diff --git a/Packages/Clustering/rmsds-align.py b/Packages/Clustering/rmsds-align.py
new file mode 100644
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+++ b/Packages/Clustering/rmsds-align.py
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+# !/usr/bin/env python3
+
+"""
+rmsds-align.py: Calcuate 2D RMSD using different alignment and rmsd selections.
+
+The purpose of this tool is to calcuate pairwise RMSD for a selection after
+aligning using a different selection. This script supports upto 2 trajectories.
+
+Anees Mohammmed Keedakkatt Puthenpeedikakkal, 2022
+"""
+
+"""
+
+  This file is part of LOOS.
+
+  LOOS (Lightweight Object-Oriented Structure library)
+  Copyright (c) 2013 Tod Romo, Grossfield Lab
+  Department of Biochemistry and Biophysics
+  School of Medicine & Dentistry, University of Rochester
+
+  This package (LOOS) is free software: you can redistribute it and/or modify
+  it under the terms of the GNU General Public License as published by
+  the Free Software Foundation under version 3 of the License.
+
+  This package is distributed in the hope that it will be useful,
+  but WITHOUT ANY WARRANTY; without even the implied warranty of
+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+  GNU General Public License for more details.
+
+  You should have received a copy of the GNU General Public License
+  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+"""
+
+
+import sys
+import argparse
+import loos
+import loos.pyloos
+
+
+def fullhelp():
+    print("""
+SYNOPSIS
+
+Calculate a pair-wise RMSD for a trajectory (or two trajectories) with
+different align and rmsd selections.
+
+
+DESCRIPTION
+
+This tool calculates the pairwise RMSD between each structures in a trajectory
+after aligning using a selection which is different from the RMSD selection.
+This tool can be used for two different trajectories also. This tool is similar
+to rmsds, except rmsds uses same selection for alignment and pairwise
+RMSD calculation.
+
+The transformation matrix that aligns align_selection_2 is used to transform
+align_selection_1, followed by RMSD calcuation using rmsd_selection_1 to
+rmsd_selection_2. This is looped over the all the frames in the
+trajectory (or for selected --range1 and --range2)
+
+EXAMPLES
+
+python3 rmsds-align.py model.pdb simulation.dcd > rmsd.asc
+
+This example uses all alpha-carbons and every frame in the trajectory
+(equivalent to rmsds).
+
+
+python3 rmsds-align.py --model2 inactive.pdb --traj2 inactive.dcd active.pdb
+active.dcd > rmsd.asc
+
+This example uses all alpha-carbons and compares the "inactive" simulation
+with the "active" one.
+
+
+python3 rmsds-align.py  --align 'resid <= 20 && name== "CA"' --rmsd 'resid > 25
+ && name =~ "^(C|CA|CB|O|N)$"' model.pdb simulation.dcd > rmsd.asc
+
+This example uses only first 20 alpha carbons for alignment and pairwise RMSD
+is calculated for all the backbone atoms with resid > 25.
+
+
+python3 rmsds-align.py --align 'resid <= 20 && name== "CA"' --align2
+'resid >=25 && resid <=44 && name == "CA"' --rmsd 'resid > 25 && resid < 50 &&
+name =~ "^(C|CA|CB|O|N)$"' --rmsd2 'resid < 25 && name =~ "^(C|CA|CB|O|N)$"'
+--model2 inactive.pdb --traj2 inactive.dcd active.pdb active.dcd > rmsd.asc
+
+This complex example first aligns active’s first 20 alpha-Cs with inactive’s
+alpha-Cs with resid >=25 and resid <=44. Pairwise RMSD is calculated between
+active’s backbone (with resid’s in 25-49) and inactive’s backbone with
+resid <25.
+
+
+NOTES
+
+When using two trajectories, the selections must match both in number of atoms
+selected and in the sequence of atoms (i.e. the first atom in the align/rmsd
+selection is matched with the first atom in the align2/rmsd2 selection.)
+
+SEE ALSO
+rmsd2ref, rmsds
+
+          """)
+
+
+class FullHelp(argparse.Action):
+    def __init__(self, option_strings, dest, nargs=None, **kwargs):
+        kwargs['nargs'] = 0
+        super(FullHelp, self).__init__(option_strings, dest, **kwargs)
+
+    def __call__(self, parser, namespace, values, option_string=None):
+        fullhelp()
+        parser.print_help()
+        setattr(namespace, self.dest, True)
+        parser.exit()
+
+
+header = " ".join(sys.argv)
+parser = argparse.ArgumentParser(description="Calculate 2D RMSD using"
+                " different alignment and rmsd selections.")
