aRMSD
After the installation of aRMSD, this primer outlines the comparison
of two conformers of a small molecule. Briefly, functionality beyond
basic use is indicated, too.
setup of aRMSD
It is recommended to install and use aRMSD within a virtual
environment of Python 3.11 (or above). Either download the .zip archive,
or clone the GitHub repository. By
the command of
pip install .
within this folder, pyproject.toml resolves the program’s dependencies
on pypi.org. Be aware this support requires up to
about 0.8GB of permanent memory. When successful, the installation
provides the CLI armsd (all lowercase) as a new command.
workflow overview
The following tree diagram recapitulates key points of the workflow on
.xyz data. Files M1.xyz and M2.xyz can be found in folder
examples.
├── reading input structures, for instance M1.xyz and M2.xyz
│
│
├── Consistency Checks and Structural Modification
│ ├── 0 to remove and exclude all hydrogens from the analysis
│ ├── 1 to remove all hydrogens bound to carbon
│ └── 3 to include all hydrogens in the analysis
│
│
├── Symmetry Adjustment & Sequency Matching
│ ├── visual inspection, any number or sequence of
│ │ ├── s to ave a .png (optional)
│ │ ├── left mouse button (LMB) to drag the scene
│ │ ├── Ctrl + LMB to roll the scene
│ │ ├── Shift + LMB to pan the scene
│ │ ├── mouse reel to zoom the scene
│ │ ├── r to return scene to a home position
│ │ ├── 3 toggle on/off stereoscopic anaglyph representation
│ │ └── q to quit and close the current widget
│ │
│ ├── any number or sequence of symmetry operations
│ │ ├── 1 for an inversoin at the origin
│ │ ├── 2 for a reflection on the xy plane
│ │ ├── 3 for a reflection on the xz plane
│ │ ├── 4 for a reflection on the yz plane
│ │ ├── 5 for a rotation around the x axis
│ │ ├── 6 for a rotation around the y axis
│ │ ├── 7 for a rotation around the z axis
│ │ └── 8 do not edit the relative orientation, show the molecules again
│ │
│ └── decide on the current alignment
│ └── 10 to save the current alignment for the next step
│
│
├── decide over the program'ś matching algorithm used
│ ├── -1 continue with the current choice, or
│ ├── -2 change ge matching algorithm or solver
│ │ ├── -10 to leave the for the next upper level of hierarchy
│ │ ├── -1 to show detail;s of the currently used algorithm
│ │ ├── 1 use absolute distance between the atoms
│ │ ├── 2 use a combination of absolute and relative distances
│ │ ├── 3 use random permutations / brute force
│ │ ├── 4 use 'Hungarian' solver for the permutation matrix
│ │ └── 5 use 'aRMSD' solver for the permutation matrix (standard)
│ │
│ └── decide on the current atom match
│ ├── visual inspection (see above)
│ └── decide on the current state
│ ├── 0 to continue, because it is reasonably well aligned, or
│ └── return to manual adjustment of the initial alignment
│
│
└── Kabsch Algorithm, Statistics & Visualization
├── -1 Perform the Kabsch alignment (default), or
├── -2 Change the weighting function with either
│ ├── 0 for geometric / unweighted (default)
│ ├── 1 for x-ray scattering factors (Mo K\alpha)
│ ├── 2 atomic masses
│ ├── 3 total number of electrons
│ ├── 4 number of core electrons
│ ├── 5 spherical electron densities
│ ├── 6 LDA electron densities
│ └ -10 to return to the upper menu (then needs new a -1 for the test)
│
└── collect the results
├── 0 to visualize the results in a aRMSD representation
├── 1 visualize structural superposition
├── 2 perform statistics investigation of bond lengths and angles (plots)
├── 3 show RMSD results
├── 4 intrerpolate between the structures (cart., 10 steps)
├── 5 generate the permanent aRMSD_out.log file
└── 20 export structure data, in either number or sequence of
├── 0 export superposition in two '.xyz' files
├── 1 export superposition in one '.xyzs' file
├── 2 export aRMSD representation in one '.xyzs' file
└── -10 to return to the upper menu
reference outputs
optional permanent record aRMSD_logfile.out
aRMSD allows to recapitulate the analysis in a permanent record, file
aRMSD_logfile.out. In the flow chart, this is option 5 of section
“collect the results”. Below is the summary of the successful Kabsch
test with example data M1.xyz and M2.xyz:
+------------------------------------------------------------------------------+
| aRMSD - automatic RMSD Calculator (version 1.0.0) |
| Arne Wagner, Norwid Behrnd (2026) |
| |
| A brief description of the program can be found in the manual and in: |
| A. Wagner, PhD thesis, University of Heidelberg, 2015. |
| |
| Cite this program by: |
| A. Wagner, H.-J. Himmel, J. Chem. Inf. Model, 2017, 57, 428-438 |
| (doi: 10.1021/acs.jcim.6b00516), |
| source (http://www.github.com/nbehrnd/armsd), and version used. |
+------------------------------------------------------------------------------+
14-Jul-2026
*** Log file about the superposition of structures ***
"Model"... M1.xyz
"Reference"... M2.xyz
* Consistency establishment between the structures:
The basic approach is to subsequently remove hydrogen atoms
until the same number of atoms is found in both molecules.
