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Submission Details

Submission Title

Fitting 1AON.pdb to the GroEL 7.7 A density map

Submission Authors

  • Radhakrishna Bettadapura
  • Qin Zhang
  • Chandrajit Bajaj

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

Submission Comments

We use the electrostatics potential of the crystal structure for the purposes of rigid-body fitting, i.e., the electrostatics potential is correlated with the cryo-EM density map under various rigid-body transformations. The potential is computed using a suitable Poisson-Boltzmann solver such as APBS. In this case, however, electrostatics fitting proves inferior to blurred map fitting. The uploaded results thus correspond to blurred density map fitting.

See the attached document for details.

GroEL7A.pdf describes the fitting of GroEL.

F2Fit.pdf describes the software used for fitting. F2Fit will eventually be available from the CVC software page: http://www.cs.utexas.edu/~bajaj/cvc/software.shtml

In all fitting experiments, VolumeRover was used for segmentation, F2Fit for fitting, and TexMol for visualization. Additionally, UCSF Chimera was used to select, isolate and save protein chains.

Files

Submitted Maps:

Submitted PDB Models:

Other files:



Images and screenshots


Representative Image:

Screenshots and other example images:

Submission Details

Submission Title

Fitting 1AON.pdb to the GroEL 7.7 A density map

Submission Authors

  • Radhakrishna Bettadapura
  • Qin Zhang
  • Chandrajit Bajaj

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

Submission Comments

We use the electrostatics potential of the crystal structure for the purposes of rigid-body fitting, i.e., the electrostatics potential is correlated with the cryo-EM density map under various rigid-body transformations. The potential is computed using a suitable Poisson-Boltzmann solver such as APBS. In this case, however, electrostatics fitting proves inferior to blurred map fitting. The uploaded results thus correspond to blurred density map fitting.

See the attached document for details.

GroEL7A.pdf describes the fitting of GroEL.

F2Fit.pdf describes the software used for fitting. F2Fit will eventually be available from the CVC software page: http://www.cs.utexas.edu/~bajaj/cvc/software.shtml

In all fitting experiments, VolumeRover was used for segmentation, F2Fit for fitting, and TexMol for visualization. Additionally, UCSF Chimera was used to select, isolate and save protein chains.

Files

Submitted Maps:

Submitted PDB Models:

Other files:



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