Re: [ccp4bb] Strange diffraction images
Beware twinning tests with pseudo translation! Intensity stats are distorted.. What does SFCHECK suggest? It pre-selects data for testing.. Eeanor Green, Todd wrote: I have a case that is similar to this, or at least visually similar by diffraction pattern(ie. strong/weak intensities). I think my situation is due to a pseudo-translation. I say this my defining of pseudo translation as basically something other than pure translation(ie. some translation and some degree (albeit slight) of rotation). In my case, the crystals (I THINK!) are P23(and i guess you would say pseudo I23). There are assemblies at 0,0,0 and 0.5,0.5,0.5. The translated assembly at 0.5,0.5,0.5 is slightly misaligned(by a small rotation) with the assembly at the origin but near to perfect. If it were perfect it'd be I23. But since it is not, it is reduced to the Primitive cell. When indexing, if you don't include the more diffuse, lower intensity spots, you will lock on the I-cell. If you include them then you get right cell, as you would suspect. I included pictures. These are 2 regions of a single diffraction pattern with spot predictions for the indicated Bravais lattice. You can easily see the sharper more dense spots versus the more diffuse less intense ones. In the second shot, you can see that the orthorhombic cell fits much better than either of the cubic cells but that's another issue which is related to my questions last week. So to muddy the water a little, my case could be pseudo-cubic altogether. I'm still working on all of that. As a side note, Xtriage doesn't think things are twinned as was suggested for one some of the other diffraction patterns discussed earlier today. -Todd -Original Message- From: CCP4 bulletin board on behalf of Jacob Keller Sent: Mon 8/27/2007 10:44 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Strange diffraction images What a beautiful and interesting diffraction pattern! To me, it seems that there is a blurred set of spots with different cell dimensions, although nearly the same, underlying the ordered diffraction pattern. A possible interpretation occurred to me, that the ordered part of the crystal is supported by a less-ordered lattice of slightly different dimensions, which, because the crystal is a like a layer-cake of 2-d crystals, need not be commensurable in the short range with the ordered lattice. The nicely-ordered cake part of the crystal you solved, but the frosting between is of a different, less ordered nature, giving rise to the diffuse pattern which has slightly different lattice spacing. I would have to see more images to know whether this apparent lattice-spacing phenomenon is consistent, but it at least seems that way to me from the images you put on the web. I would shudder to think of indexing it, however. All the best, Jacob Keller ps I wonder whether a crystal was ever solved which had two interpenetrating, non-commensurable lattices in it. That would be pretty fantastic. ==Original message text=== On Mon, 27 Aug 2007 5:57:45 am CDT Mark J. van Raaij wrote: In general, I think we should be careful about too strong statements, while in general structures with high solvent diffract to low-res, there are a few examples where they diffract to high res. Obviously, high solvent content means fewer crystal contacts, but if these few are very stable? Similarly, there are probably a few structures with a high percentage of Ramachandran outliers which are real and similarly for all other structural quality indicators. However, combinations of various of these probably do not exist and in any case, every unusual feature like this should be described and an attempt made to explain/analyse it, which in the case of the Nature paper that started this thread was apparently not done, apart from the rebuttal later (and perhaps in unpublished replies to the referees?). With regards to our structures 1H6W (1.9A) and 1OCY (1.5A), rather than faith, I think the structure is held together by a real mechanism, which however I can't explain. Like in the structure Axel Brunger mentioned, there is appreciable diffuse scatter, which imo deserves to be analysed by someone expert in the matter (to whom, or anyone else, I would gladly supply the images which I should still have on a tape or CD in the cupboard...). For low-res version of one image see http://web.usc.es/~vanraaij/diff45kd.pngand http://web.usc.es/%7Evanraaij/diff45kd.pngand http://web.usc.es/~vanraaij/diff45kdzoom.pngtwo http://web.usc.es/%7Evanraaij/diff45kdzoom.pngtwo possibilities I have been thinking about: 1. only a few of the tails are ordered, rather like a stack of identical tables in which four legs hold the table surfaces stably together, but the few ordered tails/legs do not contribute much to the diffraction. This raises the question why some tails should be stiff and others not; perhaps traces of a metal or other
Re: [ccp4bb] Strange diffraction images
There is also one case of a protein structure that I am aware of, where a
similar problem has been tackled (the phenomenon is also known as
one-dimensional disorder, according to A.J.C. Wilson - yes, the one how
invented the plot).
