As soon as your structure is solved and refined, you'll receive ...

... a .res file

You can open this file with many visualization programs to view your molecule. You will also need this file to create images, for example for your master's or doctoral thesis. The following programs are recommended:

  • Olex2 (open source, freeware): A very comprehensive program, which is used by many crystallographers as well. In Olex2, all functions that are relavant for viewing your molecule are found in the menus "Work" and "View". In the menu "View" you can select a style that is used to display your molecule (wireframe, spacefill, ball-and-stick, polyhedra, etc.). In "Work" you will find the submenu "Draw", which allows to select the atom labels you want to display. Here, you also find options to save your image (.png, .bmp, .ps) and an option to convert your image to a POV-Ray file. POV-Ray is a free rendering tool for creating high-resolution graphics. Note: In the "Work" menu you will find an option to rename single or multiple atoms (rename = change the atom labels we assigned). Of course you can use this function, as long as you are aware that this may lead to serious errors. Here is an example: Assume that the bond length between the atoms Mn1 and O3 was kept constant (within certain limits) during refinement (such constraints or restraints may be needed to generate a stable model of your compound). If you now change the labels of the two atoms, the command to set the bond length to a certain value may no longer work. The command has to be adjusted by manually editing the .res file. All commands we use are explained in the SHELXL manual. Important note: For publications, the atom labels in your image must match the atom labels in the cif file (see the Publication section of this website), i.e. if your structure is to be published and atom labels are to be changed, you must talk to us.

  • ORTEP3 (freeware): This program is only for visualizing your structure and creating images for your thesis or for publication. Options to change labels are not found here. The program is a bit older and could use a new look. Nevertheless, it contains all functions to display your molecule in an appealing way (e.g. calculating a centroid in the geometric center of a Cp ring and displaying the Cp-metal bond as a single line between the metal and the Cp centroid). From a crystallographic point of view, the program is structured intuitively. The sidebar contains all the options to precisely place your molecule in space (note: right-clicking on the sidebar opens a dialog, which offers the possibility to limit the rotation angle to a few degrees - thus allowing a proper alligment in space). The "Contents" menu contains options that allow you to specify exactly which parts of your structure you want to display (asymm. unit, whole cell, selection of a so-called PART of a disordered group). If certain parts of your structure are generated by crystallographically imposed symmetry operations, care should be taken: The "growing" function will automatically generate the symmetry-equivalent parts of your structure. In consequence, your whole molecule will be displayed after "growing". As for the other programs listed here, this only works satisfactorily for neutral molecules. For salts (separated cation and anion) it often happens that only one of the two parts (cation or anion) is completed by applying symmetry. As a result, it appears as if the overall charge balance was incorrect. However, this is due to a deficiency in the "growing" algorithm. In the "Style" and "Lables" menus, you may customize color settings and choose the atom labels to be displayed. Be careful when using the "Calculate" menu, which allows you to display calculated distances and angles. The errors calculated here are not exactly correct as some of the files needed for a correct caluculation are missing. With the itmes in the "File" menu, you may convert your .res file to an .xyz file (for DFT calculations) or export the image of your structure as a POV-Ray file.

  • Mercury (freeware): The official visualization program of the Cambridge Crystallographic Data Centre. This program is particularly useful for visulizing multiple structures and for a comparative analysis (e.g.: for comparing Ni-C bond lengths in all nickel alkyl complexes deposited in the CSD up to now). Some features are useful for displaying organic molecules: Delocalized aromatic rings, for example, can be represented with a circle in the ring. Hydrogen bonding networks can be expanded by simply clicking on one of the atoms within the network. Solvents in the crystal lattice may be easily hidden (right click on the solvent and select "Hide Molecule"). The program has a very efficient graphical interface that allows to display many molecules at the same time, which is of advantage for creating packing diagrams. The representation of planes is also very well implemented: you may choose to represent Miller planes or planes through certain atoms and determine angles and distances between these planes (as in all other programs: without reliable errors). Provided you also installed POV-Ray (a freely available rendering tool), you can render your structural image directly in Mercury. A particularly noteworthy feature of Mercury: You may generate STL or VRML files, which may be used to print your stucture with a 3D printer. The university's computing center has 3D printers for printing 3D models of you structure for a fee.

... a .docx file

An ordinary MS-Word file that contains a lot of information about your crystal, the actual measurement and the refinement. This file serves as your starting point for creating a table summarizing the most important crystallographic data. Such a table is required for publication and is usually reproduced in the Supporting Information (a template can be found in the Publication section of this website). In the .docx file you will also find the atomic positions (x,y,z) for each atom (ISAM), the ADPs (anisotropic displacement parameters) for each atom and several bond lengths, bond angles and torsion angles (each with a standard deviation). Please use these values and standard deviations in your disscussion. The values displayed by most visualization programs are unreliable. If you need more values (e.g. distance to a plane, angles between planes), you better come by with a piece of paper and a pencil. Unfortunately, some of these values can only be transferred via copy-paste, i.e. to transfer these values to your computer it is most often easier to transcribe directly from our screen.

... a preliminary checkcif.pdf file

This file is created by a check routine, which checks that the essential requirements for publication of your structure are met. Since the check routine is improved on a regular basis, we have to create an up-to-date checkcif.pdf file shortly before publication. The up-to-date file is then submitted along with your manuscript. The preliminary checkcif.pdf file is supplied for guidance only. You may use the preliminary checkcif.pdf file to assess whether complications may arise during the review process. In case you see a Level B Alert in your checkcif.pdf, complications are possible. In rare cases, Level C Alerts may lead to questions from a reviewer as well. By commenting the checkcif prior to publication, we actually need to justify why an alert shows up in a particular case. Level G Alerts are for your information only, i.e. these are no "real alerts". Level A Alerts appear in case of critical discrepancies between theory and the diffraction experiment. If this is indeed the case, you won't receive a .res file nor a checkcif.pdf, i.e. you should never see a Level A Alert. Nevertheless, you will be informed that your structure could not be refined satisfactorily. Still, you will receive a simple picture of your structure, so you can at least check if the convectivity of the atoms is in line with your expectations.


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Most recent amendment: January 07th 2022
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