Model_building_of_human_Hgb_beta_subunit - I2PC/scipion-courses GitHub Wiki

Once we have the refined atomic structure of the human Hgb alpha-subunit, the beta-subunit should being modeled in a similar way. Follow the next workflow steps and repeat the process to generate the structure of the human Hgb beta-subunit, highligthed in the general workflow and detailed below. Take into account UniPROTKB sequence IDs and recommendations for the human Hgb beta-subunit in modeling tutorial and do not forget to validate your structure (validation steps are omitted in this schema).

Modeling_beta_subunit

To get the homology model of the haemoglobin beta subunit follow the same steps applied to get the first model of the alpha subunit (Scipion protocol chimerax-model from template. Complete the small form to get access to Modeller:

Modeller menu (step 6.b)

Once you have the retrieved models, select one of them, for instance #3.2. Realize that in this case you are going to have HEME groups also: Modeller menu (step 6.b)

Delete the additional HEME group and save the model anyway:

1.- Rename model #3.2 as #4.

  • rename #3.2 id #4

2.- Save chain A of the renamed model in tmp folder.

  • save /tmp/chainA.cif format mmcif models #4

3.- Open saved chain A as model #4; hide the rest of the models and observe that HEME group is still missing.

  • open /tmp/chainA.cif

4.- Select the extra HEME group and delete it.

  • select #4/A:148

  • del sel

5.- Save this new model #4 as the beya subunit of the human Haemoglobin.

  • scipionwrite #4 prefix Hgb_beta_