Resources about Crystallography
- Frequently Asked Questions
- User Manuals for Operating IMSERC's Diffractometers and their Software
- Single Crystal Crystallography Facility Files
- Structure Validation/Publication
- Crystallographic Websites
- Association and Organizations
- Synchrotron Resources
- Crystallographic Supplies
Frequently Asked Questions
1. How do I get crystals?
2. I think I have crystals, now what?
3. How do I fill out the sample submission form for Crystallographic service?
4. My crystals are air/temperature/light/time-sensitive, how should I handle them?
5. What happens to my samples when you are done with the experiment?
6. I left my sample in the queue and haven’t heard anything. What’s going on?
7. How do you decide what instrument/wavelength to use for my sample?
8. Can you run my chiral single crystal sample on an instrument with Mo-radiation?
9. Where do I get my data?
10. Is this structure publishable?
11. What do I need in order to publish this structure?
12. How can I tell if this structure has already been published?
13. How do I solve my own structures?
14. How do I run my own single crystal data collections?
15. My samples need to go to a synchrotron facility, such as APS or ALS. Can you help?
User Manuals for Operating IMSERC's Diffractometers and their Software
- STADI MP
- STADI P
- Synergy systems
- STADI VARI
- Installation Instructions of Freeware Crystallographic Software
- Olex2 - A guide for Chem432 students
- Notes on Olex2 – Ilia Guzei’s user manual for Olex2
- Olex2 Cheat Sheet – Quick reference card of commands
- SHELX official wikis and manuals
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
- 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
- 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)
- Crystals@Otterbein – symmetry and packing visualizations and other crystallographic resources
- Symmetry Tutorial – A PowerPoint based tutorial developed by Bruce Foxman. An excellent guide to the International Tables
- X-Forum – A web forum devoted to all things crystallographic
- 2014 International Year of Crystallography
- The ACA Summer Course for Chemical Crystallography
Association and Organizations
- American Crystallographic Association
- International Union of Crystallography
- US National Committee for Crystallography