[phenixbb] Unknown atoms revisitied

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Thu Sep 6 18:20:05 PDT 2007

> Does the atom type have to be a known element or can it something like
> element X as seen in some pdb files?
> An example from 1aqn:
> HETATM 1951  UNK UNX   277      -4.541  50.540  38.754  0.25 13.93           X 
> HETATM 1952  UNK UNX   278      -4.443  49.701  37.169  1.00 15.64           X 
Pavel is correct, but I'll add a some more details.

If you want to use these atoms in refinement, you have to decide
what scattering type to use. That has to be one of the symbols
published in the International Tables for Crystallography, Volume C
(see cctbx/eltbx/xray_scattering/it1992.cpp under $PHENIX or

Regarding the .cif file:

 SIN             N      N    N         0.000
                 |      |    |
                 |      |    this must be a valid "energy type" (see below)
                 |      this must be a valid scattering type symbol (Int. Tab.)
                 this can be anything you want

mon_lib/ener_lib.cif defines energy types (phenix.where_mon_lib_list_cif
shows the path to mon_lib). You can define other energy types in
additional .cif files you give to phenix.refine, using the same syntax
as in the central ener_lib.cif.

Regarding the .pdb file:

HETATM 1952  UNK UNX   278      -4.443  49.701  37.169  1.00 15.64           X
             |   |                                                           |
             |   this must match the data_comp_UNX                           |
             |                     this must match _chem_comp_atom.type_symbol
             this must match _chem_comp_atom.atom_id

You cannot use X in columns 77-78 because it must match
_chem_comp_atom.type_symbol, and that in turn must be a valid
scattering type symbol. However, you can leave the column blank.
I think I'll change phenix.refine to treat the X like a blank,
then you don't have to remove it. But in the current release
you have no choice.


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