Diamond Version 5 User Manual: Distances and angles

Measuring and reporting distances, angles, and torsion angles

This article in brief:
- Measuring distances, angles, and torsion angles
- About reported distances, angles, and torsion angles
- Measuring distances etc. between centroids (dummy atoms)

Previous article: Distances around a selected atom
Next article: Extended geometric infos: Angles between planes etc.

Measuring Distances, Angles, and Torsion Angles

You can interactively measure:

- distances between two atoms each,

- angles between three angles each,

- torsion angles between four angles each.

For that, Diamond uses a special mode, the measure mode, where you click on two, three, or four atoms, rsp. to get the corresponding value. The distances are given in Angstroems, the angles in degrees, both with standard uncertainties, if standard uncertainties are available with the structural parameters. The geometric informations (the value itself and the atoms concerned, including symmetry operations) will be stored with the Diamond document and can be used, for example, to export them as geometric parameters, e.g. in CIF format as geom_dist_....

The result is given in a yellowish info window and is stored in the list of reported distances and can be inspected later e.g. in the data sheet or in the table of reported distances. The measuring mode for angles measures the angle at the second of three clicked atoms each. The third measuring mode measures torsion angles between four atoms each.

To enter the measure mode for distances, choose the Measure Distances command from the Tools menu, or press the corresponding button in the Measure toolbar:

The same command can also be used to end the measure mode if it is currently active. The measure mode can also be deactivated by pressing the Escape key.

In the "distance measurement" mode, the mouse cursor changes to an arrow with a ruler symbol. You now have to click on two atoms; the first atom will have a '1', the second atom a '2' to indicate the order of selections. When the second atom is selected, a small tool tip window close to the mouse cursor will display the corresponding distance between the two atoms, along with some additional information about the two atoms. The information window will vanish if you move the mouse cursor, however, the corresponding distance will be listed in the "Table of Reported Distances" which can be displayed in the Tables pane.

Screenshot of measuring the interatomic distance between atom #1 "O 11" and atom #2 "C 26" with the result shown in a special info tip window...

...the measured distances can be surveyed via the Table of reported distances. The properties pane shows more details about this "reported distance".

Use the command Table -> Reported Distances from the View menu to show the table of reported distances, if you want to follow the measured informations. The table of reported distances contains a list of previously measured distances or distance values that have been imported from a CIF (geom_dist_... etc.). New distance values will be appended to the end of the list.

Entering the measure mode for angles and torsion angles is similar: Choose the Measure Angles or Measure Torsion Angles command, rsp., from the Tools menu, or press the corresponding buttons from the Measure toolbar:

and

To measure a distance, click with the left mouse button on the two atoms, one after the other. After the second click the distance will be calculated and the information added to the list. If the distance has already been caught, the corresponding row in the list will be selected.

To measure an angle, you must click on three atoms, one after the other. The second atom is the atom at the apex of the angle.

To measure a torsion angle, you must click on four atoms, one after the other. The torsion angle is calculated as described in Klyne, W. & Prelog, V. (1960), Experientia, 16, 521. The vector direction from the second to the third atom is the viewing direction, and the torsion angle is the angle of twist required to superimpose the projection of the vector from the second to the first atom onto the projection of the vector from the third to the fourth atom. Clockwise torsions are positive, counterclockwise torsions are negative.

Informations about each reported or measured distance

For distances, angles, and torsion angles, the measure window uses different formats. This is the format for distances:

Informations about each reported or measured angle

If three atoms #1, #2, and #3 are clicked one after the other, atoms #1 and #3 define the two atoms at the sides of the angle, atom #2 is the atom at the apex.

Informations about each reported or measured torsion angle

Compare the definition of the torsion angle above.

Editing the list of distances, angles, or torsion angles

To copy the selected rows from the list - for example into a spreadsheet -, use the Copy Table command from the context menu of the table of reported distances (or angles or torsion angles, rsp.). To delete one or more distances, angles, or torsion angles, rsp., select the corresponding rows, and use the Delete command.

About reported distances, angles, and torsion angles

A Diamond document uses several lists for geometric informations about the current structure data set:

Reported distances
The "reported distances" usually derive from data of the CIF category GEOM, which is used to specify the geometry of the structural model as derived from the atomic sites. The distance informations are taken from the CIF child categories about covalent bond distances (_geom_bond...) as well as from contact distances (_geom_contact...). The "reported distances" can be complemented with the above described measured distances as well as distance informations from the table of (calculated) distances.

Reported angles
The "reported angles" usually derive from the CIF child category for interatomic angles (_geom_angle...), and - like interatomic distances - can be complemented with measured angles and calculated angles from the table of (calculated) angles.

Reported torsion angles
The "reported torsion angles" usually derive from the CIF chilc category for torsion geometry (_geom_torsion data) and can be complemented with measured torsion angles.

Tables of reported distances, angles, and torsion angles

The reported geometric informations can be listed in the data pane by the corresponding commands in the Table sub-menu of the View menu. Each row in the table comprises informations about the two, three, or four atoms involved and the distance and angle information. More details are available from the properties pane - usually below the table of reported geometric information. (See screenshot of table of reported distances above.)

Distance, angle, and torsion angle informations in the data sheet

The "comprehensive" configuration of the data sheet summarizes all informations available "reported" distance, angle, and torsion angle informations.

The following is a screenshot of the data sheet of the sample document "COD-1500005-one-Co(NH3)6-molecule.diamdoc". The section "Selected geometric informations" lists the interatomic distances that have been imported from a list of "_geom_dist..." informations in a CIF file or have been created in Diamond by measuring distances or have been created by copying from the table of (calculated) distances. The list of distance informations is followed by a list of angle informations.

About reported H-bond infos

At this place, we also mention the Reported H-bond infos, which typically come from "geom_hbond..." loops in a CIF file. For historical reasons, these H-bond infos appear twice in a Diamond structure data set - once as the mentioned "reported H-bond infos" and second as "connection parameters".

A "reported H-bond info" contains three distance (d_D,H, d_H,A, d_D,A) and one angle (D,H,A) information about the three atoms donor, H-atom, and acceptor.

The "comprehensive" configuration of the data sheet lists the "reported H-bond infos" in the section "Selected hydrogen bonds" (see below), whereas the H-bond connection parameters are listed in the "H-bond parameters" section.

Measuring distances etc. between centroids (dummy atoms)

A special case is the measuring of distances (or angles) between centroids or - more in general - with the help of dummy atoms. This is explained on the Diamond web site: https://www.crystalimpact.de/diamond/howto_centroids_distances.htm

Previous article: Distances around a selected atom
Next article: Extended geometric infos: Angles between planes etc.

[1] COD: 9000684. Hazen, R. M.; Finger, L. W.; "Crystal structure and compressibility of zircon at high pressure crystal No. 1, 1 atm - before P"; American Mineralogist, 64, 196-201 (1979)
[2] COD: 1500005. Ritu Bala, Raj Pal Sharma, Rajni Sharma, Juan M. Salas, Miguel Quiroos, William T.A. Harrison; "Cationic cobaltammines as anion receptors: Synthesis, characterization an X-ray structure of bis-(hexaamminecobalt(III)) tris-(hydrogenarsenate) tetrahydrate"; Journal of Molecular Structure, 828, 174-180 (2007).