[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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