<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi,<br><br>At the Molecular Modelling Group (<a href="http://www.molecular-modelling.ch/">http://www.molecular-modelling.ch/</a>) in Lausanne, Switzerland, we've developed a Chimera extension with 3 functionalities:<br> * GUI for CHARMM setups: inspect, clean up and prepare molecules for use with CHARMM<br> * GUI for the EADock docking software: setup a receptor, a ligand, choose the docking parameters that suit your needs, and run your docking<br> * access to the S3DB database, a database containing more than 250 manually curated complexes<br><br>The extension is reaching the end of the test phase and we plan on releasing it soon. However, coming closer to the release day brought up several questions:<br><br>1) We needed a slightly modified version of the writeMol2 function (in writeMol2.py), and had to include a modified version of the writeMol2 and midas package in our extension. Of course we're not claiming any intellectual property on any of those two modified files, but is it a problem to integrate them into our extension?<br><br>2) More or less the same situation appears for the rotamers window, from which we took a part to integrate it in part of our extension that allows a user to fix residues with missing atoms. We basically copied and pasted the code we needed. The problem is slightly different since this isn't a built-in function of Chimera, as opposed to writeMol2, for example. But again, is that a problem?<br><br>3) We plan to add some features to the awesome ViewDock extension that is already part of Chimera. However, we really only want to implement shortcut commands that are helpful when using EADock, but since ViewDock is already so complete, it makes no sense to start from scratch. We see two options: either extend the ViewDock extension with our features, or inherit a large part of the ViewDock extension and customize it in our own extension. Option 1 seems possible only if the owner of the ViewDock extension agrees to integrate our features in his extension and brings up questions of supporting/updating those features, whereas option 2 brings up the question already mentioned above.<br><br>Could someone let us know what the standard policy is to deal with those issues?<br><br>Thanks,<br><br>Sébastien Cuendet</body></html>