On Tue, Jul 26, 2011 at 11:48 PM, Francois Berenger
Thanks for the workaround Pavel. However, I just wanted to know if it could be done using geometry only with phenix.pdbtools. If it was possible and fast, I or some colleague may have needed to wrap the functionality into some code as a compiled library.
Maybe I should rather look for some tool that can add sidechains to a backbone model (without introducing clashes in the process).
Try PULCHRA (http://www.pirx.com/pulchra/index.shtml) - since it is open-source, we distribute it with Phenix (phenix.pulchra). My guess is it won't be able to avoid all clashes for a poor starting structure, but it is incredibly fast, and it can even start from C-alpha coordinates alone. It appears to only work with a single chain at a time, but a little bit of scripting will fix that problem. -Nat