value is 2, a conversion need to be performed. Using the code can help organizing batch script for checking and (eventually) converting large number of PDB files.
4. Converting the PDB into the standard PDB format.
To convert a PDB file from the old to the standard format of ATOM and HETATM records, invoke the script convert_molaris_old_pdb_to_new_pdb.py by giving as parameters the name of the PDB file that needs to be converted and the output PDB file name. For example:
convert_molaris_old_pdb_to_new_pdb.py input.pdb output.pdb