Comparison_validation_scores - I2PC/scipion-courses GitHub Wiki

Modeling workflow to detail the structure of the whole molecule of the human Hgb that we have obtained previously by applying symmetry. Validate it in the same way as we have validated previously each one of the Hgb subunits.

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Run the validation protocols detailed in modeling tutorial: Phenix Validation cryoEM and Phenix EMRinger. Then, compare your validation results with those obtained with the pair map and structure downloaded from databases using the following workflow:

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1. Step 30: Import the structure of PDB ID 5NI1 using the protocol pwem-import atomic structure (appendix):

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2. Step 1a: Import the map of EMDB ID EMD-3488 using the protocol pwem-import volumes according to the original map header coordinates (appendix):

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3. Step 31: Automatic fitting of map and structure with the protocol phenix-dock in map (appendix):

3. Step 32: Check that map and structure are fitted with the protocol chimerax-rigid fit (appendix):

Complete the fitting and save the fitted atomic structure in Scipion with the next command lines:

• fitmap #3 inMap #2
• scipionwrite #3 prefix 5ni1_fitted_

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4. Step 33: Validation of the refined atomic structure with Phenix Validation cryoEM protocol (appendix):

Scipion Summary:

Compare these validation values with those observed in the Haemoglobin PDB full validation report. Are they identical?

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5. Step 34: Validation of the refined atomic structure regarding to the map EMD-3844 with Phenix EMRinger protocol (details in modeling tutorial and protocol appendix)

Scipion Summary:

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Comparison of validation scores Compare the validation scores obtained for your own whole structure with those score values obtained for the published human Hgb (PDB ID 5ni1).

Try to complete the next validation table with your own scores. Is your model of the human Hgb better or worse than the published one?

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