Check: Trame, CB mcKay, DB (2001). Acta Cryst. D57, 1079-1090.
Boaz
- Original Message -
From: George M. Sheldrick [EMAIL PROTECTED]
Date: Monday, August 27, 2007 18:49
Subject: Re: [ccp4bb] Strange diffraction images
To: CCP4BB@JISCMAIL.AC.UK
Some small molecule crystallographers have specialized in
solving and
refining structures that, exactly as you describe it, consist of
two (or
more) interpenetrating, non-commensurable lattices. The usual
approach is
to decribe the crystal in up to six dimensional space. The
programs SAINT
and EVALCCD are able to integrate such diffraction patterns and
SADABS is able to scale them. However the case in point is
probably
commensurate.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
On Mon, 27 Aug 2007, Jacob Keller wrote:
What a beautiful and interesting diffraction pattern!
To me, it seems that there is a blurred set of spots with
different cell dimensions, although
nearly the same, underlying the ordered diffraction pattern. A
possible interpretation occurred to
me, that the ordered part of the crystal is supported by a
less-ordered lattice of slightly
different dimensions, which, because the crystal is a like a
layer-cake of 2-d crystals, need not
be commensurable in the short range with the ordered lattice.
The nicely-ordered cake part of the
crystal you solved, but the frosting between is of a
different, less ordered nature, giving rise
to the diffuse pattern which has slightly different lattice
spacing. I would have to see more
images to know whether this apparent lattice-spacing
phenomenon is consistent, but it at least
seems that way to me from the images you put on the web. I
would shudder to think of indexing it,
however.
All the best,
Jacob Keller
ps I wonder whether a crystal was ever solved which had two
interpenetrating, non-commensurable
lattices in it. That would be pretty fantastic.
Jacob,
Some small molecule crystallographers have specialized in
solving and
refining structures that, exactly as you describe it, consist of two
interpenetrating, non-commensurate lattices. The usual approach is
to index the diffraction pattern in multiple dimensional space
('superspace'). The programs SAINT and EVALCCD are able to
integrate
diffraction patterns in up to six dimensions, SADABS is able to
scale
them and the refinement is almost always performed with
Petricek's
program JANA2000:
http://www-xray.fzu.cz/jana/Jana2000/jana.html
However the case in point is probably commensurate.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
Phone: 972-8-647-2220 ; Fax: 646-1710
Skype: boaz.shaanan‎
Re: [ccp4bb] Strange diffraction images
Some small molecule crystallographers have specialized in solving and
refining structures that, exactly as you describe it, consist of two (or
more) interpenetrating, non-commensurable lattices. The usual approach is
to decribe the crystal in up to six dimensional space. The programs SAINT
and EVALCCD are able to integrate such diffraction patterns and
SADABS is able to scale them. However the case in point is probably
commensurate.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
On Mon, 27 Aug 2007, Jacob Keller wrote:
What a beautiful and interesting diffraction pattern!
To me, it seems that there is a blurred set of spots with different cell
dimensions, although
nearly the same, underlying the ordered diffraction pattern. A possible
interpretation occurred to
me, that the ordered part of the crystal is supported by a less-ordered
lattice of slightly
different dimensions, which, because the crystal is a like a layer-cake of
2-d crystals, need not
be commensurable in the short range with the ordered lattice. The
nicely-ordered cake part of the
crystal you solved, but the frosting between is of a different, less
ordered nature, giving rise
to the diffuse pattern which has slightly different lattice spacing. I would
have to see more
images to know whether this apparent lattice-spacing phenomenon is
consistent, but it at least
seems that way to me from the images you put on the web. I would shudder to
think of indexing it,
however.
All the best,
Jacob Keller
ps I wonder whether a crystal was ever solved which had two interpenetrating,
non-commensurable
lattices in it. That would be pretty fantastic.
