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I've been working on another CIF file, this time for (-)-threo-methylphenidate based on Pharma Res, 1995 (sadly the relevant crystallography data isn't supplied in the free preview at Springer). I have several questions relating to this file, the most pressing is that so far I have this loop:

loop_
_atom_site_label
_atom_site_chemical_conn_number
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_adp_type
_atom_site_B_iso_or_equiv
_atom_site_type_symbol
N1   1    -0.8852(9) 0.120(1)   -1.0300(8) Biso 3.1(2) N
H1a  2    -0.9650000 0.08500000 -1.0010000             H
H1b  3    -0.8800000 -0.0800000 -1.0330000             H
C2   4    -0.739(1)  0.049(2)   -0.940(1)  Biso 3.9(2) C
H2   5    -0.7460000 -0.0800000 -0.9360000             H
C3   6    -0.614(1)  0.092(1)   -0.988(1)  Biso 5.1(3) C

that is generating this error in enCIFer:

Too many or too few data values in the loop

which I'm going to take a stab in the dark and say that it's because two fields (Biso & $B_{eq}$ value) aren't supplied for each atom in this loop (namely it is missing from the hydrogen atoms). The problem is that the paper I cited didn't specify these for hydrogen atoms. Should I use separate loops for hydrogen & other atoms (i.e., one loop for hydrogens, another for the other atoms)? I ask because I fear that this might make molecular modelling software treat the hydrogens & the other atoms as being part of separate molecules.

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  • $\begingroup$ Most software I've used gets the atomic positions from the CIF and then interprets molecular identity from connected components and/or the asymmetric unit. $\endgroup$
    – Geoff Hutchison
    May 2, 2015 at 2:41
  • $\begingroup$ My understanding of the CIF format is exactly what you describe. You must provide everything you declare, so your current loop fails for the reason you suspect. $\endgroup$
    – Geoff Hutchison
    May 2, 2015 at 2:42
  • $\begingroup$ So can dots (.) be used where the missing data is so that this error won't appear? $\endgroup$
    – Josh Pinto
    May 2, 2015 at 3:00
  • $\begingroup$ It looks like the structure model equally was published in 1998JOC1785 which is entry NODBIR here. Submitting the .cif to checkcif reveals some alerts, but not a "too few / to many atoms". Some positional disorder, but ok. $\endgroup$
    – Buttonwood
    May 25, 2021 at 21:58

1 Answer 1

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Your loop defines 8 records. That works fine for heavy elements. However, the lines with hydrogen atoms have only 6 items. That's the reason why this error is reported (all you records are not multiplier of 8).

Usually in refinement the hydrogen atom's $U_{iso}$ is 1.2–1.5 bigger than this of atom to which the H is bound (smaller 1.2 for more constrained movements like on aromatic carbons, bigger 1.5 for aliphatic)

Try something like this:

N1   1    -0.8852(9) 0.120(1)   -1.0300(8) Biso 3.1(2) N
H1a  2    -0.9650000 0.08500000 -1.0010000 Biso 4.     H
H1b  3    -0.8800000 -0.0800000 -1.0330000 Biso 4.     H
C2   4    -0.739(1)  0.049(2)   -0.940(1)  Biso 3.9(2) C
H2   5    -0.7460000 -0.0800000 -0.9360000 Biso 4.     H
C3   6    -0.614(1)  0.092(1)   -0.988(1)  Biso 5.1(3) C
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