| Download
and Installation
Follow first the
simple registration
and download steps (you need to download the tutorial separately)!
In addition to
the Python programs, the ModeHunter_Tutorial_1.4 directory contains
also a number of additional files and a directory:
- 4AKE_chain_a_ca.pdb:
adenylate kinase C-alpha atom representation.
- adkin_monomer_30_pseudoatoms.pdb:
coarse grained model coordinates.
- adkin_monomer_30_pseudoatoms.psf
: coarse grained model connectivities.
- 7DGQ_chain_3_AF2.pdb: AlphaFold2 structure prediction (based on amino acid sequence corresponding to chain 3 of PDB ID 7DGQ), aligned with
- 30673_iso_0.0664.situs: Situs-formatted cryo-EM map (EMD 30673, 5A resolution, surface iso level 0.0664) in a different conformation.
- 7DGQ_chain_3_true.pdb: The true (known) structure of the AF2 model that can be used for validation.
- tutorial.script: A
documented and shell executable text file that explains the individual
tutorial steps.
- solutions:
directory with expected output files of the tutorial for comparison.
- tutorial.log: the expected tutorial script output in the command shell
|
| Script and Solutions
Please try out the above
mentioned tutorial.script and, especially, read the documentation
within this file. You can execute the script by
entering: "./tutorial.script" in a terminal window (command shell). (If
the executable or the python programs do not run, you may have to
adjust /bin/env/python to point to the local python version, or
edit the script by adding executables to the beginning of lines where
.py files are executed.) You can compare the files on your system with
those in the solutions directory and with the expected output in tutorial.log. The overall workflow is documented in
the script file and should be
self-explanatory from the program output in the command shell.
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