Hi,
Am 15.07.2010 um 00:58 schrieb Robert Hanson:
> I'm pretty sure you are wrong about the word "must" there. Can you find that
> specific requirement in the second of those references?
You are right I can't find a specific requirement for the atom name. I have to
admit I was annoyed that some program choked on the pdb file written by jmol.
sorry.
Angel found something in the pdb version 2.2, appendix 3 and the internet has a
version for us all: http://structure.usc.edu/pdb/
Alex
> -- (The first is simply a description of what some programs spit out.)
> Nonetheless, it simplifies the code anyway to do this, so the following logic
> is in for Jmol 12.0.RC25:
>
> boolean startInColumn13 =
>
> elementSymbol.length() == 2
> || atomName.length() == 4
> || atomName.firstCharacterIsDigit
>
>
> Bob
>
>
> On Wed, Jul 14, 2010 at 11:14 AM, Alexander Rose
> <[email protected]> wrote:
> Hi,
>
> there is a mistake in the write('PDB') output:
>
> ATOM 1 N LEU A 1 -20.262 -10.014 -0.741 1.00 45.64
> N # original pdb atom line
> ATOM 2 CA LEU A 1 -20.917 -11.314 -0.405 1.00 45.20 C
>
> ATOM 1 N LEU A 1 -20.262 -10.014 -0.741 0.00 45.63
> N # after jmol write('PDB')
> ATOM 2 CA LEU A 1 -20.917 -11.314 -0.405 0.00 45.20 C
>
>
> http://bmerc-www.bu.edu/needle-doc/latest/atom-format.html#pdb-atom-name-anomalies
> http://www.wwpdb.org/documentation/format32/sect9.html#ATOM
>
> the atom name must be located in column 13-16 and column 13 & 14 contain the
> _right justified_ atomic symbol. However, jmol left justies it.
>
>
> Alex
>
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>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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