[ccp4bb]: ARP/wARP 6.0 and/or REFMAC5 problem

[Clemens Vonrhein <vonrhein@globalphasing.com>]

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Dear all,

trying to build a structure with I atoms in it I encountered the
following:

  - the recommendation from ARP/wARP is to add existing metal atoms
    (or anything else for that matter) as residue IUM to the end of
    the PDB file

  - for I I then get a line like

ATOM      1  I   HET Y5504     -37.821 -22.501  -6.363  0.76 73.74  53       I

    which I _think_ is correct PDB syntax?

  - REFMAC5 now has problems with that and after going through the
    source (make_crd.f) and trying to follow the logic I _think_ what
    happens is that

    * because REFMAC5 knows the residue type (IUM = Uranyl) it tries
      to be very clever

    * the atom " I  " seems to match somehow a DNA???

    * the error is:

  ----- refmac.log -------------------------------------------------
  I am reading library. Please wait.
                mon_lib.cif
  WARNING : residue: Id  5504  chain:YY   - not found in the library
                    program will create complete description for:Id
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:XX-XXX-XX
  --------------------------------
  WARNING : Id  YY5504  : wrong definition of first atom of the tree
  ----- refmac.log -------------------------------------------------


My questions: 

  - has anyone managed to get this ARP/wARP feature (IUM metal atoms)
    working with atoms that require a single character in the atom
    specifier (especially I)?

  - do I have to use IUM residue type? It seems to be hardcoded in
    ARP/wARP somewhere, because with other residue types it keeps
    waters close to the metals/iodine.

  - anyway I can tell REFMAC5 to use the I.cif file for this specific
    atom?

Thanks for any hint.

Cheers

Clemens

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