If the number of atoms is identical and the atom types belong
to the same group in the periodic table, the molecules are
considered as consistent.
No disorder in the structures was found.
Initial number of atoms in "Model"... 20 (7 H atoms)
Initial number of atoms in "Reference"... 20 (7 H atoms)
Consistency between the structures was established:
The number of atoms in "Model"... 20 (7 H atoms)
The number of atoms in "Reference"... 20 (7 H atoms)
No further modifications were performed.
Final global atom count (number of hydrogens retained)... 20 (7 H atoms)
* Transformation of the molecules into "Standard Orientation":
1. The center of mass was shifted to the Cartesian origin.
2. The moment of inertia tensor was constructed, diagonalized
and the eigenvectors rotated on the x, y and z axes.
* Details of the matching process:
Structures were matched... True
Applied matching algorithm... distance
Solver used for matching... hungarian
Solution of the matching problem... regular
Number of highest deviations to be shown... 5
The highest deviations were between the pairs... [Angstrom]
H-3 -- H-3 0.51015
H-5 -- H-5 0.53917
H-6 -- H-6 0.57063
O-20 -- O-20 0.59831
O-17 -- O-17 0.72209
The RMSD after the initial matching was [Angstrom].. 0.21395
* Kabsch alignment:
# General settings
Substructures were defined... False
Weighting function for Kabsch algorithm... none
Consideration of multi-center-contributions... False
# Differentiation criteria and color information
Number of colors for aRMSD plot... 19
Maximum RMSD value for color projection [Angstrom].. 0.7
Threshold for bond comparison [Angstrom]... 0.02
Number of distance pairs above threshold... 13
Percentage of the colored intersections... 9.999999999999998
Color for shorter bonds in "Model" vs. "Reference"... #006400 [HEX]
Color for longer bonds in "Model" vs. "Reference"... #CD0000 [HEX]
Number of bonds below threshold... 13
Color of "Model"... #CD0000 [HEX]
Color of "Reference"... #006400 [HEX]
Final rotation matrix from 'Standard Orientation':
|-0.99992015 -0.01135453 -0.00554716|
U = |+0.01155612 -0.99921955 -0.03777234|
|-0.00511394 -0.03783343 +0.99927097|
# This matrix aligns Model with Reference.
# U already includes all custom symmetry operations!
* Final Quality of the Superposition:
RMSD (Kabsch test, refined superposition [Angstrom])... 0.20274
Superposition R^2 (dimensionless)... 0.99499
Cosine similarity (dimensionless)... 0.99827
d values for the GARD calculation... 0.3, 1.2
GARD score (dimensionless)... 0.80828
For an introduction into the GARD calculation, see J. C. Baber,
D. C. Thompson, J. B. Cross and C. Humblet, J. Chem. Inf. Model.,
2009, 49, 1889-1900, doi: 10.1021/ci9001074.
