Chain_merge_symmetrization

Modeling workflow to built the structure of the asymmetric unit and the structure of the whole molecule of the human Hgb by applying symmetry (detailed in the general modeling workflow):

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1. Step 11a: Merging of chains A and B of human Hgb alpha and beta subunits, respectively, with ChimeraX operate protocol (details in p. 89-93 and Appendix 5 of the modeling tutorial)

If you want to have HBA-refined and HBB_refined (red arrows 2 and 3, respectively) go for instructions to Fig. 62 of the modeling tutorial.

Once you have opened the ChimeraX GUI, merge the chains A and B and save the final asymmetric unit writing in the command line:

• scipioncombine #3,4
• scipionwrite #5 prefix asymmetric_unit_model_

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2. Step 12a: Manual flexible fitting with CCP4 Coot, if needed, in the overlapping area between chains A and B

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3. Step 13a: Automatic flexible fitting with Phenix Real space refine, if needed, in the overlapping area between chains A and B

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4. Step 14a: Building of the whole human Hgb molecule by applying symmetry to the asymmetric unit with ChimeraX operate protocol (details in p. 93-95 and Appendix 5 of the modeling tutorial)

Once you have opened the ChimeraX GUI, apply symmetry, rename chains and save the whole structure as a unique model writing in the command line:

• sym #3 C2 copies true
• save /tmp/chains_C_D.cif format mmcif models #4.2
• open /tmp/chains_C_D.cif
• Old chimerax versions
  • setattr #5/A c chains_id C
  • setattr #5/A r chains_id C
  • setattr #5/B c chains_id D
  • setattr #5/B r chains_id D
• New version chimerax
  • setattr #5/A chain chain_id C
  • setattr #5/B chain chain_id D
• scipioncombine #3,5
• scipionwrite #6 prefix whole_model_

5. Step 15a: Manual flexible fitting with CCP4 Coot, if needed, in the overlapping area between asymmetric units

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6. Step 16a: Automatic flexible fitting with Phenix Real space refine, if needed, in the overlapping area between asymmetric units

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Once we have the asymmetric unit or the whole macromolecule modeled, we can submit our map and model to databases:

7. Step 17a: Preparation of files to send them to databases (all of them are saved in the appropriate format in a specific folder). (Details in p. 99-103 and Appendix 28 of the modeling tutorial)

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8. Step 17b: Identification of unmodeled parts of the map using the map subtraction protocol (Details in p. 96-99 and Appendix 4 of the modeling tutorial)