From owner-chemistry@ccl.net Sat Mar 9 16:42:00 2013 From: "Radoslaw Kaminski rkaminski.rk_+_gmail.com" To: CCL Subject: CCL: Standardization of a crystal structure Message-Id: <-48395-130309135541-27340-ZkeF3V/qE0wGQhVn1pSqhw-x-server.ccl.net> X-Original-From: Radoslaw Kaminski Content-Type: multipart/alternative; boundary=047d7b604fbad67c8504d7827b64 Date: Sat, 9 Mar 2013 19:55:10 +0100 MIME-Version: 1.0 Sent to CCL by: Radoslaw Kaminski [rkaminski.rk#,#gmail.com] --047d7b604fbad67c8504d7827b64 Content-Type: text/plain; charset=ISO-8859-1 What is also worth noting is that the standard setting of the space group no. 14 is P2(1)/c, though you might see the P2(1)/n and P2(1)/a in the literature. In many cases it does not matter (it's the same space group). However, under some circumstances a non-standard setting is rather preferred. Just a comment:) Radek 2013/3/5 Jacco van de Streek jacco.vandestreek::sund.ku.dk < owner-chemistry---ccl.net> > > Sent to CCL by: Jacco van de Streek [jacco.vandestreek/a\sund.ku.dk] > > Could any one explain, what is meant > > by standardization of a crystal structure. > > What is probably meant is the standardisation of the unit-cell parameters > and the space group. Crystallographers have a set of conventions (i.e. > rules that are not based on any physics) regarding what a standard set of > unit-cell parameters should look like. For example, if the unit-cell > lengths a, b and c are equivalent by (but not related by) symmetry, some > conventions state that the unit-cell parameters should be labeled such that > ab>c, as with all arbitrary conventions, they are a matter of > taste). For unit cells with two angles identical to 90 degrees based on the > space-group symmetry, the convention is that the remaining angle should be > called beta (or gamma according to some other conventions). > > Space-group symmetry can also be standardised. For space group number 14, > the standard setting is P 1 21/c 1 with the inversion at the origin, for > example. > > Most standardisation also includes the atomic coordinates: it is > convenient if the atomic coordinates are reported in such a manner that > they form a connected molecule without the need to apply the space-group > symmetry (including translations) to generate symmetry-related copies, and > the fractional coordinates of the centre of mass of the molecule should all > be in the range [0, 1> (perhaps even in the range [0,1/2> or whatever, > depending on the space-group symmetry). Also the number of atoms that > should be reported is usually standardised to be restricted to the smallest > set required to reconstruct the entire crystal structure (by applying the > space-group symmetry). > > The standardisation may also include the atom labeling itself. > > > Can it be used directly on the crystal structures > > obtained from experiments. (without changing the original information) > > In principle, yes. In practice, some programs may either change the number > of decimals (because they choose to save all files with a fixed number of > decimal places, ignoring the input) and your coordinates may either gain > some meaningless trailing zeros or lose some semi-meaningful fourth or > fifth decimal, and some programs may omit the estimated standard deviations > on the atomic coordinates, or even on the unit-cell parameters. When you > want to do an energy minimisation anyway, this should not make any > difference, as these estimated standard deviations do not affect the final > result anyway. > > > Also, please suggest any free wares that can > > do this. > > WinGX: > > http://www.chem.gla.ac.uk/~louis/software/wingx/ > > Platon: > > http://www.cryst.chem.uu.nl/spek/ > > Best wishes, > -- > Dr Jacco van de Streek > Department of Pharmacy > University of Copenhagen> > > -- Radoslaw Kaminski, M.Sc. Eng. Ph.D. Student Crystallochemistry Laboratory Department of Chemistry University of Warsaw Pasteura 1, 02-093 Warszawa, Poland http://www.chem.uw.edu.pl/people/RKaminski/ --047d7b604fbad67c8504d7827b64 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable What is also worth noting is that the standard setting of the space group n= o. 14 is P2(1)/c, though you might see the P2(1)/n and P2(1)/a in the liter= ature. In many cases it does not matter (it's the same space group). Ho= wever, under some circumstances a non-standard setting is rather preferred.=

Just a comment:)

Radek


201= 3/3/5 Jacco van de Streek jacco.vandestreek::= sund.ku.dk <owner-chemistry---ccl.net>

Sent to CCL by: Jacco van de Streek [jacco.vandestreek/a\sund.ku.dk]
> Could any one explain, what is meant
> by standardization of a crystal structure.

What is probably meant is the standardisation of the unit-cell parame= ters and the space group. Crystallographers have a set of conventions (i.e.= rules that are not based on any physics) regarding what a standard set of = unit-cell parameters should look like. For example, if the unit-cell length= s a, b and c are equivalent by (but not related by) symmetry, some conventi= ons state that the unit-cell parameters should be labeled such that a<b&= lt;c (or a>b>c, as with all arbitrary conventions, they are a matter = of taste). For unit cells with two angles identical to 90 degrees based on = the space-group symmetry, the convention is that the remaining angle should= be called beta (or gamma according to some other conventions).

Space-group symmetry can also be standardised. For space group number 14, t= he standard setting is P 1 21/c 1 with the inversion at the origin, for exa= mple.

Most standardisation also includes the atomic coordinates: it is convenient= if the atomic coordinates are reported in such a manner that they form a c= onnected molecule without the need to apply the space-group symmetry (inclu= ding translations) to generate symmetry-related copies, and the fractional = coordinates of the centre of mass of the molecule should all be in the rang= e [0, 1> (perhaps even in the range [0,1/2> or whatever, depending on= the space-group symmetry). Also the number of atoms that should be reporte= d is usually standardised to be restricted to the smallest set required to = reconstruct the entire crystal structure (by applying the space-group symme= try).

The standardisation may also include the atom labeling itself.

> Can it be used directly on the crystal structures
> obtained from experiments. (without changing the original information)=

In principle, yes. In practice, some programs may either change the n= umber of decimals (because they choose to save all files with a fixed numbe= r of decimal places, ignoring the input) and your coordinates may either ga= in some meaningless trailing zeros or lose some semi-meaningful fourth or f= ifth decimal, and some programs may omit the estimated standard deviations = on the atomic coordinates, or even on the unit-cell parameters. When you wa= nt to do an energy minimisation anyway, this should not make any difference= , as these estimated standard deviations do not affect the final result any= way.

> Also, please suggest any free wares that can
> do this.

WinGX:

http://www.chem.gla.ac.uk/~louis/software/wingx/

Platon:

http://www.= cryst.chem.uu.nl/spek/

Best wishes,
--
Dr Jacco van de Streek
Department of Pharmacy
University of Copenhagen



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--
Radoslaw Kaminski, M.Sc= . Eng.
Ph.D. Student
Crystallochemistry Laboratory
Department of C= hemistry
University of Warsaw
Pasteura 1, 02-093 Warszawa, Poland
h= ttp://www.chem.uw.edu.pl/people/RKaminski/ --047d7b604fbad67c8504d7827b64--