Frequently Asked Questions

Can I use OpenStructure modules from python?

That's definitely possible, provided you have set the proper environment variables. On Linux you need to set LD_LIBRARY_PATH to the directory containing the libraries and PYTHONPATH to the directory containing the python modules. For a 64 bit platform this would look like:

export PYTHONPATH=/path/to/bundle/lib64/openstructure
export LD_LIBRARY_PATH=/path/to/bundle/lib64

On a 32bit system, the exchange lib64 for lib.

On MacOS X, you only need to set the PYTHONPATH. No need to set DYLD_LIBRARY_PATH.

How do I load a crappy PDB file?

The easiest way is to use the fault_tolerant option of LoadPDB. If you set the value to true, it will load the structure and just skip erroneus records:

ent=io.LoadPDB('pdb_with_errors.pdb', fault_tolerant=True)

How do I load all PDB files in a directory?

The python glob module can be used to match files in a certain directory against a glob pattern. Then use LoadPDB as you normally would.

import glob
for pdb_file in glob.glob(os.path.join(dir_path, '*.pdb')):
  pdbs.append(io.LoadPDB(os.path.join(dir_path, pdb_file)))

Where Do I Get Help?

First, search the documentation on the website. If you don't find the answer you were looking for, you may want to ask on the users mailing list. Please make sure to read the posting guidelines first.

Which licensing does Openstructure come with?

Openstructure is released under GNU-LGPL license

Which software libraries does Openstructure depend on?

Openstructure depends on the following software libraries to implement its functionality:

Why another molecular Viewer?

Openstructure is not aiming to be a Viewer, but more a computational structural biology framework, a toolkit. It features nice graphics, though!