I checked, and here is the code for that. Jmol is ignoring the matrices and
just using the Jones-Faithful operators:
private void remark290() throws Exception {
while (readHeader(true) != null && line.startsWith("REMARK 290")) {
if (line.indexOf("NNNMMM OPERATOR") >= 0) {
while (readHeader(true) != null) {
String[] tokens = getTokens();
if (tokens.length < 4)
break;
if (doApplySymmetry || isbiomol)
setSymmetryOperator(tokens[3]);
}
}
}
}
On Thu, Nov 27, 2014 at 1:41 PM, Robert Hanson <[email protected]> wrote:
> REMARK
> 290
> REMARK 290 CRYSTALLOGRAPHIC
> SYMMETRY
> REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21
> 1
> REMARK
> 290
> REMARK 290 SYMOP
> SYMMETRY
> REMARK 290 NNNMMM
> OPERATOR
> REMARK 290 1555
> X,Y,Z
> REMARK 290 2555
> -X,Y+1/2,-Z
> REMARK
> 290
> REMARK 290 WHERE NNN -> OPERATOR
> NUMBER
> REMARK 290 MMM -> TRANSLATION
> VECTOR
> REMARK
> 290
> REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
> TRANSFORMATIONS
> REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE
> ATOM/HETATM
> REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE
> CRYSTALLOGRAPHICALLY
> REMARK 290 RELATED
> MOLECULES.
> 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
> REMARK
> 290
> REMARK 290 REMARK:
> NULL
> ..
> REMARK
> 350
> ...
> REMARK
> 500
> ...
> CRYST1 40.960 18.650 22.520 90.00 90.77 90.00 P 1 21 1
> 2
> 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 0.024414 0.000000 0.000328
> 0.00000
> SCALE2 0.000000 0.053619 0.000000
> 0.00000
> SCALE3 0.000000 0.000000 0.044409
> 0.00000
>
>
> On Thu, Nov 27, 2014 at 11:25 AM, Hans Horn <[email protected]> wrote:
>
>> Thx Bob!
>>
>> Where should these remarks go in the PDB file?
>>
>> H.
>>
>>
>> On 11/27/2014 9:20 AM, Robert Hanson wrote:
>>
>> 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
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
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>> with Interactivity, Sharing, Native Excel Exports, App Integration & more
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>>
>>
>> _______________________________________________
>> Jmol-users mailing
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>>
>>
>>
>>
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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
>
>
--
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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