Hello, I am learning how to use PanDDA and would appreciate some clarifications on the modeling and refining steps. I realize that maybe some questions will be too obvious, but I would appreciate the confirmation of my guesses so I might learn to do it the correct way.
I managed to get to step 13 of the tutorial (https://pandda.bitbucket.io/pandda/tutorials.html#) (but with my data). After step 11 in my pandda-export folder, I have the following files: File name: Remarks: 1 ensemble-model.log 2 ensemble-model.pdb Contains both bound and ground-state 3 ensemble-model-restraints.log 4 ensemble-model-restraints.phenix.params 5 ensemble-model-restraints.refmac.params 6 pandda-input.mtz Does not contain the "event density" of ligand 7 pandda-input.pdb Does not contain ligand 8 pandda-model.pdb Contains bound state of ligand 9 pandda-output.mtz Does not contain the "event density" of ligand 10 pandda-output-event-001.mtz Contains the "event density" of ligand In the file ensemble-model.pdb I see water and ligand on the same spot. My protein normally has water in that site, but if the ligand is bound - there is no water. Further modeling is required for my structures and thus I move on to step 13 where I get confused. I have highlighted in bold the instructions of the tutorial. 1. Generation of restraints for refinement (giant.make_restraints) It says: "...The output restraint files can then be fed to giant.quick_refine, which then either runs phenix or refmac (see below)." Should I skip this step as I already have the phenix.params and refmac.params files? 1. Quick-and-easy refinement (giant.quick_refine) To make refinement more straightforward, giant.quick_refine can be used to refine the models. A normal refinement will look like giant.quick_refine input.pdb input.mtz ligand.cif restraints.params Which files should I use here? The pandda-input.pdb, pandda-input.mtz ligand.cif and ensemble-model-refmac.params? If the .params file is for the ensemble, should I rather use then ensebmle-model.pdb, padda-output-event-001.mtz ligand.cif and ensemble-model-refmac-params? If I want to include additional parameterization for the refmac, do I manually add instructions in the .params file? For example, if I want to increase the weight parameter? 2. Splitting the ensemble model (giant.split_conformations) Should it be done on the output of the step 13.2? 3. (Re-)modelling of the bound-/ground-states (coot) The ground-state conformations should be modelled into a ground-state ("reference") dataset/map (e.g. "*-ground-state-average-map.native.ccp4" from pandda.analyse). I do not have any file in the format ....native.ccp4 Should I do it with the file pandda-input.pdb with pandda-input.mtz? The bound-state conformations of the protein are modeled into the appropriate event maps, as in pandda.inspect. Should I use the files pandda-model.pdb with pandda-ouput-event-001.mtz? However, if you want to edit both structures simultaneously (e.g. to add a molecule that is the same in both states), then this should be done to the combined ensemble model. Should I use ensemble-model.pdb with pandda-output-event-001.mtz? 4. Re-merging single-state models for refinement. After you have re-modelled the bound- and ground-states of the protein, you need re-assemble the ensemble model for refinement. giant.merge_conformations ground-state.pdb bound-state.pdb Maybe it will be more clear which exact files to use here once I go through steps 1-4, but if there is something I should be aware of during this step - please let me know. Please let me know if you any of my questions should be clarified more. I will greatly appreciate any help I can get with this! Best regards, Vladyslav ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
