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Resources about Crystallography

Frequently Asked Questions

1. How do I get crystals?

There are many ways to grow crystals of your target materials. They can form spontaneously in reaction vessels or NMR tubes, or they can take weeks of careful recrystallization attempts to appear. Check with others in your lab who might have had success in growing crystals, or view the IMSERC Crystallization Guide for tips on recrystallization techniques. Additional resources are available on the web.

2. I think I have crystals, now what?

Once you suspect you have crystals, bring the vial to the Crystallography lab (BG60/62) for a visual assessment on the polarized light microscopes. Crystallography staff members will tell you if your sample is crystalline and if it might succeed on the diffractometer. You will need to fill out a sample submission form (see Question #3 below) and leave your crystals together with the form at the end of the queue in the lab. See staff members if you need assistance. Remember to leave your sample in a clearly labeled vial and to fill out the form completely. Follow the instruction if your crystals are sensitive to ambient conditions, please follow instructions below (see Question #4).

3. How do I fill out the sample submission form for Crystallographic service?

Log on to NUcore and choose the appropriate service, i.e., single crystal service request or powder diffraction service request. Fill out the form, add to your cart and remember to click “purchase” to complete the submission. Return to your form and print the PDF file. Read full detailed instructions .

4. My crystals are air/temperature/light/time-sensitive, how should I handle them?

If your samples will decompose rapidly under ambient conditions, please leave them in a safe place in your lab. Fill out a sample submission form (see Question #3), select 'Call' as location on the form, and leave it in the queue. You must contact a Crystallography staff member to arrange a time to bring your samples to the lab for data collection. If your samples decay rapidly over time, see a staff member as soon as possible to arrange a day for the data collection.

5. What happens to my samples when you are done with the experiment?

Some air- or temperature-sensitive samples may decompose while we are working with them but we do our best to preserve the bulk of the material submitted so that we can return it to you for further analysis. If you know you will need your sample or the specific crystal used for the data collection returned, talk to a staff member and we will save what material we can. Unused material is deposited in the sample return box on the bench by the queue and may be picked up at any time. We empty the boxes approximately every two weeks, so be sure to retrieve your sample as soon as possible after the experiment.

6. I left my sample in the queue and haven’t heard anything. What’s going on?

The most likely explanation is that your sample is still waiting its turn in the queue. You will be notified when your sample is into data collection or if your sample did not diffract well enough for data collection. If your crystals were not of good enough quality for data collection, your sample submission form will be set aside by the queue, and a note given on the form why the sample did not work. We will also send an email or notification through NUcore. If you are concerned, feel free to contact a Crystallography staff , or come by the BG60/62 lab .

7. How do you decide what instrument/wavelength to use for my sample?

IMSERC maintains a wide range of single crystal and powder diffractometers that can be used on various types of samples. In general, MoKα or AgKα radiation is good for strong diffracting crystals, heavy X-Ray absorbers, and/or small unit cells. CuKα radiation is useful for weak diffracting crystals, large unit cells and/or light-atom chiral molecules. After years of experience, Crystallography staff members have a good feel for which materials will work best on a particular instrument. If your sample fails on one of the less-powerful diffractometers, we will switch to a higher intensity instrument and try again.

8. Can you run my chiral single crystal sample on an instrument with Mo-radiation?

It depends. Absolute stereochemistry of light-atom materials cannot be determined with Molybdenum radiation. Molecules with no atoms heavier than Na and with no known chiral centers must be run on one of the Cu instruments. Relative stereochemistry can always be determined, so samples that diffract well enough and have at least one known chiral center can be run on the Mo instrument. Likewise, the anomalous signal used to determine chirality is large enough with MoKα radiation for molecules containing atoms heavier than Na, so samples containing a heavy atom can be run on one of the Mo instruments.

9. Where do I get my data?

When a structure refinement is complete, IMSERC Crystallography staff send a notification through NUcore and upload the necessary files for structure viewing, analysis, and publication to ReciprocalNet . Typical files include a report document (MS Word format), and a Crystallographic Information File (CIF file). These files contain all the information you need to view your structure, create figures, and publish the data. See the file information page for more details.

10. Is this structure publishable?

We always strive to collect publishable data every time we put a crystal on the diffractometer; however, not every structure will be suitable for publication. If you have received a structure report from us (MS Word document), then we believe your data can be published on some level. Specific journals have certain requirements for accepting crystal structures, so not every journal will accept every structure produced. Crystallography staff will work with you during the publication process to ensure your data will pass the review. Please keep in mind that a “perfect” checkCIF report is very rare – especially for the complex structures produced by researchers at Northwestern. If your checkCIF report has errors – even A-level alerts – this does not mean the structure cannot be published. It does, however, indicate the need for comments in the text or supporting information to explain the warnings. Crystallography staff typically provide such comments in the CIF file and in the report document that you can use in your publications. If you have any doubts or concerns, please speak with a staff member.

