I'm pretty sure you are wrong about the word "must" there. Can you find that
specific requirement in the second of those references? -- (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
>
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Sprint
> What will you do first with EVO, the first 4G phone?
> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
--
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
------------------------------------------------------------------------------
This SF.net email is sponsored by Sprint
What will you do first with EVO, the first 4G phone?
Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
