[ccp4bb]: trouble with metals in Refmac5 under OSX

[Patrick Loll]

Hi all,

I fear I'm becoming vexed.

I'm attempting to run a Refmac5 refinement, using an input file containing a cadmium ion. The program stumbles on the metal, reporting:

WARNING : atom :CD CD BB 101 is absent in the library
WARNING : CD BB 101 : first atom of the tree is absent
WARNING : CD BB 101 : last atom of the tree is absent

(I've included a little more of the surrounding text from the logfile at the bottom of this message)

The metal is clearly the offender, since I can delete it from the pdb file and the program runs OK.

Curiously, I encounter this problem on my OSX machine, but when I copy the input pdb and mtz files to an Irix machine, the job runs with no problem, using the SAME input files. Both platforms are running ccp4 5.0.2 & ccp4i 1.3.20. This is the first refinement job I've tried on the OSX machine since installing the package some months ago; I wonder if I made some grievous blunder when installing the programs?

I've tried a large number of format permutations when specifying the metal in the PDB file, including the following (I've included a line showing a water molecule to give some sense of the register):

ATOM 1531 OW0 HOH Z 183 22.638 4.457 32.105 1.00 44.15 O

ATOM 1532 CD CD B 101 25.170 -8.966 56.029 1.00 38.11 CD
ATOM 1532 Cd CD B 101 25.170 -8.966 56.029 1.00 38.11 CD
ATOM 1532 CD CD B 101 25.170 -8.966 56.029 1.00 38.11 CD
HETATM 1532 CD CD B 101 25.170 -8.966 56.029 1.00 38.11 CD
HETATM 1532 CD CD B 101 25.170 -8.966 56.029 1.00 38.11 CD
ATOM 1532 CD CD B 101 25.170 -8.966 56.029 1.00 38.11 CD

The first version looks correct to me, but all versions give the same error. The structure factor file ATOMSF is indeed present in /sw/lib/ccp4-5.0.2/data/atomsf.lib (and yes, it does contain an entry for CD!).

Any ideas?

Thanks,

Pat

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Here's a little more text cut & pasted from the logfile:

.
.
.

Input file :/Users/loll/Documents/science/ferritin/Cpd8/Matt-Final/Cpd8/xtal1/
------------------------------
--- LIBRARY OF MONOMERS ---
_lib_name mon_lib
_lib_version 4.3
_lib_update 11/06/03
------------------------------
NUMBER OF MONOMERS IN THE LIBRARY : 2432
with complete description : 449
NUMBER OF MODIFICATIONS : 43
NUMBER OF LINKS : 64
I am reading libraries. Please wait.
- energy parameters
- monomer"s description (links & mod )

FORMATTED OLD file opened on unit 45
Logical name: ATOMSF, Filename: /sw/lib/ccp4-5.0.2/data/atomsf.lib


Spacegroup information obtained from library file:
Logical Name: SYMINFO Filename: /sw/lib/ccp4-5.0.2/data/syminfo.lib

Number of atoms : 1532
Number of residues : 346
Number of chains : 3
I am reading library. Please wait.
mon_lib.cif
--------------------------------
--- title of input coord file ---

PDB_code:xxxx
PDB_name:----
PDB_date:XX-XXX-XX
--------------------------------
WARNING : atom :CD CD BB 101 is absent in the library
WARNING : CD BB 101 : first atom of the tree is absent
WARNING : CD BB 101 : last atom of the tree is absent

Spacegroup information obtained from library file:
Logical Name: SYMINFO Filename: /sw/lib/ccp4-5.0.2/data/syminfo.lib

End of this subr
Number of chains : 2
Total number of monomers : 345
Number of atoms : 1531
Number of missing atoms : 0
Number of rebuilt atoms : 0
Number of unknown atoms : 0
Number of deleted atoms : 0

Number of bonds restraints : 1375
Number of angles restraints : 1850
Number of torsions restraints : 938
Number of chiralities : 204
Number of planar groups : 242
IERR = 1


There is error. See above
===> Error: Fatal error. Cannot continue


---------------------------------------------------------------------------------------
Patrick J. Loll, Ph. D. (215) 762-7706
Associate Professor FAX: (215) 762-4452
Department of Biochemistry & Molecular Biology
Director, Biochemistry Graduate Program
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA 19102-1192 USA

[EMAIL PROTECTED]