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KnotPull - a simplifier for 3D structures
KnotPull reduces a user provided 3D structure, to simplify it, while preserving the topology of the chain. It has been successfully used for knot detection in proteins and chromatin chains.
It can return either a final, simplified structure, or a .pdb formatted trajectory of consecutive simplifications performed.
Install
pip install knot_pull
(older versions) pip install --index-url https://test.pypi.org/simple/ knot_pull
If installing with pip --user knot_pull_check and knot_pull_show
will be installed in your user base
(python -c "import site; print(site.USER_BASE)"), e.g.
$HOME/.local/bin/knot_pull_check
Running
To run on a specific chain of a local pdb file:
knot_pull_check -o -k -c A 3ris.pdb
To run on a local xyz file (with format idxyz; chains separated by a line with "END"):
knot_pull_check -o from_xyz.pdb -k 05.xyz
To run on by structure id from RCSB PDB (without creating an output file):
knot_pull_check -k 4mcb
To show coloured trajectory in PyMOL (if installed):
knot_pull_show my_output_file.pdb
If PyMOL is not available in system path it can be specified as the second argument
Output
If no output-modifying flag is specified [e.g. -q], the output will look similar to:
>knot_pull_check -k 4mcb
#LOG: data format: online
#LOG: got coordinates: 452 bead(s)
#LOG: finished smoothing: 2 chain(s)
Final topology: [8, 8]:
[3_1](A) U [3_1](B)
#DT codes: [4(+), 6(+), 2(+)](A) U [-4(+), -6(+), -2(+)](B)
where:
- number of beads is the number of read-in data points and additional "dummy" coordinates added to fill in long gaps in the structure
- number of chains is based on selected/available chain names in the structure
- square brackets in the "Final topology line" indicate the number of coordinates in each chain after smoothing
- next line gives the Alexander-Briggs notation of knots in each chain. Chains separated by a "#" are linked, separated by "U" are not.
- DT codes show the simplified Dowker code found for each chain. Sign in the parenthesis after each crossing indicates crossing direction as in skein relations: if reoriented so that both lines point up, "+" indicates that the one going left-to-right is on top, "-" - the one right-to-left.
Help:
usage: knot_pull_check [-h] [-p] [-t] [-f {pdb,xyz,guess}] [-k] [-c CHAIN]
[-o [OUTPUT]] [-s [SAVE]]
[infile]
Simplify the 3D structure while preserving the topology
positional arguments:
infile Structure file which will be used
optional arguments:
-h, --help show this help message and exit
-p, --preserve_resnums
Keep original numbering
-t, --trajectory Write out all steps of the simplification [default is
1]
-f {pdb,xyz,guess}, --format {pdb,xyz,guess}
Input file format: xyz or pdb [default is guess]
-k, --detect_knot Calculate the knot Dowker notation and assign the knot
type
-c CHAIN, --chain CHAIN
Specify which chain(s) you want to simplify. Multiple
chains should be separated by commas.
-b BEGIN, --begin BEGIN
Smooth and analyze only part of the structure: specify
the first bead to be considered. '-b 4' will start
from the 4th bead, '-b i4' will start from the
residue/coordinate with id 4. When specified, only the
first chain from selected/present will be used.
-e END, --end END Smooth and analyze only part of the structure: specify
the first bead to be considered. '-e 104' will
disregard beads from 105th forward, '-e i104' will
disregard residue/coordinates with id >=105. When
specified, only the first chain from selected/present
will be used.
-o [OUTPUT], --output [OUTPUT]
Specify the output file. Format is guessed based on
extension [default pdb]. For stdout use "-". Empty
argument makes an '_out.pdb' file. If this option is
missing just the last frame will be shown (sets
trajectory to 0)
-q, --quiet Nothing except the knot type (if calculated) will be
written to the screen
