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Hello Raik-- > > 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? Presuming the input pdb residue nums are consistent with the overall sequence, you can use psfGen.seqToPSF (follow an example in eginput/PSF_generation/*.py) and then initialize coordinate values using protocol.initCoords. > > 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? You shouldn't use many if any xplor.command calls. You use the IVM to group (ivm.IVM.group()) your previously determined regions into rigid bodies. Then you might try the protocol in eginput/gb1_rdc/anneal.py. > > 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! Unfortunately, the documentation is a bit sparse. I will try to assist you as necessary. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iEYEARECAAYFAkpUimMACgkQPK2zrJwS/lZN7ACbBdbG+kx/7AQA7p+CncRN+As5 u0QAnAt0KDDOEpfMZe03Dwgs5EMSMVuO =M4KB -----END PGP SIGNATURE-----
