Flexible_fitting - I2PC/scipion-courses GitHub Wiki

• Flexible Fitting in general

Modeling workflow to refine the initial model of the alpha subunit of the human haemoglobin according to the map asymmetric unit (lower part of the alpha subunit modeling workflow):

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1. Step 9a: Interactive flexible fitting or refinement with CCP4 Coot protocol (details in modeling tutorial and protocol appendix)

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Relevant information:

• To display a specific map and select its density level (Fig. 11.3 (A) of the modeling tutorial)
• To select a specific map for refinement (Fig. 11.3 (B, C) of the modeling tutorial)
• To assess the fitting of the atomic structure regarding a specific map (Fig. 11.3 (D) of the modeling tutorial)
• To remove the MET first residue of the atomic structure (Fig. 11.4 of the modeling tutorial)
• To edit the coot.ini file to perform a semi-automatic refinement (Fig. 11.5 of the modeling tutorial)
• To observe the rearrangement of the TYR residue 141 in the atomic structure (Fig. 11.6 of the modeling tutorial)
• To save the refined atomic structure in Scipion: Press key w

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2. Step 10a: Automatic flexible fitting or refinement with Phenix Real space refine protocol (details in modeling tutorial and protocol appendix)

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3. Step 10b: Automatic flexible fitting or refinement with CCP4 Refmac protocol (details in modeling tutorial and protocol appendix)

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