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cryoFIT / cryo_fit2

cryo_fit2 source codes, test files, live at .../phenix-xxxx/modules
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how to include ligands in cryo_fit2 #11

Closed GangyuSun closed 1 year ago

GangyuSun commented 2 years ago

Hi, Is there any method to give the ligand restraint file to cryo_fit2? The restraint file is not supported by the default PHIL of cryo_fit2. the erros is something like : Sorry: Fatal problems interpreting model file: Number of atoms with unknown nonbonded energy type symbols: 59 Please edit the model file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. Thanks for any help!

girodat commented 2 years ago

Hi Gangyu,

Sorry to say we currently don't have any ligand support in cryo_fit2. We are going to work on generating methods/libraries for cryo_fit ligands but haven't implemented it yet. Often it is best to use cryo_fit or cryo_fit2 to model large scale conformational changes and then use ligand fitting tools in phenix to properly position ligands such as Elbow or LigandFit etc.

Thanks, Dylan

GangyuSun commented 2 years ago

Okay, got it! Thanks for your response! Gangyu