+
+parser.add_argument('model', help="Model")
+
+parser.add_argument('traj', help="Trajectory")
+
+parser.add_argument('--model2',
+                    help="Model for 2nd trajectory (default = model)",
+                    default=None)
+
+parser.add_argument('--traj2',
+                    help="2nd trajectory (default = traj)",
+                    default=None)
+
+parser.add_argument('--align',
+                    help="Align selection for 1st trajectory (default = CA)",
+                    default='name == "CA"', type=str)
+
+parser.add_argument('--align2',
+                    help="Align selection 2nd trajectory (default = align)",
+                    default=None, type=str)
+
+parser.add_argument('--rmsd',
+                    help="RMSD selection for 1st trajectory"
+                    "(default = (C|O|N|CA))",
+                    default='name =~ "^(C|O|N|CA)$"', type=str)
+
+parser.add_argument('--rmsd2',
+                    help="RMSD selection for 2nd trajectory (default = rmsd)",
+                    default=None, type=str)
+
+parser.add_argument('--precision',
+                    help="Write out matrix coefficients with this many digits "
+                    "(default = 2)", default=2, type=int)
+
+parser.add_argument('--range1',
+                    help="Range of frames to use from the first trajectory "
+                    "[FORMAT - skip:stride:stop, stop is optional] "
+                    "(default = 0:1:last)", default='0:1', type=str)
+
+parser.add_argument('--range2', help="Range of frames to use from the second "
+                    "trajectory [FORMAT - skip:stride:stop, stop is optional] "
+                    "(default = range1)",
+                    default=None, type=str)
+
+parser.add_argument('--fullhelp',
+                    help="Print detailed description of all options",
+                    action=FullHelp)
+
+args = parser.parse_args()
+
+# In case of only one trajectory is given as input
+if args.rmsd2 is None:
+    args.rmsd2 = args.rmsd
+
+if args.align2 is None:
+    args.align2 = args.align
+
+if args.model2 is None:
+    args.model2 = args.model
+
+if args.traj2 is None:
+    args.traj2 = args.traj
+
+if args.range2 is None:
+    args.range2 = args.range1
+
+
+# Organizing range of frames to consider in trajectories
+range_1 = args.range1.split(":")
+range_2 = args.range2.split(":")
+
+# In case only skip and stride is given as input for traj
+if len(range_1) == 2:
+    select_1 = range(int(range_1[0]), len(args.traj), int(range_1[1]))
+# In case only skip, stride and stop are given
+elif len(range_1) == 3:
+    select_1 = range(int(range_1[0]), int(range_1[2]), int(range_1[1]))
+else:
+    print("Error in range")
+    sys.exit(0)
+
+
+# In case only skip and stride is given as input for traj2
+if len(range_1) == 2:
+    select_2 = range(int(range_2[0]), len(args.traj2), int(range_2[1]))
+# In case only skip, stride and stop are given
+elif len(range_1) == 3:
+    select_2 = range(int(range_2[0]), int(range_2[2]), int(range_2[1]))
+else:
+    print("Error in range")
+    sys.exit(0)
+
+# Model and Trajectory
+model = loos.createSystem(args.model)
+traj = loos.pyloos.Trajectory(args.traj, model, iterator=select_1)
+model2 = loos.createSystem(args.model2)
+traj2 = loos.pyloos.Trajectory(args.traj2, model2, iterator=select_2)
+
+# Align and RMSD selection definitions
+align_selection_1 = loos.selectAtoms(model, args.align)
+align_selection_2 = loos.selectAtoms(model2, args.align2)
+
+rmsd_selection_1 = loos.selectAtoms(model, args.rmsd)
+rmsd_selection_2 = loos.selectAtoms(model2, args.rmsd2)
+
+# Print input
+print("# Align1 - ", args.align)
+print("# Align2 - ", args.align2)
+print("# RMSD1 - ", args.rmsd)
+print("# RMSD2 - ", args.rmsd2)
+print("# Traj-range1 - ", args.range1)
+print("# Traj-range2 - ", args.range2)
+
+
+for frame in traj:
+    ref_align = align_selection_1.copy()
+    ref_target = rmsd_selection_1.copy()
+
+    for frame in traj2:
+        # Find transformation matrix that aligns align_selection_2
+        # onto ref_align(align_selection_1)
+        trans_matrix = ref_align.alignOnto(align_selection_2)
+        # Tranform matrix
+        transform = loos.XForm(trans_matrix)
+        # Apply the tranform to ref_target(rmsd_selection_1)
+        ref_target.applyTransform(transform)
+        # Calculate the RMSD between rmsd_selection_2 and
+        # ref_target(rmsd_selection_1)
+        rmsd_value = rmsd_selection_2.rmsd(ref_target)
+        # Print RMSD
+        print(round(rmsd_value, args.precision), "", end='')
+
+    print("")