* Decomposition into different atom types absolute relative
[Angstrom] [%]
C (# 9) 0.11504 (08.48)
H (# 7) 0.20942 (28.10)
O (# 4) 0.31464 (63.42)
z-matrix properties:
# z-matrices are created for both molecules, based on
# (3 N - 1) bond distances, (3 N - 2) bond angles and
# (3 N - 3) dihedral angles. Both the total RMSD and
# the relative contributions are calculated.
RMSD [Angstrom]... 0.38087
Contribution of distances... 22.96 [%]
Contribution of angles... 43.52 [%]
Contribution of dihedral angles... 33.52 [%]
* Evaluation of structural parameters:
# 1. The RMSE values are the root-mean-square errors
# between the corresponding properties of the two structures.
# 2. The R**2 values are the the correlation coefficients
# between the two data sets.
Number of bonds... 20
R**2 of linear correlation (dimensionless)... 0.95576
RMSE [Angstrom]... 0.05050
Number of bond types... 3
R**2 of linear correlation (dimensionless)... 0.95576
RMSE [Angstrom]... 0.03130
Number of angles... 62
R**2 of linear correlation (dimensionless)... 0.75591
RMSE [degrees]... 2.84310
Number of dihedrals... 148
R**2 of linear correlation (dimensionless)... 0.99617
RMSE [degrees]... 4.26160
*** End of log file ***
CLI log of a successful comparison
Except vtk widgets to visualize the structures, and diagrams by
matplotlib, the program lives in the CLI. Depending on your setup
used, it is possible that lines with program options are visually
truncated and in consequence, accidentally missed. It is for this reason
why the complete dialog on the CLI for a Kabsch test of structures files
M1.xyz and M2.xyz is provided below.
The two test data are provided by the GitHub repository (folder
examples), the Kabsch test was run in an instance of Linux
Debian 13/trixie with Python 3.13.5.
================================================================================
aRMSD (version 1.0.0, 2026)
================================================================================
A. Wagner, University of Heidelberg (2015, 2017),
forked by N. Behrnd (2018)
--------------------------------- Description ----------------------------------
Key features:
* Parses data from various file formats
* Establishes consistency and matches coordinate sequences of two molecules
* Aligns two molecular structures based on the Kabsch algorithm
* Supports different weighting functions for the superposition
* Supports error propagation for experimental structures
* Generates different visualization types of the superposition results
* Writes outfiles that can be passed to other programs
* The original version was created by A. Wagner under Windows. You find it
hosted on GitHub: https://github.com/armsd/aRMSD.
* You are using a derivative fork based on the former, developed under Linux
by N. Behrnd, hosted on GitHub: https://github.com/nbehrnd/aRMSD.
*** Cite this program as:
A. Wagner, H.-J. Himmel, J. Chem. Inf. Model, 2017, 57, 428-438
(doi: 10.1021/acs.jcim.6b00516); with address and version of aRMSD used.
Release dates of the individual modules:
- core module: '2026-07-14'
- plot module: '2026-07-03'
- log module: '2026-07-14'
Module check:
- numpy '2.5.1'
- VTK '9.6.2'
- matplotlib '3.11.0'
- uncertainties '3.2.3'
- openbabel '3.2.1'
--------------------------------------------------------------------------------
Enter the file name with extension for the first file (comp./model)
>> M1.xyz
> 'M1.xyz' has been loaded successfully! (#Atoms: 20)
Enter the file name with extension for the second file (exp./reference)
>> M2.xyz
> 'M2.xyz' has been loaded successfully! (#Atoms: 20)
--------------------------------------------------------------------------------
... Files have been loaded!
--------------------------------------------------------------------------------
> Checking for coordinate standard deviations...
... No standard deviations were found!
--------------------------------------------------------------------------------
Checking length unit of xyz coordinates ...
The coordinate unit is [Angstrom]
Checking length unit of xyz coordinates ...
The coordinate unit is [Angstrom]
> The current status was saved successfully!
--------------------------------------------------------------------------------
================ Consistency Checks and Structural Modification ================
--------------------------------------------------------------------------------
> Performing consistency checks ... (Number of atoms: 20, 20)
There are (7 & 7) H atoms in the molecules
> The structures of both molecules are consistent.
--------------------------------------------------------------------------------
What should happen to the remaining 7 H-atoms?
--------------------------------------------------------------------------------
Info: The exclusion of H-atoms in RMSD calculations is recommended if
they were not located and refined in the X-ray experiment
--------------------------------------------------------------------------------
0 ... remove all hydrogen atoms (7)
3 ... keep all hydrogen atoms
--------------------------------------------------------------------------------
>> Enter your choice: 3
> The molecules were rotated into 'Standard Orientation' ...
> The current status was saved successfully!