11. What do I need in order to publish this structure?

Different journals have different requirements for reporting crystallographic data. And of course, much depends on how you wish to report your structures. Typically, CIF files are required for submission as supporting information. Some journals may require you to submit the CIF file to a database prior to publication, e.g., database such as the Cambridge Structural Database (CSD) or Inorganic Crystal Structure Database (ICSD). The best course of action is to check the journal’s requirements early in the writing process and speak with a staff member if you need assistance in preparing files for publication. Most journals contains notes for authors on how to publish results, and these typically include information for crystal structure reports.

12. How can I tell if this structure has already been published?

The Cambridge Structural Database contains information on published crystal structures of compounds containing at least one carbon atom. The chemistry department maintains a site license to the CSD and a copy of the database can be obtained from Crystallography staff. We will provide a copy of the CD and license information for you to install on your local machine. Additionally, a copy can be found on the IMSERC terminal server for remote login use. Check CSD for more information. Information for inorganic structures that have been published can be found in the ICSD.

13. How do I solve my own structures?

If you have experience solving and refining your own crystal structures, Crystallography staff members are happy to provide you with the raw data necessary for you to do this. If you are interested in learning how to solve and refine your own structures, you can attend the Chem435 class in 'X-Ray Crystallography' offered in the Winter Quarter. Speak with IMSERC Crystallography staff if you are interested in attending the class.

14. How do I run my own single crystal data collections?

If you have successfully completed the Chem435 course, or have prior experience in operating a single crystal diffractometer, contact IMSERC Crystallography staff to schedule training. Diffractometers are available for student use during select weekdays and all weekend. Once you have been checked-out on an instrument, you may reserve time through NUcore.

15. My samples need to go to a synchrotron facility, such as APS or ALS. Can you help?

If your crystals are deemed unsuitable for IMSERC facility diffractometers , your first step should be to attempt to recrystallize them. If after repeated attempts, your samples are still too small for data collection at Northwestern, Crystallography staff will make arrangements to have data collected at the APS or by our collaborators at ALS. Due to the nature of scheduling at APS or ALS beamlines, rush data collections cannot be performed. Please budget your time accordingly. Additionally, please remember that crystals exhibiting twinning and diffuse scattering pathologies will not be made better by exposure to synchrotron radiation.

User Manuals for Operating IMSERC's Diffractometers and their Software

Single Crystal Crystallography Facility Files

Structures that have been solved and refined by IMSERC Crystallography staff will be uploaded to ReciprocalNet and deposited in the appropriate directory on the IMSERC file server . An e-mail will notify you that your files are ready for you to view or download.

Files uploaded on Reciprocal Net

  • Compound.cif – This is the CIF file that should be submitted as supporting information when publishing a structure. This is a versatile file that can be read by many software programs for visualization and analysis. Additionally, this file can be edited and a full report created using publCIF. The program enCIFer can also be used to edit and check a CIF file
  • Compound.doc – this is the report document that details the experimental and structural parameters. Much of the information in this report can be used in the experimental sections of your publications or supporting information
  • Compound.res – the results file from the final refinement cycle. This is a versatile file type that can be read by Mercury, PLATON and other molecular graphics and structure analysis programs
  • Compound.hkl – the data file used for the refinements. This file includes the hkl indices, Fobs and sigma(Fobs) for each reflection. If the crystal was twinned, this will have twin component information in it as well
  • Compound.fcf – a CIF-style file containing your reflection data. Some journals now require submission of the fcf file along with the cif file

Other files available from the file server

  • Compound.lst – the listing file of the final least-squares refinement cycles and contains information about the structure and about the quality of the data
  • Compound.pdb – Protein Data Bank format file contains atom positions in Cartesian coordinates (not unit cell dependent). Can be read by multiple molecular graphics programs. Does not contain symmetry information
  • Compound.prp – this is the log file of XPREP and contains information about the matrix used if your data were transformed to a standard setting as well as intensity data as a function of resolution – useful to see how well your crystal diffracted
  • Compound.p4p – generated during the data integration stage and contains information pertaining to the diffraction experiment
  • Compound.raw – contains the raw data from the integration, can be read by XPREP and SADABS or other crystallographic software programs

Databases

  • ReciprocalNet -a distributed crystallography network for researchers, students and the general public. All staff-collected data is available through Reciprocal Net. ReciprocalNet can be used as an internal CIF repository tool for NU researchers
  • WebCSD – The web-based version of the Cambridge Structural Database. (can only be accessed from the Northwestern network)
  • Inorganic Crystal Structure Database (web version) – Database of Inorganic Materials (can only be accessed from the Northwestern network)
  • ICDD -The International Centre for Diffraction Data

