Hans,
OK, I got it. Very simple fix. See
http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
By the way, Jmol is guessing at the origin and setting of that unit cell.
Jmol can read the Jones-Faithful data in the PDB record 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
That's guaranteed to work.
Bob Hanson
On Tue, Nov 29, 2011 at 9:49 PM, Robert Hanson <[email protected]> wrote:
> Oh, I guess I did not actually try it with your file. I didn't realize it
> was a complete model!
>
> Ah, that's a problem! Well, I can tell you why that is. Jmol presumes that
> a PDB file is a protein and saves hugely on processing by assuming that
> there are no special positions. Therefore it does not check to see if atoms
> are on top of each other after symmetry transformations. But in your case
> this isn't really a PDB file, it's an inorganic crystal file.
>
> You sure you don't want to use CIF format -- like everyone else ;) ?
>
> I have an idea, though. Let me think about this....
>
> Bob
>
>
>
>
> On Tue, Nov 29, 2011 at 4:59 PM, Hans Horn <[email protected]> wrote:
>
>> Robert,
>>
>> neat!
>>
>> when I do that with the pdb file posted, I see 10 atoms in the unit cell.
>> However, when I write it out (e.g. as xyz) I get 72 atoms.
>> Why's that?
>>
>> Is there a way to save the unit cell as 3*3 matrix?
>>
>> thx,
>> H.
>> On 11/29/2011 1:45 PM, Robert Hanson wrote:
>>
>> sure.
>>
>> load xxx.pdb {1 1 1}
>>
>> gives you a full unit cell.
>>
>> unitcell on
>>
>> gets you the unit cell
>>
>> axes on
>>
>> gets you a,b,c axes for the unit cell.
>>
>>
>>
>> On Tue, Nov 29, 2011 at 3:03 PM, Hans Horn <[email protected]> wrote:
>>
>>> Folks,
>>>
>>> I have a pdb file :
>>>
>>> #############
>>> 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
>>>
>>> ############
>>>
>>> I'd like to see the unit cell displayed, as well as the atoms in the
>>> unit cell generated and displayed.
>>> Is this possible using jmol?
>>>
>>> Thx.,
>>> H.
>>>
>>>
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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
>>
>>
>> ------------------------------------------------------------------------------
>> All the data continuously generated in your IT infrastructure
>> contains a definitive record of customers, application performance,
>> security threats, fraudulent activity, and more. Splunk takes this
>> data and makes sense of it. IT sense. And common
>> sense.http://p.sf.net/sfu/splunk-novd2d
>>
>>
>>
>> _______________________________________________
>> Jmol-users mailing
>> [email protected]https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> All the data continuously generated in your IT infrastructure
>> contains a definitive record of customers, application performance,
>> security threats, fraudulent activity, and more. Splunk takes this
>> data and makes sense of it. IT sense. And common sense.
>> http://p.sf.net/sfu/splunk-novd2d
>> _______________________________________________
>> 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
>
--
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
------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure
contains a definitive record of customers, application performance,
security threats, fraudulent activity, and more. Splunk takes this
data and makes sense of it. IT sense. And common sense.
http://p.sf.net/sfu/splunk-novd2d
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