--------------------------------------------------------------------------------
=================== Symmetry Adjustments & Sequence Matching ===================
--------------------------------------------------------------------------------
-6 Set number of deviations which are highlighted in the plot (current = 5)
-5 Load the saved status (save point available: 'True')
-4 Change plot settings
-3 Manually swap atoms in Model structure
-2 Change matching algorithm or solver
-1 Match molecular sequences based on current alignment
--------------------------------------------------------------------------------
Current matching algorithm : 'distance'
Current matching solver : 'hungarian'
Structures were matched : 'False'
--------------------------------------------------------------------------------
0 ... exit the menu (no return)
1 ... inversion at the origin
2 ... reflection at the xy plane
3 ... reflection at the xz plane
4 ... reflection at the yz plane
5 ... rotation around the x axis
6 ... rotation around the y axis
7 ... rotation around the z axis
8 ... show the molecules again
--------------------------------------------------------------------------------
10 ... save current changes (status was saved: 'True')
20 ... export structures
--------------------------------------------------------------------------------
> Results are now shown in a separate window.
... To continue, quit the pop-up window with 'q'.
> To save the scene as *.png, press 's'.
>> Enter your choice: 3
> Reflection of 'Model' structure at the xz-plane ...
--------------------------------------------------------------------------------
=================== Symmetry Adjustments & Sequence Matching ===================
--------------------------------------------------------------------------------
-6 Set number of deviations which are highlighted in the plot (current = 5)
-5 Load the saved status (save point available: 'True')
-4 Change plot settings
-3 Manually swap atoms in Model structure
-2 Change matching algorithm or solver
-1 Match molecular sequences based on current alignment
--------------------------------------------------------------------------------
Current matching algorithm : 'distance'
Current matching solver : 'hungarian'
Structures were matched : 'False'
--------------------------------------------------------------------------------
0 ... exit the menu (no return)
1 ... inversion at the origin
2 ... reflection at the xy plane
3 ... reflection at the xz plane
4 ... reflection at the yz plane
5 ... rotation around the x axis
6 ... rotation around the y axis
7 ... rotation around the z axis
8 ... show the molecules again
--------------------------------------------------------------------------------
10 ... save current changes (status was saved: 'True')
20 ... export structures
--------------------------------------------------------------------------------
> Results are now shown in a separate window.
... To continue, quit the pop-up window with 'q'.
> To save the scene as *.png, press 's'.
>> Enter your choice: 4
> Reflection of 'Model' structure at the yz-plane ...
--------------------------------------------------------------------------------
=================== Symmetry Adjustments & Sequence Matching ===================
--------------------------------------------------------------------------------
-6 Set number of deviations which are highlighted in the plot (current = 5)
-5 Load the saved status (save point available: 'True')
-4 Change plot settings
-3 Manually swap atoms in Model structure
-2 Change matching algorithm or solver
-1 Match molecular sequences based on current alignment
--------------------------------------------------------------------------------
Current matching algorithm : 'distance'
Current matching solver : 'hungarian'
Structures were matched : 'False'
--------------------------------------------------------------------------------
0 ... exit the menu (no return)
1 ... inversion at the origin
2 ... reflection at the xy plane
3 ... reflection at the xz plane
4 ... reflection at the yz plane
5 ... rotation around the x axis
6 ... rotation around the y axis
7 ... rotation around the z axis
8 ... show the molecules again
--------------------------------------------------------------------------------
10 ... save current changes (status was saved: 'True')
20 ... export structures
--------------------------------------------------------------------------------
> Results are now shown in a separate window.
... To continue, quit the pop-up window with 'q'.
> To save the scene as *.png, press 's'.
>> Enter your choice: 10
> The current status was saved successfully!
