Finishing Up

1. Finishing Up • Complete discussion of CIF • Molecular Geometry Parameters • s.u.'s • Producing Tables. • RECIPROCALNET

2. Programs for Working with cif • Publcif • Available from http://journals.iucr.org/sercives/cif/publcif • A nice cif editor. • Encifer • Available from http://www.ccdc.cam.ac.uk/free_services/encifer • Both an editor and checker

3. Verifying cif's • PLATON can be used to check a cif—start PLATON with the ciffile as input • Provides three levels of errors • A errors are serious and must be addressed • B errors are less serious • C errors may or may not be real • PLATON validation must always be viewed with a grain of salt as it can be completely incorrect.

4. IUCr services • If you do not have PLATON you can email your cif to checkcif@iucr.org • The cif should be the body of the email • You will get a report back in several minutes • If you place the manuscript in the cif you can obtain a copy of the manuscript back by mailing to printcif@iucr.org

5. Cif generation at Purdue • The program cifgen is used to create a cif. • Unfortunately all the table programs run from a different software package call MOLEN • The data in this package is stored in a binary (non text) file and cannot be read by humans • There is software to go from SHELXTL to MOLEN which is best run automatically during table creation. • There is the cif xl.cif produced by SHELXL which has the structure but it incomplete

6. Reflection Data in Cif • A second cif file is produced called xl.fcf • This contains the h,k,l, Fobs, σF, and Fcalc. • This does not need to be routinely submitted to most journals.

7. Publishing Structures with CIF • The IUCr journals require that the entire manuscript be in one cif. • Most of the ACS journals require that a single cif be included as supplementary material. • Some journals require that the cif be deposited with the Cambridge Crystallographic Data Centre (CCDC) when the manuscript is submitted. This is done at their website www.ccdc.cam.ac.uk. • Be sure you edit the authors before submitting.

8. Distances and Angles • Angles and distances are calculated as we saw earlier using formulas based on dot products of non-orthogonal coordinates • In general the distances and angles are obtained from the xl.cif file produced by SHELX.

9. S.U.'s on Geometric Parametes • There are many ways to calculate these. • For example • Use the variances or co-variances? • Should the errors in the cell constants be included? • At one time the s.u.'s were multiplied by the goof parameter but there is no statistical reason for doing this and the procedure has disappeared.

10. What are s.u.'s from least squares • Essentially the s.u.'s are a measure of how changing a parameter effects the results of the least squares. • Heavy atom structures • The heavy atoms will always have small s.u. • The light atoms will have higher s.u.'s than in an organic structure—they make less difference in the final r-factor. • The s.u.'s on hydrogen atoms are always an order of magnitude greater than carbon.

11. S.U.'s vs standard deviations • It is possible to determine the standard deviation of geometric parameters • There is no question that the s.u.'s are an under estimate of the standard deviation. • They are off by at least √2 • Always use 3 x s.u. when comparing geometric parameters!

12. Other Geometry Calculations • Torsion Angles • Least Square Planes • Calculates the best plane through a series of atoms • Provides statistics on how planar the arrangement is • Can calculate distance of an atom to the plane • Calculate the angles between the planes. • Centroid—simply average the coordinates

13. Producing Tables at Purdue • Everything is in a program called tables. • Does many things for you. • Converts SHELX data to MOLEN and does various analyses • Uses history collected during structure solution and refinement • Needs to know if DENZO or EVAL was used. • Creates input and runs prequest to add data to a local Cambridge Structural Database. • Creates all the table files

14. Creates the label for the cd disk • Creates the cd disk • Archives the data to another hard disk • Runs a web browser to create a RECIPROCAL net file system • Loads files to the RECIPROCAL net

15. Table Files • Most files are in rtf (rich text format) which can be read with any word processor. • RTF files • exp.rtf – a description of the procedures used. • data.rtf –a brief data table • inorganic.chem – a short table needed for the journal Inorganic Chemistry • bond.rtf –a table of bond distances • angle.rtf –a table of bond angles

16. xyz.rtf – atom positions • u.rtf – anisotropic adp's • torsion.rtf – torsion angles. • fofc.rtf – observed and calculated data • hydro.rtf – hydrogen bonding • CIF files • ciffile.dat – the cif file • fofc.dat – the cif of the data • Absolute Configuration Files • ent.txt – the output of the Bijvoet analysis • RS.txt – a list of the RS configuration of enantiomorphic atoms

17. Miscellaneous Files • .pdb – a file in the Protein Database Format. Can be used for input to ChemDraw • .mol – a file in another crystallographic format

18. Archiving • All the important files including all the raw data are written to a cd. • This file is given to the user and is the only output provided • This is the only place the raw data is archived • The files are copied to a different disk reached by /old/home/temp/strucname. • The table and other files are written to the RECIPROCALNET • Some data is stored in a local csd database.

19. RECIPROCAL NET • This is a distributed data base and lab management system. • Created at IU • Used by 18 labs world wide • Everything is done over the web • All structures are kept on this • All data is password protected for 5 years or until publish • Each group is entitled to 1 or more accounts for access

20. What is on RECIPNET • All the table files needed to work on or publish a structure • A JAVA graphics system for looking at results • Some tables summarizing the crystallographic data. • This can be searched by anyone for public structures and by a user after logging in for his structures.