Oct 16, 2023
Model building, validation, and visualization
- 1Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
Protocol Citation: Minghao Chen 2023. Model building, validation, and visualization. protocols.io https://dx.doi.org/10.17504/protocols.io.j8nlkw77wl5r/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: June 06, 2023
Last Modified: May 31, 2024
Protocol Integer ID: 82925
Keywords: ASAPCRN
Funders Acknowledgement:
Aligning Science Across Parkinson’s (ASAP) initiative
Grant ID: ASAP-000350
Abstract
Model building, validation, and visualization
Model building
Model building
Generate a model by
[1] existing model in PDB
[2] creating a homology model by SWISS-MODEL
[3] creating a ab-initial model by AlphaFold
Do the flexible model fitting by [ISOLDE]
Roughly fit the secodary structures into the map
Do model fitting manually in [Coot] or automatically in [Phenix]
Repeat the model fitting until the coordinates fit the map resonably
Validation
Validation
Validate the quality of the models by using the validation tools in Phenix and the online validation service provided by wwPDB (https://www.wwpdb.org/validation/validation-reports)
Make sure the statistics, particularly the Ramachandran plot, Rotamers, R.m.s. deviations and B-factors are resonable.
Visualization
Visualization
Visualize the models and maps by [ChimeraX]
Create figures by [Adobe Illustrator]
Create movies by [iMovie]