Jacob,
Some small molecule crystallographers have specialized in solving and
refining structures that, exactly as you describe it, consist of two
interpenetrating, non-commensurate lattices. The usual approach is
to index the diffraction pattern in multiple dimensional space
('superspace'). The programs SAINT and EVALCCD are able to integrate
diffraction patterns in up to six dimensions, SADABS is able to scale
them and the refinement is almost always performed with Petricek's
program JANA2000:
http://www-xray.fzu.cz/jana/Jana2000/jana.html
However the case in point is probably commensurate.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
Re: [ccp4bb] Strange diffraction images
I am still eagerly awaiting a biomacromolecular quasicrystal with a five-fold
symmetric diffraction
pattern. It seems that this is entirely possible, if one gets roughly
Penrose-tile shaped oligomers
somehow. But wow, how would you solve that thing? I guess one would have to
modify software from
the small molecule or matsci folks.
Jacob
==Original message text===
On Mon, 27 Aug 2007 11:19:15 am CDT George M. Sheldrick wrote:
Some small molecule crystallographers have specialized in solving and
refining structures that, exactly as you describe it, consist of two (or
more) interpenetrating, non-commensurable lattices. The usual approach is
to decribe the crystal in up to six dimensional space. The programs SAINT
and EVALCCD are able to integrate such diffraction patterns and
SADABS is able to scale them. However the case in point is probably
commensurate.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
On Mon, 27 Aug 2007, Jacob Keller wrote:
What a beautiful and interesting diffraction pattern!
To me, it seems that there is a blurred set of spots with different cell
dimensions, although
nearly the same, underlying the ordered diffraction pattern. A possible
interpretation occurred to
me, that the ordered part of the crystal is supported by a less-ordered
lattice of slightly
different dimensions, which, because the crystal is a like a layer-cake of
2-d crystals, need not
be commensurable in the short range with the ordered lattice. The
nicely-ordered cake part of the
crystal you solved, but the frosting between is of a different, less
ordered nature, giving rise
to the diffuse pattern which has slightly different lattice spacing. I would
have to see more
images to know whether this apparent lattice-spacing phenomenon is
consistent, but it at least
seems that way to me from the images you put on the web. I would shudder to
think of indexing it,
however.
All the best,
Jacob Keller
ps I wonder whether a crystal was ever solved which had two interpenetrating,
non-commensurable
lattices in it. That would be pretty fantastic.
Jacob,
Some small molecule crystallographers have specialized in solving and
refining structures that, exactly as you describe it, consist of two
interpenetrating, non-commensurate lattices. The usual approach is
to index the diffraction pattern in multiple dimensional space
('superspace'). The programs SAINT and EVALCCD are able to integrate
diffraction patterns in up to six dimensions, SADABS is able to scale
them and the refinement is almost always performed with Petricek's
program JANA2000:
http://www-xray.fzu.cz/jana/Jana2000/jana.html
However the case in point is probably commensurate.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
===End of original message text===
***
Jacob Keller
Northwestern University
6541 N. Francisco #3
Chicago IL 60645
(847)467-4049
[EMAIL PROTECTED]
***
Re: [ccp4bb] Strange diffraction images - PS
Apologies, part of my previous message was missing and part
appeared twice. Here is another try:
Jacob,
Some small molecule crystallographers have specialized in solving and
refining structures that, exactly as you describe it, consist of two
interpenetrating, non-commensurate lattices. The usual approach is
to index the diffraction pattern in multiple dimensional space
('superspace'). The programs SAINT and EVALCCD are able to integrate
diffraction patterns in up to six dimensions, SADABS is able to scale
them and the refinement is almost always performed with Petricek's
program JANA2000:
http://www-xray.fzu.cz/jana/Jana2000/jana.html
However the case in point is probably commensurate.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
Re: [ccp4bb] Strange diffraction images
Very dumb question perhaps:
If there were two interpenetrating lattices of slightly different cell
dimensions, would we not
expect that the indexing program would leave out a lot of the spots as
unpredicted or uncovered?
Could someone clarify with respect to the diffraction pattern that has just
been posted (diff45..png)?
