PDB dump format

ilya ily... at gmail.com
Sat Oct 11 22:01:09 UTC 2008

Hello all!

I noticed that when cp2k dumps pdb it prints name field of ATOM record
(cols 13-16) right aligned.
Many viewers don't like it because the format desc says
Notes on atom naming
The atom name is a four-character field that may be subdivided into
atomic symbol (A2), "remoteness indicator" (A1), and "branch
designator" (A1) subfields, as detailed below. The atom name may be
subdivided into the following subfields:

Name                 Format 	Description

atomic symbol 	         A2 	Right-justified atomic symbol, e.g. " C".

remoteness indicator 	A1 	Greek letter distance abbreviation. In order
of increasing distance, these are "A" for alpha, "B" for beta, "G" for
gamma, "D" for delta, "E" for epsilon, "Z" for zeta, and "H" for eta.

branch designator 	A1 	digit designating the branch direction; left
blank if the sidechain is unbranched.

OK... may be it's stupid viewers (accelrys!!!) because they don't know
about symbol field, but it would be nice to correct this for fast
viewing (and make it more std complaint).

The easy solution it just print everything left aligned (although it's
not strict standard complaint, most viewers understand it)
The second solution is to parse the name (in case input specified not
in pdb) and print according to the std, but maybe it's complex and



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