================= OpenStructure molecular modelling framework ================== OpenStructure provides a modular, flexible, molecular modelling environment which allows to integrate, process and visualize information of different origin such as sequences, alignments and 3D structures. Please refer to www.openstructure.org for more information and documentation. Thank you for you interest and enjoy the straightforward way of handling protein structure data! Please do not hesitate to contact us for feedback or troubleshooting: openstructure-users@maillist.unibas.ch If you like our software and have used it in your research project, please cite the following paper on OpenStructure: M. Biasini, T. Schmidt, S. Bienert, V. Mariani, G. Studer, J. Haas, N. Johner, A.D. Schenk, A. Philippsen and T. Schwede, OpenStructure: an integrated software framework for computational structural biology, Acta Cryst., 2013 If you use the code or binary in OpenStructure to compute lDDT scores, please also cite the following reference: V. Mariani, M. Biasini, A. Barbato, T. Schwede, lDDT : A local superposition- free score for comparing protein structures and models using distance difference tests, Bioinformatics, 2013 If you use the code in OpenStructure to compute QS scores, please also cite the following reference: M. Bertoni, F. Kiefer, M. Biasini, L. Bordoli, T. Schwede, Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology, Scientific Reports, 2017 ================= The OpenStructure Team =======================================
Studer Gabriel
authored
Simon found issues when reading and writing CONECT statements in PDB io and provided code to fix it. yay Reading: OpenStructure did not read CONECT statements at all. By default, it still doesnt. Many PDB files out there don't provide these statements and we really don't want to rely on them. We rather want to assign connectivity based on the chemical component dictionary from the PDB. However, a valid use case are novel compounds that are not in the component dictionary. Reading connect statements can now be enabled in the pdb reader through the IOProfile. This may give issues in processing after reading. OpenStructure implements processors that are responsible for connectivity. Now that we build some of the connectivity already at the reading stage, this might cause trouble. To remedy most of the nightmares that can come out of that, the processors can now optionally skip connectivities between Hetatoms. Writing: That was a plain bug when writing CONECT statements for bond orders > 1.