--------------------------------------------------------------------------------
=================== Symmetry Adjustments & Sequence Matching ===================
--------------------------------------------------------------------------------
-6 Set number of deviations which are highlighted in the plot (current = 5)
-5 Load the saved status (save point available: 'True')
-4 Change plot settings
-3 Manually swap atoms in Model structure
-2 Change matching algorithm or solver
-1 Match molecular sequences based on current alignment
--------------------------------------------------------------------------------
Current matching algorithm : 'distance'
Current matching solver : 'hungarian'
Structures were matched : 'False'
--------------------------------------------------------------------------------
0 ... exit the menu (no return)
1 ... inversion at the origin
2 ... reflection at the xy plane
3 ... reflection at the xz plane
4 ... reflection at the yz plane
5 ... rotation around the x axis
6 ... rotation around the y axis
7 ... rotation around the z axis
8 ... show the molecules again
--------------------------------------------------------------------------------
10 ... save current changes (status was saved: 'True')
20 ... export structures
--------------------------------------------------------------------------------
>> Enter your choice: -1
--------------------------------------------------------------------------------
The geometric RMSD of the current alignment is: 0.214 A
The 5 most disordered atom pairs are:
Entry Pair Distance / A
5 H-3 -- H-3 0.510
4 H-5 -- H-5 0.539
3 H-6 -- H-6 0.571
2 O-20 -- O-20 0.598
1 O-17 -- O-17 0.722
--------------------------------------------------------------------------------
=================== Symmetry Adjustments & Sequence Matching ===================
--------------------------------------------------------------------------------
-6 Set number of deviations which are highlighted in the plot (current = 5)
-5 Load the saved status (save point available: 'True')
-4 Change plot settings
-3 Manually swap atoms in Model structure
-2 Change matching algorithm or solver
-1 Match molecular sequences based on current alignment
--------------------------------------------------------------------------------
Current matching algorithm : 'distance'
Current matching solver : 'hungarian'
Structures were matched : 'True'
--------------------------------------------------------------------------------
0 ... exit the menu (no return)
1 ... inversion at the origin
2 ... reflection at the xy plane
3 ... reflection at the xz plane
4 ... reflection at the yz plane
5 ... rotation around the x axis
6 ... rotation around the y axis
7 ... rotation around the z axis
8 ... show the molecules again
--------------------------------------------------------------------------------
10 ... save current changes (status was saved: 'True')
20 ... export structures
--------------------------------------------------------------------------------
> Results are now shown in a separate window.
... To continue, quit the pop-up window with 'q'.
> To save the scene as *.png, press 's'.
>> Enter your choice: 10
> The current status was saved successfully!
--------------------------------------------------------------------------------
=================== Symmetry Adjustments & Sequence Matching ===================
--------------------------------------------------------------------------------
-6 Set number of deviations which are highlighted in the plot (current = 5)
-5 Load the saved status (save point available: 'True')
-4 Change plot settings
-3 Manually swap atoms in Model structure
-2 Change matching algorithm or solver
-1 Match molecular sequences based on current alignment
--------------------------------------------------------------------------------
Current matching algorithm : 'distance'
Current matching solver : 'hungarian'
Structures were matched : 'True'
--------------------------------------------------------------------------------
0 ... exit the menu (no return)
1 ... inversion at the origin
2 ... reflection at the xy plane
3 ... reflection at the xz plane
4 ... reflection at the yz plane
5 ... rotation around the x axis
6 ... rotation around the y axis
7 ... rotation around the z axis
8 ... show the molecules again
--------------------------------------------------------------------------------
10 ... save current changes (status was saved: 'True')
20 ... export structures
--------------------------------------------------------------------------------
>> Enter your choice: 0
> Exiting symmetry transformation menu ...
--------------------------------------------------------------------------------
================= Kabsch Algorithm, Statistics & Visualization =================
--------------------------------------------------------------------------------
-10 Exit aRMSD
-8 Plot aRMSD color map
-7 Change general RMSD settings
-6 Add/remove bond
-4 Change plot settings
-3 Define two substructures (structures are defined: 'False')
-2 Change weighting function
-1 Perform Kabsch alignment (required for all functions)
--------------------------------------------------------------------------------
Current weighting function : 'none'
Calculate mcc contribution : 'False'
Kabsch alignment performed : 'False'
