On Oct 17 2004, Miguel wrote:
Bugs item #1048504, was opened at 2004-10-17 01:25 Message generated for change (Comment added) made by migueljmol You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=1048504&group_id=23629
Peter,
Bob filed a bug report saying: -------- Initial Comment: I tried opening a file Peter suggested from http://journals.iucr.org/e/issues/2004/10/00/EAtxtisscontsbdy.html (inorganic compounds-- Acta Cryst. (2004). E60, i120-i123) (checkCIF/PLATON results: No syntax errors found) But nonetheless, Jmol does not read
http://scripts.iucr.org/cgi-bin/sendcif?hb6095sup1 --------
One of the problems I had with this file was the termination of the loop_ constructs.
I spent a few minutes at the iucr web site and tried to figure out the .cif specification for loops ... but was unable to find an answer.
Q: What terminates a loop in CIF?
see reply to Bob
The loops in the aforementioned file are smashed together, without intervening comments or white space ... as in:
loop_ _atom_site_label _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_U_iso_or_equiv _atom_site_adp_type _atom_site_calc_flag _atom_site_refinement_flags _atom_site_occupancy _atom_site_disorder_assembly _atom_site_disorder_group _atom_site_type_symbol Sr 0.3333 0.6667 0.1667 0.0145(3) Uani d S 1 . . Sr N 0.0000 0.0000 0.0820(3) 0.0182(10) Uani d S 1 . . N C 0.0000 0.0000 0.0000 0.0126(14) Uani d S 1 . . C loop_ _atom_site_aniso_label _atom_site_aniso_U_11 _atom_site_aniso_U_22 _atom_site_aniso_U_33 _atom_site_aniso_U_12 _atom_site_aniso_U_13 _atom_site_aniso_U_23 Sr 0.0131(3) 0.0131(3) 0.0172(4) 0.00654(15) 0.000 0.000 N 0.0179(16) 0.0179(16) 0.019(2) 0.0089(8) 0.000 0.000 C 0.009(2) 0.009(2) 0.020(4) 0.0044(10) 0.000 0.000 _geom_special_details
Q: Is this a valid file?
yes. whitespace is any combination of th whitespace characters and can be as little as a newline. CIF is NOT a line-oriented format anymore than C or Java is
Thanks for your help.
I have written what I hope will become the definitive parser for CIF. Ask Billy to mail it to you. You can easily lift the parsing routine.
P.
Miguel
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