fixed for Jmol 12.1.11 and 12.0.13 (only a bug for non-PDB files using WRITE
PDB)
Will upload shortly as
http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
On Thu, Sep 9, 2010 at 6:18 PM, Oliver Stueker <
[email protected]> wrote:
> Hi,
>
> I just noticed that Jmol 12.0.11 writes PDB files that don't match to the
> specification.
>
> for example: (col header for orientation)
> 1 2 3 4 5 6 7
> 8
>
> 12345678901234567890123456789012345678901234567890123456789012345678901234567890
> HETATM 1 S1 UNK 1 -7.220 -0.405 0.015 1.00 0.00
> S
> HETATM 2 H2 UNK 1 -8.120 0.570 0.003 1.00 0.00
> H
> HETATM 3 C3 UNK 1 -5.719 0.638 0.001 1.00 0.00
> C
> HETATM 4 H4 UNK 1 -5.731 1.260 -0.885 1.00 0.00
> H
> HETATM 5 H5 UNK 1 -5.730 1.283 0.870 1.00 0.00
> H
> HETATM 6 C6 UNK 1 -4.472 -0.244 0.011 1.00 0.00
> C
> HETATM 7 H7 UNK 1 -4.491 -0.903 -0.852 1.00 0.00
> H
> HETATM 8 H8 UNK 1 -4.490 -0.880 0.892 1.00 0.00
> H
> HETATM 9 C9 UNK 1 -3.183 0.582 -0.000 1.00 0.00
> C
> HETATM 10 H10 UNK 1 -3.173 1.223 -0.880 1.00 0.00
> H
> HETATM 11 H11 UNK 1 -3.172 1.246 0.862 1.00 0.00
> H
>
>
> One can see that the resName already starts in column 17 though in that
> column one should find the altLoc with the
> result that from column 17 everything is shifted 1 character to the left.
>
> I have created the file by loading a GAMESS-US output file (in case that
> makes any difference) and using the command:
> write coords pdb "myFile.pdb" ;
>
> Oliver
>
>
> ------------------------------------------------------------------------------
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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
------------------------------------------------------------------------------
Automate Storage Tiering Simply
Optimize IT performance and efficiency through flexible, powerful,
automated storage tiering capabilities. View this brief to learn how
you can reduce costs and improve performance.
http://p.sf.net/sfu/dell-sfdev2dev
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