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Mastering CIFs for Crystallographic Data: Tools and Guidelines

Learn to create, edit, and validate CIF files efficiently using various software programs. Understand CIF structure, data naming conventions, and the submission process. Enhance your crystallography skills with practical insights.

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Mastering CIFs for Crystallographic Data: Tools and Guidelines

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  1. CIF's • CIFs from SHELX • CIFs from MOLEN • Working with CIFS • ENCIFER • PUBLCIF • PLATON Validation

  2. CIF from SHEX • If the command ACTA is included in the SHELX input the program will generate two files. • One is xl.cif • This is a cif with everything SHELX knows • It does not know about details of the data collection, structure solution, etc. • The other is xl.fcf • This contains the Fo and Fc data • This is not simply .hkl reformated

  3. CIF's from MOLEN • MOLEN is the old NONIUS software • Use the local commands endprep or rendprep to go from SHELX to MOLEN • Program to generate cif is cifgen or rcifgen. • This program will create a full cif file called ciffile.dat • This is a full cif ready to go.

  4. Parts of a cif • Every cif must have a data_name command at the start. • Name can be either a compound id or global. • There can only be one global data section and this must be at the start. • The idea is as follows • Global • Compound I • Compound II • etc

  5. To build a Multi-structure CIF • Use the idfull.cif cif as the first cif part. • Append the other id.cif's after this. • Note the global data covers all the compounds included. • If there is more than one data_global then the cif will fail all format checking and be rejected!

  6. Acta Cryst Submission • It is possible to submit an entire manuscript in a cif • In fact this is the only way of submitting to Acta Cryst Journals. • The Global section will contain the manuscript and other items needed for publication • Look at a cif.

  7. Bonds and Angles to be published loop_ _geom_angle_atom_site_label_1 _geom_angle_atom_site_label_2 _geom_angle_atom_site_label_3 _geom_angle _geom_angle_site_symmetry_1 _geom_angle_site_symmetry_2 _geom_angle_site_symmetry_3 _geom_angle_publ_flag C4 N3 C2 117.2(3) . . . ? O91 N9 O92 124.6(3) . . . ? O91 N9 C9 117.7(3) . . . ? O92 N9 C9 117.6(3) . . . ? C2 C1 C10 119.8(3) . . . ?

  8. PUBLCIF • This is a free program that allows you to edit both the cif and the publication data at the same time • Exists for all operating systems • Available from the IUCr

  9. ENCIFER • This is a free cif editor available from the CCDC • It allows easy changes to the cif. • It checks the cif format and some basic input • DOES NOT check for consistency of most numbers • Also has a display function for molecular graphics

  10. PLATON • PLATON has the most complete cif checking facility. • It can be used locally if you have a copy of PLATON or by uploading the cif to the web site http://checkcif.iucr.org/ • To use locally start platon by platon xxx.cif and use the validation function from the menu.

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