Structure Validation/Publication

Crystallographic Software

  • CrystAlis Pro – Single crystal diffraction data reduction and structure analysis. Software is available to registered IMSERC users only and it can be downloaded from the ‘imsercdata.northwestern.edu\public’ folder as described under the 'Data Access' section on our FAQ page. Software features include:
    • Automated analysis of the data can be conducted in parallel to the ongoing data collection with near instant experiment feedback by utilizing a single integrated package for diffractometer control and data analysis
    • Fast reliable feedback during the initial stages of sample analysis. Unit cells typically appear within one or two frames and can be searched for via CellCheckCSD or a local database automatically. “What is this?” tool can determine connectivity in seconds, allowing you to make fully informed decisions without wasting valuable instrument time. A wide variety of tools are available to assist you in visualising, identifying and solving problems quickly, e.g. Ewald3D - a new fast 3-dimensional diffraction viewer
    • SMX or PX? CrysAlisPro contains separate workflows to fit their differing needs and approaches
    • Fast support and solutions. CrysAlisPro facilitates effective remote support both scientific and technical with full diagnostic readouts and detailed log files for remote diagnosis and solving of issues
    • Support of non-standard experiments including high pressure data collections, variable temperature and multi-wavelength experiments, powder experiments (data collection and processing), automatic screening or full data collections of several in situ protein crystals, highly absorbing samples, up to 8-fold twinned samples, charge density measurements, and absolute structure determination, to name a few
  • Bruker APEX3 – Single crystal diffraction data reduction and structure analysis. Software is available to registered IMSERC users only and it can be downloaded from the ‘imsercdata.northwestern.edu\public’ folder as described under the 'Data Access' section on our FAQ page. Software features include:
    • Comprehensive software package for single crystal X-ray diffraction (SC-XRD)
    • Twin handling of up to eight domains
    • Intrinsic Phasing (ShelXT) solves the vast majority of structures in seconds
    • XRD 2 routine to collect powder data from capillary or flat samples
  • Bruker TOPAS – Profile and structure analysis software for powder diffraction. Software is available to registered IMSERC users only and it can be accessed through IMSERCs Terminal Server as described under the 'Software' section on our FAQ page. Software features include:
    • Single Line Fitting
    • Indexing (LSI and LP-Search methods)
    • Whole Powder Pattern Decomposition (Pawley and Le Bail methods)
    • Ab-initio structure determination in direct space from powder and single crystal data
    • Whole Powder Pattern Decomposition (Pawley and Le Bail methods)
    • Rietveld structure refinement
    • Quantitative Rietveld analysis
  • Bruker EVA – Phase analysis and evaluation of powder diffraction data. Software is available to registered IMSERC users only and it can be accessed through IMSERCs Terminal Server as described under the 'Software' setion on our FAQ page. Software features include:
    • Highly sophisticated residual search with respect to already identified phases, thus greatly improving analysis of minor phases Support of Variable Counting Time (VCT) and Dynamic Beam Optimization (DBO) data for highly accurate trace phase analysis thanks to significantly decreased Lower Limits of Detection (LLoD)
    • Simultaneous search in multiple reference databases
    • Grouping of candidate patterns phases to handle the ever-increasing number of similar or nearly identical reference database entries
    • Phase identification and accurate quantitative phase analysis based on RIR (reference intensity ratios) values
  • Olex2 – Structure solution/refinement GUI (Freeware)
  • GSAS-II – Crystallography data analysis software for single crystal and powder data (Freeware)
  • STOE WinX POW – Powder Diffraction Software Package. Software is available to registered IMSERC users only and it can be accessed through IMSERCs Terminal Server as described under the 'Software' section on our FAQ page. Software features include:
    • Graphics incl. Peak Search, Smoothing, Background Subtraction
    • 3D Graphics
    • Raw data handling with Import/Export of data in various formats
    • Profile Fitting
    • Indexing and Lattice Constants Refinement
    • Theoretical Pattern Generation
    • Size/Strain Analysis
    • Crystallinity Analysis
    • Retained Austenite Analysis
  • Cambridge Crystallographic Data Centre (CCDC) Freeware – Freeware with tutorials from CCDC for:
    • enCIFer – CIF checking, editing and visualization software
    • Mercury – Crystal Structure Visualization and Exploration Made Easy. Advanced features in Mercury are available to Northwestern members only after activation of Mercury
    • CSDSymmetry - The most complete collation of observed molecular and crystallographic symmetry properties to date
  • PLATON – Multi-system program for structure analysis (Freeware)
  • WinGX – Multi-system GUI for structure solution and analysis (Freeware)
  • JANA – Structure solution/refinement program for Modulated Structures (Freeware)
  • publCIF – CIF editor and publication wizard (Freeware)

Crystallographic Websites

Association and Organizations

Synchrotron Resources

Crystallographic Supplies

Videos