Raji
-Included Message--
Some small molecule crystallographers have specialized in solving and
refining structures that, exactly as you describe it, consist of two (or
more) interpenetrating, non-commensurable lattices. The usual approach is
to decribe the crystal in up to six dimensional space. The programs SAINT
and EVALCCD are able to integrate such diffraction patterns and
SADABS is able to scale them. However the case in point is probably
commensurate.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
On Mon, 27 Aug 2007, Jacob Keller wrote:
What a beautiful and interesting diffraction pattern!
To me, it seems that there is a blurred set of spots with different cell
dimensions, although
nearly the same, underlying the ordered diffraction pattern. A possible
interpretation occurred to
me, that the ordered part of the crystal is supported by a less-ordered
lattice of slightly
different dimensions, which, because the crystal is a like a layer-cake of
2-d crystals, need not
be commensurable in the short range with the ordered lattice. The
nicely-ordered cake part of the
crystal you solved, but the frosting between is of a different, less
ordered nature, giving rise
to the diffuse pattern which has slightly different lattice spacing. I would
have to see more
images to know whether this apparent lattice-spacing phenomenon is
consistent, but it at least
seems that way to me from the images you put on the web. I would shudder to
think of indexing it,
however.
All the best,
Jacob Keller
ps I wonder whether a crystal was ever solved which had two
interpenetrating, non-commensurable
lattices in it. That would be pretty fantastic.
Jacob,
Some small molecule crystallographers have specialized in solving and
refining structures that, exactly as you describe it, consist of two
interpenetrating, non-commensurate lattices. The usual approach is
to index the diffraction pattern in multiple dimensional space
('superspace'). The programs SAINT and EVALCCD are able to integrate
diffraction patterns in up to six dimensions, SADABS is able to scale
them and the refinement is almost always performed with Petricek's
program JANA2000:
http://www-xray.fzu.cz/jana/Jana2000/jana.html
However the case in point is probably commensurate.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
-End of Included Message--
Re: [ccp4bb] Strange diffraction images
The left-out spots would be the diffuse spots, which I assume were not
indexed/integrated. The
sharp spots were presumably used to solve the structure.
JPK
==Original message text===
On Mon, 27 Aug 2007 11:36:08 am CDT Raji Edayathumangalam wrote:
Very dumb question perhaps:
If there were two interpenetrating lattices of slightly different cell
dimensions, would we not
expect that the indexing program would leave out a lot of the spots as
unpredicted or uncovered?
Could someone clarify with respect to the diffraction pattern that has just
been posted (diff45..png)?
Raji
-Included Message--
Some small molecule crystallographers have specialized in solving and
refining structures that, exactly as you describe it, consist of two (or
more) interpenetrating, non-commensurable lattices. The usual approach is
to decribe the crystal in up to six dimensional space. The programs SAINT
and EVALCCD are able to integrate such diffraction patterns and
SADABS is able to scale them. However the case in point is probably
commensurate.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
On Mon, 27 Aug 2007, Jacob Keller wrote:
What a beautiful and interesting diffraction pattern!
To me, it seems that there is a blurred set of spots with different cell
dimensions, although
nearly the same, underlying the ordered diffraction pattern. A possible
interpretation occurred to
me, that the ordered part of the crystal is supported by a less-ordered
lattice of slightly
different dimensions, which, because the crystal is a like a layer-cake of
2-d crystals, need not
be commensurable in the short range with the ordered lattice. The
nicely-ordered cake part of the
crystal you solved, but the frosting between is of a different, less
ordered nature, giving rise
to the diffuse pattern which has slightly different lattice spacing. I would
have to see more
images to know whether this apparent lattice-spacing phenomenon is
consistent, but it at least
seems that way to me from the images you put on the web. I would shudder to
think of indexing it,
however.
All the best,
Jacob Keller
ps I wonder whether a crystal was ever solved which had two
interpenetrating, non-commensurable
lattices in it. That would be pretty fantastic.
