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Submission Details

Submission Title

automatic multiple fitting using MultiFit

Submission Authors

  • Keren Lasker

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

Submission Comments

=Input: emd_5137.map, 3LOS_A.pdb; Output: mmcpn_closed_state_model_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 the SymmRef method.

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

=Running times (on a single CPU):

  1. Step 2 run for 4:41 minutes

  2. Step 3 run for less then a minute

=The commands used to run multifit:

  1. Generate a parameters file: $IMP/tools/imppy.sh python $IMP/modules/symm_multifit/bin/build_symm_multifit_params.py -- 8 3LOS_A.pdb emd_5137_top.mrc 4.3 1.33 0.468 -128 -128 -128

  2. Generate a surface file for the intput subunit: $IMP/tools/imppy.sh perl $IMP/modules/symm_multifit/bin/runMSPoints.pl 3IYF_A.pdb

  3. Run the modeling $IMP/modules/symm_multifit/bin/symm_multifit multifit.param.top

  4. The output file (multifit.output) holds 10 top solutions (number of solutions is a parameter), each containing transformations to build the ring and the cross-correlation score. The records are sorted by the cross-correlation score.

  5. alternatively, one can use the webserver: http://modbase.compbio.ucsf.edu/multifit/

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_5137.map, 3LOS_A.pdb; Output: mmcpn_closed_state_model_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 the SymmRef method.

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

=Running times (on a single CPU):

  1. Step 2 run for 4:41 minutes

  2. Step 3 run for less then a minute

=The commands used to run multifit:

  1. Generate a parameters file: $IMP/tools/imppy.sh python $IMP/modules/symm_multifit/bin/build_symm_multifit_params.py -- 8 3LOS_A.pdb emd_5137_top.mrc 4.3 1.33 0.468 -128 -128 -128

  2. Generate a surface file for the intput subunit: $IMP/tools/imppy.sh perl $IMP/modules/symm_multifit/bin/runMSPoints.pl 3IYF_A.pdb

  3. Run the modeling $IMP/modules/symm_multifit/bin/symm_multifit multifit.param.top

  4. The output file (multifit.output) holds 10 top solutions (number of solutions is a parameter), each containing transformations to build the ring and the cross-correlation score. The records are sorted by the cross-correlation score.

  5. alternatively, one can use the webserver: http://modbase.compbio.ucsf.edu/multifit/

Files

Submitted Maps:

Submitted PDB Models:

Other files:



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