The trouble, as Eleanor and Garib correctly point out, has nothing to do with the formatting of the PDB file, nor is it related to anything in the way OS X does, well, anything (the reason I saw a difference between Irix and OS X was that I had slightly different assortments of monomer libraries on the two machines). As an aside, there IS also a file named Cd.cif, and OS X clearly seemed to be choosing the correct file based upon the case of the residue name.
A note to those using Hampton Screen 2 condition # 34, or other cadmium-containing buffers: The CD1 monomer library is for HYDRATED cadmium ions; if you don't have a hydration shell defined as part of the residue, you need to have a monomer library file for a naked ion (the CD_EL.cif file referred to by Eleanor below; if you don't have one (I didn't in 5.0.2), you can infer the format from files used for other ions, e.g., CA.cif for calcium...)
Begin forwarded message:
From: Garib Murshudov <[EMAIL PROTECTED]>
Unforutunately residue name CD clashes with cytidine and residue name for cadmium is CD1. I should make list of
all elements.
Garib
[EMAIL PROTECTED]
There does seem to be a potential problem there:
There is a "residue" Cd with name Cd in
/y/programs/xtal/ccp4-6.0/ccp4-6.0/lib/data/monomers/c/CD.cif
Cd C 'Cytidine ' DNA 30 19
pesky DNA...
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