Re: [ccp4bb]: cannot calculate structure factors

["David J. Schuller" <djs63@cornell.edu>]

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On Fri, 14 Feb 2003, Richard Baxter wrote:

> I have received a veritable flood of replies suggesting that my PDB file
> contains misaligned atom names.
> So my final question is about the other atom names in my PDB file that
> might give me trouble, the iron ions FE, and the four porphyrin nitrogens
> NA, NB, NC and ND. Currently these are all left justified to column 14 of
> the PDB record. Will this be correct to identify them as iron rather than
> flourine, and nitrogens rather than sodium, niobium and neodynium?

If you would actually go to the RCSB site and read the PDB file spec,

you would find that atom names should contain the element abbreviation 
right-justified in columns 13-14.  So elements with one letter names (C, 
O, N, S) should start in column 14.  Elements with two letter names (Mg, 
Fe, Br, Ca) should start in column 13.

You will find some exceptions to this where the PDB does not follow their 
own guidelines, such as hydrogen atoms and NAD cofactors.  This is not my 
fault.

Cheers,

=======================================================================
"Reductionism is one of those words that makes me want
    to reach for my revolver." - Richard Dawkins 
=======================================================================
                        David J. Schuller
                        modern man in a post-modern world
                        MacCHESS, Cornell University
                        djs63@cornell.edu