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Submission Details

Submission Title

automatic multiple fitting using MultiFit

Submission Authors

  • Keren Lasker

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Submission Comments

=Input: emd_5001.map, 3CAU_A.pdb; Output: groel_model_from_res4_multifit.pdb

=An automated protocol:

  1. The density was split into two rings along the Z axis using simple map manipulations commands in the em module of IMP.

  2. An ensemble of symmetric models for the top ring were generated using MultiFit. These models maximize fit to the map ,geometric complementarity between interacting subunits and maintain C8 symmetry.

  3. The top ranked model, was refined using a combination of the SymmRef method (refinement of symmetric complexes by geometric and energetic constraints) and EM fitting.

  4. The refined model was the fitted to the bottom ring, and the combined model of the two rings was deposited.

=Accuracy: the deposited model is very close to the reference structure, with a Ca-RMSD lower than 1 A.

=Running times (on a single CPU): 1. Step 2 run for approximately 4 minutes. 2. Step 3 run for approximately 10 minutes.

Files

Submitted Maps:

Submitted PDB Models:

Other files:



Images and screenshots


Representative Image:

Screenshots and other example images:

Submission Details

Submission Title

automatic multiple fitting using MultiFit

Submission Authors

  • Keren Lasker

(hint: click '+' to add more items)

Submission Comments

=Input: emd_5001.map, 3CAU_A.pdb; Output: groel_model_from_res4_multifit.pdb

=An automated protocol:

  1. The density was split into two rings along the Z axis using simple map manipulations commands in the em module of IMP.

  2. An ensemble of symmetric models for the top ring were generated using MultiFit. These models maximize fit to the map ,geometric complementarity between interacting subunits and maintain C8 symmetry.

  3. The top ranked model, was refined using a combination of the SymmRef method (refinement of symmetric complexes by geometric and energetic constraints) and EM fitting.

  4. The refined model was the fitted to the bottom ring, and the combined model of the two rings was deposited.

=Accuracy: the deposited model is very close to the reference structure, with a Ca-RMSD lower than 1 A.

=Running times (on a single CPU): 1. Step 2 run for approximately 4 minutes. 2. Step 3 run for approximately 10 minutes.

Files

Submitted Maps:

Submitted PDB Models:

Other files:



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