Index of /xplor-nih/methodsMolBiol
Name Last modified
0README.txt 2018-03-12 15:58
README.txt 2018-03-12 15:58
bicelles_hnc.tbl 2017-05-03 16:17
bicelles_nc.tbl 2017-05-03 16:17
bicelles_nh.tbl 2017-05-03 16:17
chapter.pdf 2017-12-15 16:58
dihedral.tbl 2017-05-03 16:17
fold.py 2019-04-01 14:09
gb1.seq 2017-05-03 16:17
methodsMolBiol.tar.gz 2019-09-04 12:22
noe.tbl 2017-05-03 16:17
refine.py 2019-04-01 14:01
tmv107_hnc.tbl 2017-05-03 16:17
tmv107_nc.tbl 2017-05-03 16:17
tmv107_nh.tbl 2017-05-03 16:17
Example of molecular dynamics/simulated anneanling structure determination using
distance, torsion angle, and bond-vector orientation (from RDCs) restraints, as
described in detail in:
C.D. Schwieters, G.A. Bermejo, ``Protein Structure Elucidation from NMR
Data with the Program Xplor-NIH,'' Methods Mol Biol. 1688, 311-340 (2018).
[available here as chapter.pdf]
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Run the following programs (in the order in which they appear):
# Generate a PSF file from sequence.
seq2psf gb1.seq
# Calculate a set of structures starting from extended conformations.
xplor -py fold.py > fold.log
# Return a symbolic link to the top-scoring structure calculated by fold.py.
getBest -num 1 -symlinks
# Calculate a set of structures by refining the top-scoring one from fold.py.
xplor -py refine.py > refine.log
[ Running these commands requires that the Xplor-NIH helper programs
are in your PATH. This can be accomplished by adding the bin
directory of the Xplor-NIH distribution to your PATH, or using the
-symlinks option to ./configure so that the commands are available
from a directory already in your PATH. ]
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fold.py is exactly as presented in the reference, except for the following changes:
* The nstructures variable has been added at the very beginning to specify the
wanted number of structures.