Overview – Why Reciprocal Net?

1. Why Reciprocal Net? Overview – Why Reciprocal Net? • The motivating force behind the Reciprocal Net is to make life easier for the crystallographer as well as to insure that the colleague he is working with can make maximum use of the information obtained from a crystal structure analysis. • Easy access to tabular information • User friendly graphics

2. Current Status • Today we have nearly 20 systems either on-line or nearing on-line status, and the software is remarkably stable. • The system is not only popular with the users of the data, but has been widely recognized by several major scientific organizations: • One of top 50 Science and Engineering sites (Scientific American) • Featured on NetWatch in Science • Featured in Chemistry (ACS general public newsletter)

3. Current Status • Reciprocal Net Site Software 0.9.0 is currently scheduled for release in July, 2005 • If time and resources permit, a minor upgrade will be released in September, 2005; likely to be labeled 1.0.0

4. Portal and Educational Content

5. Portal and Educational Content

6. Portal and Educational Content

7. Portal and Educational Content

8. Portal and Educational Content

9. What is a LIMS? What does it look like? Open a browser

10. What is a LIMS? What is a LIMS? • LIMS: Laboratory Information Management System • Records data about laboratory operations and results • Supports workflow tracking, sample status reporting, and other data-centric features (depending on the particular LIMS) • The Reciprocal Net LIMS • Designed for crystallography • Workflow based • Maintains permanent, complete history • Stores selected miscellaneous data as well as files

11. LIMS: Basic Workflow

12. LIMS: Data Structure • Many data reside in a database on the server • Per-sample data include arbitrary files supplied by users • ALL data are versioned

13. LIMS: New Samples When a new sample arrives in the facility, the procedure is: • Submit the sample into the Reciprocal Net. • Collect some data and try to determine a unit cell. • Either “failed to collect” for examinations or “collect preliminary data” and enter unit cell parameters, etc. • If the latter: collect full data, solve structure, early refinement. • “Refine structure” and submit preliminary files. • Complete refinement, fill in the blanks in the data mask, generate the graphics files and place as many files in the repository as you want.

14. Release to Public When a structure has been published: • Perform the “Release to Public” action • Perform an “Add Citation” action if there is a citation

15. LIMS: How the IUMSC benefits Benefits • Sample tracking • What is its current status • No more paper reports • Quick access to summary data about previously-determined structures • Search by unit cell parameters / volume • Search by sample provider / submitter • Search by (partial) sample number • Search by responsible crystallographer

16. LIMS: More Benefits More Benefits • Collaborating Chemists can do more for themselves • Preparation of images • Tracking their samples’ status • Answering many structure geometry questions • Ease of file exchange • Files and data are accessible from anywhere with a network connection.

17. LIMS: More Benefits The Graphics Files In order for the graphics to appear in the Reciprocal Net window, two files need to be in the repository: name.sdt and name.crt. The first contains a list of the atoms in ORTEP format, the second one a list of the atoms with cartesian coordinates, connectivity, and some other information. The generation of these two files is a little weird.

18. Generating files for graphics Overview – Why Reciprocal Net? If you have a straight-forward and “clean” molecule with Z’ = 1, and no disorders, the process is relatively simple: SHORTEP requires only a simple knowledge of some simple instructions and will proceed with not problems. In many cases however, it is desirable to have a series of name.crt and name.sdt files to represent different moieties or ignore disordered portions of a molecule. It might also be desirable to have files in which only selected hydrogen atoms are shown. XP allow to generate a name.ins file that contains precisely those atoms you want to see in the graphics application. The program shel2sdt.exe can read shelx .ins format and generate a file name.sdt, which can be read by SHORTEP.

19. shortep.exe Overview – Why Reciprocal Net? SHORTEP is a legacy program that was developed in the IUMSC when there were few other options. The name comes from the fact that it is a “shortened” version of C. Johnson’s ORTEP program. All of the atom plotting instructions are removed, but the atom manipulation routines are retained, and a fair number of new manipulation and generation options are added. Because we had standardized on a hybrid of GENLES (LANL) and ORFLS (ORNL) input formats, we were using (and still use) a unique “SDT” format. This is the nnnn.sdt file that is required for some of the graphics options in the Reciprocal Net. The SHORTEP program can read an SDT and generate additional SDT’s as well as the nnnn.crt files used in recipnet. The nnnn.crt file is the other file format that was employed, primarily to keep the file size minimized in the system.

20. Generating files for graphics Overview – Why Reciprocal Net? If one wishes to generate the files directly from a .res or .ins file nnnn.resfrom SHELX nnnn.cif nnnn.crt shel2sdt.exe shortep.exe nnnn.sdt Manipulate atoms if necessary for differentfragments of interest.

21. shel2sdt Overview – Why Reciprocal Net? shel2sdt.exe is a command line program that can be used to create the name.sdt, which can be read into shortep.exe. shel2sdt name.ins is all you need to type.

22. Read CIF Acknowledge Read in Atoms Create SDT Create CRT Exit Program SHORTEP

23. Let’s have an example Ylid Test Structure