Jacob,
Some small molecule crystallographers have specialized in solving and
refining structures that, exactly as you describe it, consist of two
interpenetrating, non-commensurate lattices. The usual approach is
to index the diffraction pattern in multiple dimensional space
('superspace'). The programs SAINT and EVALCCD are able to integrate
diffraction patterns in up to six dimensions, SADABS is able to scale
them and the refinement is almost always performed with Petricek's
program JANA2000:
http://www-xray.fzu.cz/jana/Jana2000/jana.html
However the case in point is probably commensurate.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
-End of Included Message--
===End of original message text===
***
Jacob Keller
Northwestern University
6541 N. Francisco #3
Chicago IL 60645
(847)467-4049
[EMAIL PROTECTED]
***
Re: [ccp4bb] Strange diffraction images
As a side note, Xtriage doesn't think things are twinned as was suggested for one some of the other diffraction patterns discussed earlier today. Hi Todd, Detection of twinning in the presence of pseudo translations / and or NCS parallel to the twin law is difficult and using model based techniques (RvsR statistic) could be usefull. Furthermore, I would like to point to Acta D 63, 926-930 with some pointers to literature regaring other 'weird' pathologies. HTH Peter
Re: [ccp4bb] Strange diffraction images
I believe Wayne Hendrickson's lab has had such a case with a 10-fold
symmetric mollusc hemocyanin crystal. This must have been in the early
90's and to my knowlwedge they were never able to solve the structure
even though it diffracted beyond 2 Anstrom.
I'm not sure if this work has been published but you can check the paper
describing a single domain of this protein complex or contact one of its
authors.
Bart
J Mol Biol. 1998 May 15;278(4):855-70.
Crystal structure of a functional unit from Octopus hemocyanin.
Cuff ME, Miller KI, van Holde KE, Hendrickson WA.
Jacob Keller wrote:
I am still eagerly awaiting a biomacromolecular quasicrystal with a five-fold symmetric diffraction
pattern. It seems that this is entirely possible, if one gets roughly Penrose-tile shaped oligomers
somehow. But wow, how would you solve that thing? I guess one would have to modify software from
the small molecule or matsci folks.
Jacob
==Original message text===
On Mon, 27 Aug 2007 11:19:15 am CDT George M. Sheldrick wrote:
Some small molecule crystallographers have specialized in solving and
refining structures that, exactly as you describe it, consist of two (or
more) interpenetrating, non-commensurable lattices. The usual approach is
to decribe the crystal in up to six dimensional space. The programs SAINT
and EVALCCD are able to integrate such diffraction patterns and
SADABS is able to scale them. However the case in point is probably
commensurate.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
On Mon, 27 Aug 2007, Jacob Keller wrote:
What a beautiful and interesting diffraction pattern!
To me, it seems that there is a blurred set of spots with different cell
dimensions, although
nearly the same, underlying the ordered diffraction pattern. A possible
interpretation occurred to
me, that the ordered part of the crystal is supported by a less-ordered lattice
of slightly
different dimensions, which, because the crystal is a like a layer-cake of 2-d
crystals, need not
be commensurable in the short range with the ordered lattice. The nicely-ordered cake part of the
crystal you solved, but the frosting between is of a different, less ordered nature, giving rise
to the diffuse pattern which has slightly different lattice spacing. I would
have to see more
images to know whether this apparent lattice-spacing phenomenon is consistent,
but it at least
seems that way to me from the images you put on the web. I would shudder to
think of indexing it,
however.
All the best,
Jacob Keller
ps I wonder whether a crystal was ever solved which had two interpenetrating,
non-commensurable
lattices in it. That would be pretty fantastic.
