Hi there, we have just started looking at the xplor python interface and would like to use it to stitch together a fusion protein from two structured domains connected by a linker with unknown structure.
So we use psfGen.seqToPSF(...) in order to create the psf for the complete molecule. Is there now a way to read in the two PDBs that each cover part of the total sequence and project their structure into the system? Or will we need to create a single composite PDB with fake coordinates for the linker? The second step would be to create a covalent structure for the linker and minimize the whole system together. protocol.genExtendedStructure(...) should do the trick for the linker but how do we then run a rigid body, flexible linker, rigid body minimization? Lots of xplor.command(), or is there a more pythonic way? The python interface looks quite a bit more intuitive than the classic xplor language but documentation seems a bit patchy. Sorry if we overlooked some obvious documentation! Thanks a lot in advance! Raik
