You are missing the symmetry records. Jmol does not process raw space group
names because of all the possible settings.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000
0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000
0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000
0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000
0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000
9.32500
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
On Thu, Nov 27, 2014 at 10:46 AM, Hans Horn <[email protected]> wrote:
> Folks,
>
> I have the following pdb file for an MgCl2 crystal:
>
> HEADER 09-NOV-11
> TITLE Structure 1
> REVDAT 1 09-NOV-11 0
> REMARK 4
> REMARK 4 COMPLIES WITH FORMAT V. 2.1, 25-OCT-1996
> HET UNK A 1 2
> FORMUL 1 UNK Mg3 Cl6
> CRYST1 3.596 3.596 17.590 90.00 90.00 120.00 R -3 m -1
> ORIGX1 1.000000 0.000000 0.000000 0.00000
> ORIGX2 0.000000 1.000000 0.000000 0.00000
> ORIGX3 0.000000 0.000000 1.000000 0.00000
> SCALE1 0.278087 0.160553 -0.000000 0.00000
> SCALE2 0.000000 0.321107 -0.000000 0.00000
> SCALE3 0.000000 0.000000 0.056850 0.00000
> HETATM 1 Mg1 UNK 1 0.000 0.000 0.000 1.00
> 0.00 Mg2+
> HETATM 2 Cl1 UNK 2 0.000 0.000 4.535 1.00
> 0.00 Cl1-
> END
>
> which claim to have space group 'R -3 m'.
>
> When I load it into jmol,
> e.g. via load <pdb name> {1 1 1} packed
>
> jmol insists that we have 'P 1 [P 1] #1' instead of 'R -3 m' symmetry.
>
> Somehow the CRYST1 record seems to be parsed incorrectly.
> For all I can tell the pdb file is formatted correctly.
>
> Thx.,
> Hans
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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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