--------------------------------------------------------------------------------
0 ... visualize results in aRMSD representation
1 ... visualize structural superposition
2 ... perform statistic investigation of bond lengths and angles
3 ... show RMSD results
4 ... interpolate between the structures (cart., 10 steps)
5 ... generate outfile
20 ... export structural data
--------------------------------------------------------------------------------
>> Enter your choice: -1
--------------------------------------------------------------------------------
========================= Quality of the Superposition =========================
--------------------------------------------------------------------------------
> The type of weighting function is: 'none'
---------------------------- Similarity Descriptors ----------------------------
>>> Superposition R^2 : 0.99499
>>> Cosine similarity : 0.99827
>>> GARD score : 0.80828
-------------------------- Root-Mean-Square-Deviation --------------------------
>>> RMSD : 0.20274 Angstrom
>>> - Decomposition : Individual atom types (total percentage)
C (# 9) : 0.11504 Angstrom (08.48 %)
H (# 7) : 0.20942 Angstrom (28.10 %)
O (# 4) : 0.31464 Angstrom (63.42 %)
----------------------------- Z-matrix properties ------------------------------
>>> RMSD : 0.38087
>>> - Decomposition : total percentage
distances : 22.96 %
angles : 43.52 %
dihedrals : 33.52 %
--------------------------------------------------------------------------------
================= Kabsch Algorithm, Statistics & Visualization =================
--------------------------------------------------------------------------------
-10 Exit aRMSD
-8 Plot aRMSD color map
-7 Change general RMSD settings
-6 Add/remove bond
-4 Change plot settings
-3 Define two substructures (structures are defined: 'False')
-2 Change weighting function
-1 Perform Kabsch alignment (required for all functions)
--------------------------------------------------------------------------------
Current weighting function : 'none'
Calculate mcc contribution : 'False'
Kabsch alignment performed : 'True'
--------------------------------------------------------------------------------
0 ... visualize results in aRMSD representation
1 ... visualize structural superposition
2 ... perform statistic investigation of bond lengths and angles
3 ... show RMSD results
4 ... interpolate between the structures (cart., 10 steps)
5 ... generate outfile
20 ... export structural data
--------------------------------------------------------------------------------
>> Enter your choice: 0
> Results are now shown in a separate window.
... To continue, quit the pop-up window with 'q'.
> To save the scene as *.png, press 's'.
--------------------------------------------------------------------------------
================= Kabsch Algorithm, Statistics & Visualization =================
--------------------------------------------------------------------------------
-10 Exit aRMSD
-8 Plot aRMSD color map
-7 Change general RMSD settings
-6 Add/remove bond
-4 Change plot settings
-3 Define two substructures (structures are defined: 'False')
-2 Change weighting function
-1 Perform Kabsch alignment (required for all functions)
--------------------------------------------------------------------------------
Current weighting function : 'none'
Calculate mcc contribution : 'False'
Kabsch alignment performed : 'True'
--------------------------------------------------------------------------------
0 ... visualize results in aRMSD representation
1 ... visualize structural superposition
2 ... perform statistic investigation of bond lengths and angles
3 ... show RMSD results
4 ... interpolate between the structures (cart., 10 steps)
5 ... generate outfile
20 ... export structural data
--------------------------------------------------------------------------------
>> Enter your choice: 1
> Results are now shown in a separate window.
... To continue, quit the pop-up window with 'q'.
> To save the scene as *.png, press 's'.
--------------------------------------------------------------------------------
================= Kabsch Algorithm, Statistics & Visualization =================
--------------------------------------------------------------------------------
-10 Exit aRMSD
-8 Plot aRMSD color map
-7 Change general RMSD settings
-6 Add/remove bond
-4 Change plot settings
-3 Define two substructures (structures are defined: 'False')
-2 Change weighting function
-1 Perform Kabsch alignment (required for all functions)
--------------------------------------------------------------------------------
Current weighting function : 'none'
Calculate mcc contribution : 'False'
Kabsch alignment performed : 'True'
--------------------------------------------------------------------------------
0 ... visualize results in aRMSD representation
1 ... visualize structural superposition
2 ... perform statistic investigation of bond lengths and angles
3 ... show RMSD results
4 ... interpolate between the structures (cart., 10 steps)
5 ... generate outfile
20 ... export structural data
--------------------------------------------------------------------------------
>> Enter your choice: 2
> Results are now shown in a separate window.
... To continue, quit the pop-up window with 'q'.
