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Re: [ccp4bb]: converting Xplor to PDB coordinate files

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On Thu, 10 Feb 2000, Edward Berry wrote:

> Is it the case that PDBSET keyword ELEMENT no longer works after v 3.3?
> If so, how do people convert Xplor/CNSv0.1 files to standard
> pdb format for sfall? My irons are all changing to flourines!
> (OK, it wouldn't kill me to edit manually, but automation is nice)
> ATOM  15780  FE  HEM     1      23.137 134.086  77.947  1.00 38.60      KKKK

i have seen a problem with such programs also confusing calcium with alpha

the PDB standard says: atom names in columns 13-16, with the element name
right-justified in columns 13-14.

the best way i have found of handling metals in PDB-type files between
various programs, some of which do not respect column placement, is to
use 4 letter atom names.  so instead of "FE  " i would use "FE+2" or
"FE+3".  that way programs which read the element correctly from columns
13-14 are happy (such as many CCP4 programs), programs which do not
respect column placement (such as FRODO, CNS and X-plor) will maintain the
column alignment because of the 4 letter names, and those programs which
care about atom type (such as X-plor and CNS) can be placated by writing
your topology files to support the 4 letter names.

this gets me through the various stages of model building and refinement,
and it is only when i am ready to submit coordinates to the PDB that i
would think about chopping the atom name to "FE  ", and i think you'll
find that the auto-dep procedure does that for you.

the only fly in this ointment is that the O'fficial PDB atom names for
some non-peptide groups, such as NAD, use 4 letter atom names for carbon,
oxygen and nitrogen.  this is why the special element columns were added
a few years ago.  bring this up to the folks at PDB and i think the
standard response goes something like 'mmCIF should fix this'.


It is characteristic of thoughtful people that they don't understand some
things that to others are as plain as a pikestaff.  -  A. G. Cairns-Smith
                        David J. Schuller
                        modern man in a post-modern world
                        University of California-Irvine