Home   Manual

Crystal Library


#1

Part of the Avogadro 1.1 release is significantly improved crystallography support, in large part because of work by David Lonie.

I’d like to make this even clearer by including a crystal library like the fragments library, e.g.:

crystals/
elements/
oxides/
sulfides/
ice.cif

I’m gathering a good number myself, but I’m open to suggestions. I’d like to have fairly good coverage of basic structure types (e.g., NaCl, CsCl, anatase, rutile…) and common materials (e.g., quartz, Al2O3, GaAs, etc.)

It might be nice to throw in “interesting” materials like the YBCO superconductor if there’s a freely-distributable CIF available.

Suggestions?
-Geoff


Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: [email protected]
web: http://hutchison.chem.pitt.edu/


#2

On 08/16/2011 02:20 PM, Geoffrey Hutchison wrote:

Part of the Avogadro 1.1 release is significantly improved crystallography support, in large part because of work by David Lonie.

I’d like to make this even clearer by including a crystal library like the fragments library, e.g.:

crystals/
elements/
oxides/
sulfides/
ice.cif

I’m gathering a good number myself, but I’m open to suggestions. I’d like to have fairly good coverage of basic structure types (e.g., NaCl, CsCl, anatase, rutile…) and common materials (e.g., quartz, Al2O3, GaAs, etc.)

It might be nice to throw in “interesting” materials like the YBCO superconductor if there’s a freely-distributable CIF available.

Suggestions?
-Geoff
How about some common OTC drugs like aspirin, ibuprofen, or similar. I
know these are in the CCSD, but there may be some freely distributable
versions also. I think that Cambridge does (or did) have a small
library of such molecules that were available without license for
educational purposes.
Steve Williams

Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: [email protected]
web: http://hutchison.chem.pitt.edu/


Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
user administration capabilities and model configuration. Take
the hassle out of deploying and managing Subversion and the
tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2


Avogadro-Discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/avogadro-discuss


#3

On Aug 16, 2011, at 3:30 PM, Steve Williams wrote:

How about some common OTC drugs like aspirin, ibuprofen, or similar.

You want the molecules or the crystals?

-Geoff


#4

Both would be nice. The crystals are interesting in some cases due to
intermolecular forces. I had a student maybe 10 years or do an undergraduate
pchem project (probably using dgauss) on the structure of aspirin… He could
not get good agreement on the molecular structure without including the H-bonded
dimer as present in the crystal.

Steve
----- Original Message -----
From: Geoff Hutchison [email protected]
Date: Tuesday, August 16, 2011 6:04 pm
Subject: Re: [Avogadro-Discuss] Crystal Library
To: [email protected]

On Aug 16, 2011, at 3:30 PM, Steve Williams wrote:

How about some common OTC drugs like aspirin, ibuprofen, or similar.

You want the molecules or the crystals?

-Geoff



Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
user administration capabilities and model configuration. Take
the hassle out of deploying and managing Subversion and the
tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2


Avogadro-Discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/avogadro-discuss


#5

Both would be nice. The crystals are interesting in some cases due to
intermolecular forces.

If you’re willing to make up a list (and/or find some files) I’d be glad to include both. There’s a new version of the chemical-structures project which we use for fragments, so those will get a boost for 1.1 as well.

Thanks and best regards,
-Geoff


#6

I have an email query about this pending with the support people at the
CSD. I’ll share what I learn.
Steve

On 08/17/2011 10:32 AM, Geoffrey Hutchison wrote:

Both would be nice. The crystals are interesting in some cases due to
intermolecular forces.
If you’re willing to make up a list (and/or find some files) I’d be glad to include both. There’s a new version of the chemical-structures project which we use for fragments, so those will get a boost for 1.1 as well.

Thanks and best regards,
-Geoff

Get a FREE DOWNLOAD! and learn more about uberSVN rich system,
user administration capabilities and model configuration. Take
the hassle out of deploying and managing Subversion and the
tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2


Avogadro-Discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/avogadro-discuss


#7

On Aug 17, 2011, at 11:11 AM, Steve Williams wrote:

I have an email query about this pending with the support people at the
CSD.

I suspect their answer might be “no.” But there’s always http://www.crystallography.net/ and CrystalEye (http://wwmm.ch.cam.ac.uk/crystaleye/) which should have many of these crystals.

Cheers,
-Geoff


#8

Hi! I have been trying to tile the different structures of Ice recently and found the crystal library. I was wondering where these structures were taken from? In other words, is there some source that they were taken from or did someone create the cif file? I am wondering because it appears that some of the unit cells are not correct. This is more apparent when you tile them. More specifically, Ice II does not appear to have the correct structure and Ice VI does not even have oxygen’s present.


#9

All the crystal structures (including ice) are straight from the Crystallography Open Database:
http://crystallography.net

If you have particular reports, please let me know.