Hi Peng, first off, there is Phenix mailing list for Phenix-related questions. phenix.real_space_refine is Phenix program, not CCP4 so any issues related to it are best addressed at appropriate mailing list (Phenix mailing list, that is).
To answer your you question: please send me all inputs (1.pdb, 2.mrc, reference.eff, 20161215-3.pdb) and we will solve the problem. If files are too large to send via email please use file-sharing tools such as Dropbox or Google drive (I guess QQ has something for that too, if you are in China). All the best, Pavel On Tue, Jan 3, 2017 at 6:39 PM, Peng <[email protected]> wrote: > Dear all, > > I met a problem when I tried to refine a EM structure using a reference > model in Phenix. > > I used the command > > phenix.real_space_refine 1.pdb 2.mrc reference.eff resolution=3.2 > > , but it did not work. > > > My reference.eff is following: > > refinement { > > reference_model { > > enabled = True > > reference_group { > > reference = chain A > > selection = chain A > > file_name = 20161215-3.pdb > > } > > reference_group { > > reference = chain B > > selection = chain B > > file_name = 20161215-3.pdb > > } > > reference_group { > > reference = chain C > > selection = chain C > > > file_name = 20161215-3.pdb > > } > > } > > } > > } > > > My output .log file is following: > > reference_model { > > enabled = False > > file = None > > use_starting_model_as_reference = False > > sigma = 1.0 > > limit = 15.0 > > hydrogens = False > > main_chain = True > > side_chain = True > > fix_outliers = True > > strict_rotamer_matching = False > > auto_shutoff_for_ncs = False > > secondary_structure_only = False > > reference_group { > > reference = None > > selection = None > > file_name = None > > ...... > > > It seemed my reference.eff was not recognized. > > How can I use the reference model in Phenix refinement? > > > Thanks, > > Peng > > > >
