Hi,
I have also found one glitch in the PDB output code:
If I load a xyz-file with e.g. 200 Gold-atoms into Jmol 12.0.RC22 and do:
select * ;
write COORDS PDB "gold.pdb" ;
I'll get the following:
...
HETATM 96 Au96 UNK 1 23.440 3.383 7.612 1.00 0.00 Au
HETATM 97 Au97 UNK 1 1.465 5.921 7.612 1.00 0.00 Au
HETATM 98 Au98 UNK 1 4.395 5.921 7.612 1.00 0.00 Au
HETATM 99 Au99 UNK 1 7.325 5.921 7.612 1.00 0.00 Au
HETATM 100 Au100 UNK 1 10.255 5.921 7.612 1.00 0.00
Au
HETATM 101 Au101 UNK 1 13.185 5.921 7.612 1.00 0.00
Au
HETATM 102 Au102 UNK 1 16.115 5.921 7.612 1.00 0.00
Au
...
where all columns after the atom name are shifted by one character as
soon as it runs into three-digit atom-numbers.
Oliver
On Wed, Jul 14, 2010 at 10:14, 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
--
Oliver Stueker
Post-doctoral Fellow, Theory and Modeling Group
NRC-NINT / University of Alberta, Canada
------------------------------------------------------------------------------
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
