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
------------------------------------------------------------------------------
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
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