Jacob,
Some small molecule crystallographers have specialized in solving and
refining structures that, exactly as you describe it, consist of two
interpenetrating, non-commensurate lattices. The usual approach is
to index the diffraction pattern in multiple dimensional space
('superspace'). The programs SAINT and EVALCCD are able to integrate
diffraction patterns in up to six dimensions, SADABS is able to scale
them and the refinement is almost always performed with Petricek's
program JANA2000:
http://www-xray.fzu.cz/jana/Jana2000/jana.html
However the case in point is probably commensurate.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
===End of original message text===
***
Jacob Keller
Northwestern University
6541 N. Francisco #3
Chicago IL 60645
(847)467-4049
[EMAIL PROTECTED]
***
--
==
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Dept. of Medical Microbiology Immunology
University of Alberta
1-15 Medical Sciences Building
Edmonton, Alberta
Canada, T6G 2H7
phone: 1-780-492-0042
fax:1-780-492-7521
==
Re: [ccp4bb] Strange diffraction images
I think if there had been a case of a protein quasicrystal, it would have made the cover of Nature Here are some papers about quasicrystals: 1: Proc Natl Acad Sci U S A. 1996 Dec 10;93(25):14267-70. New perspectives on forbidden symmetries, quasicrystals, and Penrose tilings. Steinhardt PJ. Quasicrystals are solids with quasiperiodic atomic structures and symmetries forbidden to ordinary periodic crystals-e.g., 5-fold symmetry axes. A powerful model for understanding their structure and properties has been the two-dimensional Penrose tiling. Recently discovered properties of Penrose tilings suggest a simple picture of the structure of quasicrystals and shed new light on why they form. The results show that quasicrystals can be constructed from a single repeating cluster of atoms and that the rigid matching rules of Penrose tilings can be replaced by more physically plausible cluster energetics. The new concepts make the conditions for forming quasicrystals appear to be closely related to the conditions for forming periodic crystals. 2: Proc Natl Acad Sci U S A. 1996 Dec 10;93(25):14271-8. Five-fold symmetry in crystalline quasicrystal lattices. Caspar DL, Fontano E. Institute of Molecular Biophysics, Florida State University, Tallahassee, 32306-3015, USA. [EMAIL PROTECTED] To demonstrate that crystallographic methods can be applied to index and interpret diffraction patterns from well-ordered quasicrystals that display non-crystallographic 5-fold symmetry, we have characterized the properties of a series of periodic two-dimensional lattices built from pentagons, called Fibonacci pentilings, which resemble aperiodic Penrose tilings. The computed diffraction patterns from periodic pentilings with moderate size unit cells show decagonal symmetry and are virtually indistinguishable from that of the infinite aperiodic pentiling. We identify the vertices and centers of the pentagons forming the pentiling with the positions of transition metal atoms projected on the plane perpendicular to the decagonal axis of quasicrystals whose structure is related to crystalline eta phase alloys. The characteristic length scale of the pentiling lattices, evident from the Patterson (autocorrelation) function, is approximately tau 2 times the pentagon edge length, where tau is the golden ratio. Within this distance there are a finite number of local atomic motifs whose structure can be crystallographically refined against the experimentally measured diffraction data. Jacob ==Original message text=== On Mon, 27 Aug 2007 2:02:36 pm CDT Bart Hazes wrote: I believe Wayne Hendrickson's lab has had such a case with a 10-fold symmetric mollusc hemocyanin crystal. This must have been in the early 90's and to my knowlwedge they were never able to solve the structure even though it diffracted beyond 2 Anstrom. I'm not sure if this work has been published but you can check the paper describing a single domain of this protein complex or contact one of its authors. Bart J Mol Biol. 1998 May 15;278(4):855-70. Crystal structure of a functional unit from Octopus hemocyanin. Cuff ME, Miller KI, van Holde KE, Hendrickson WA. Jacob Keller wrote: I am still eagerly awaiting a biomacromolecular quasicrystal with a five-fold symmetric diffraction pattern. It seems that this is entirely possible, if one gets roughly Penrose-tile shaped oligomers somehow. But wow, how would you solve that thing? I guess one would have to modify software from the small molecule or matsci folks. Jacob ==Original message text=== On Mon, 27 Aug 2007 11:19:15 am CDT George M. Sheldrick wrote: Some small molecule crystallographers have specialized in solving and refining structures that, exactly as you describe it, consist of two (or more) interpenetrating, non-commensurable lattices. The usual approach is to decribe the crystal in up to six dimensional space. The programs SAINT and EVALCCD are able to integrate such diffraction patterns and SADABS is able to scale them. However the case in point is probably commensurate. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Mon, 27 Aug 2007, Jacob Keller wrote: What a beautiful and interesting diffraction pattern! To me, it seems that there is a blurred set of spots with different cell dimensions, although nearly the same, underlying the ordered diffraction pattern. A possible interpretation occurred to me, that the ordered part of the crystal is supported by a less-ordered lattice of slightly different dimensions, which, because the crystal is a like a layer-cake of 2-d crystals, need not be commensurable in the short range with the ordered lattice. The nicely-ordered cake part of the crystal you
