Pyshifts: A Pymol Plugin for Chemical Shift-Based Analysis of Biomolecular Ensembles
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xQuartz (mac only)
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For first time PyMOL user, you will need a PyMOL license file, as PyMOL is a commercial software.
git clone https://github.com/atfrank/PyShifts.git
cd PyShifts
source setup.sh
The following commands will invoke a pymol window
pymol
In PyMOL window, go to Plugin
-> Plugin manager
-> Install new plugin
, choose Pyshifts.py
file in your local Pyshifts folder, and click OK
on the next step. You will then see a pop-up message Plugin "PyShiftsPlugin" has been installed
.
export PYSHIFTS_PATH=~/Downloads/PyShifts
export PATH=$PYSHIFTS_PATH:$PATH
export BME=~/Downloads/PyShifts/BME
export PYTHONPATH=$BME:$PATH
export LARMORD_BIN=~/Downloads/PyShifts/LarmorD_New/bin
export PATH=$LARMORD_BIN:$PATH
export LARMORCA_BIN=~/Downloads/PyShifts/LARMORCA/bin
export PATH=$LARMORCA_BIN:$PATH
conda activate pyshifts
pymol
or
source ~/.bashrc
conda activate pyshifts
pymol
Load the object to be analyzed in PyMOL, e.g. 2KOC_test.pdb
provided in test/
folder, by typing load test/2KOC_test.pdb
in pymol command line or dragging the file into PyMOL window.
Run Pyshifts through Plugin
-> Legacy Plugins
-> Pyshifts
.
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Change the
PyMOL selection/ object
entry to the name of your target object, e.g.2KOC_test
and clink onRun
. -
Go to the second tab
Error Analysis
, and click onCompare shifts
. -
Click on
Error table
orCS table
to save results.
Pyshifts has four tabs and one Exit
button. The first tab Options
include basic options for Pyshifts
, the second tab Error Analysis
performs chemical shift comparison, displays table results and provides options in different ways of sorting.
The third tab Advanced Options
contains functionality for parameter tuning. There are options on chemical shift error offset, accuracy, PyMOL rendering setting as well as machine learning clustering parameters.
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Pyshifts
(In press) : Jingru Xie, Kexin Zhang and Aaron T. Frank. "PyShifts: A PyMOL Plugin for Chemical Shift-Based Analysis of Biomolecular Ensembles." The Journal of Physical Chemistry B 118.42 (2014): 12168-12175. -
LarmorD
: Frank, Aaron T., Sean M. Law, and Charles L. Brooks III. "A simple and fast approach for predicting 1H and 13C chemical shifts: toward chemical shift-guided simulations of RNA." The Journal of Chemical Information and Modeling (2020). -
LarmorC⍺
: Frank, Aaron T., et al. "Predicting Protein Backbone Chemical Shifts From Cα Coordinates: Extracting High Resolution Experimental Observables from Low Resolution Models." Journal of chemical theory and computation 11.1 (2014): 325-331.
The PyMOL Plugin source code in this file is copyrighted, but you can freely use and copy it as long as you don't change or remove any of the copyright notices. This PyMOL Plugin is Copyright (C) 2016 by Jingru Xie , Kexin Zhang and Aaron T. Frank All Rights Reserved
Permission to use, copy, modify, distribute, and distribute modified versions of this software and its documentation for any purpose and without fee is hereby granted, provided that the above copyright notice appear in all copies and that both the copyright notice and this permission notice appear in supporting documentation, and that the name(s) of the author(s) not be used in advertising or publicity pertaining to distribution of the software without specific, written prior permission.
THE AUTHOR(S) DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR(S) BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.