---------------- The Highest Deviations in Internal Coordinates ----------------
The 3 highest deviations are printed below
Entries are: Atoms, values in the Model and Reference, difference
--------------------------------------------------------------------------------
>> Bonds (in Angstrom):
1. [C-15, C-16] 1.455 1.598 Diff. 0.14300000000000002
2. [C-8, O-17] 1.252 1.143 Diff. -0.10899999999999999
3. [C-8, C-9] 1.49 1.55 Diff. 0.06000000000000005
--------------------------------------------------------------------------------
>> Bond angles (in deg.):
1. [O-17, C-8, O-18] 119.78 128.56 Diff. 8.780000000000001
2. [O-18, C-8, O-17] 119.78 128.56 Diff. 8.780000000000001
3. [O-18, C-8, C-9] 117.731 112.809 Diff. -4.921999999999997
--------------------------------------------------------------------------------
>> Dihedral angles (in deg.):
1. [C-14, C-9, C-8, O-18] 35.01 50.081 Diff. 15.071000000000005
2. [O-18, C-8, C-9, C-14] 35.01 50.081 Diff. 15.071000000000005
3. [O-17, C-8, C-9, C-14] 144.42 130.267 Diff. -14.152999999999992
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
================= Kabsch Algorithm, Statistics & Visualization =================
--------------------------------------------------------------------------------
-10 Exit aRMSD
-8 Plot aRMSD color map
-7 Change general RMSD settings
-6 Add/remove bond
-4 Change plot settings
-3 Define two substructures (structures are defined: 'False')
-2 Change weighting function
-1 Perform Kabsch alignment (required for all functions)
--------------------------------------------------------------------------------
Current weighting function : 'none'
Calculate mcc contribution : 'False'
Kabsch alignment performed : 'True'
--------------------------------------------------------------------------------
0 ... visualize results in aRMSD representation
1 ... visualize structural superposition
2 ... perform statistic investigation of bond lengths and angles
3 ... show RMSD results
4 ... interpolate between the structures (cart., 10 steps)
5 ... generate outfile
20 ... export structural data
--------------------------------------------------------------------------------
>> Enter your choice: 3
--------------------------------------------------------------------------------
========================= Quality of the Superposition =========================
--------------------------------------------------------------------------------
> The type of weighting function is: 'none'
---------------------------- Similarity Descriptors ----------------------------
>>> Superposition R^2 : 0.99499
>>> Cosine similarity : 0.99827
>>> GARD score : 0.80828
-------------------------- Root-Mean-Square-Deviation --------------------------
>>> RMSD : 0.20274 Angstrom
>>> - Decomposition : Individual atom types (total percentage)
C (# 9) : 0.11504 Angstrom (08.48 %)
H (# 7) : 0.20942 Angstrom (28.10 %)
O (# 4) : 0.31464 Angstrom (63.42 %)
----------------------------- Z-matrix properties ------------------------------
>>> RMSD : 0.38087
>>> - Decomposition : total percentage
distances : 22.96 %
angles : 43.52 %
dihedrals : 33.52 %
--------------------------------------------------------------------------------
================= Kabsch Algorithm, Statistics & Visualization =================
--------------------------------------------------------------------------------
-10 Exit aRMSD
-8 Plot aRMSD color map
-7 Change general RMSD settings
-6 Add/remove bond
-4 Change plot settings
-3 Define two substructures (structures are defined: 'False')
-2 Change weighting function
-1 Perform Kabsch alignment (required for all functions)
--------------------------------------------------------------------------------
Current weighting function : 'none'
Calculate mcc contribution : 'False'
Kabsch alignment performed : 'True'
--------------------------------------------------------------------------------
0 ... visualize results in aRMSD representation
1 ... visualize structural superposition
2 ... perform statistic investigation of bond lengths and angles
3 ... show RMSD results
4 ... interpolate between the structures (cart., 10 steps)
5 ... generate outfile
20 ... export structural data
--------------------------------------------------------------------------------
>> Enter your choice: 5
> A logfile (aRMSD_logfile.out) has been written successfully!
--------------------------------------------------------------------------------
================= Kabsch Algorithm, Statistics & Visualization =================
--------------------------------------------------------------------------------
-10 Exit aRMSD
-8 Plot aRMSD color map
-7 Change general RMSD settings
-6 Add/remove bond
-4 Change plot settings
-3 Define two substructures (structures are defined: 'False')
-2 Change weighting function
-1 Perform Kabsch alignment (required for all functions)
--------------------------------------------------------------------------------
Current weighting function : 'none'
Calculate mcc contribution : 'False'
Kabsch alignment performed : 'True'
--------------------------------------------------------------------------------
0 ... visualize results in aRMSD representation
1 ... visualize structural superposition
2 ... perform statistic investigation of bond lengths and angles
3 ... show RMSD results
4 ... interpolate between the structures (cart., 10 steps)
5 ... generate outfile
20 ... export structural data
--------------------------------------------------------------------------------
>> Enter your choice: -10
--------------------------------------------------------------------------------
========================== Normal program termination ==========================
--------------------------------------------------------------------------------