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Nup133

These scripts demonstrate the use of IMP, MODELLER, FoXS, and Minimal Ensemble Search in the modeling of the Nup133 in the Nuclear Pore Complex (NPC). First, MODELLER is used to generate structures for the individual components in the Nup133. Then, IMP is used to fit these components together into the electron microscopy density map of Nup133.

A full description of the scripts can be found in Integrative structure-function mapping of the nucleoporin Nup133 suggests a conserved mechanism for membrane anchoring of the nuclear pore complex.

Steps (UNDER CONSTRUCTION)

First, make a directory for the output by running mkdir output. Output files that were generated when these scripts were run for the first time are also provided, in the precalculate_results directory. Then, the scripts can be run in order:

  1. Template identification: scripts/script1_build_profile.py
  2. Template(s) selection by sequence: scripts/script2_compare_templates.py
  3. Density map segmentation: scripts/script3_density_segmentation.py
  4. Template selection by fitting to a density map: scripts/script4_score_templates_by_cc.py
  5. Template alignment: scripts/script5_template_alignment.py
  6. Model building and assessment: scripts/script6_model_building_and_assessment.py and scripts/script7_pairwise_rmsd.py
  7. Multiple fitting into a density map: scripts/script8_split_density.py and scripts/script9_symmetric_multiple_fitting.py

Information

Author(s): Seung Joong Kim

Date: September 2nd, 2014

License: LGPL. This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

Last known good IMP version: build info

Testable: Yes.

Parallelizeable: No

Publications: