Re: Defining the origin of P2/n
Kurt I think that P2/n has no fixed points, and in order to keep the whole structure from shifting along the c-axis, one of the atoms has to be arbitrarily fixed. GSAS automatically fixes the first atom z-parameter (was your atom on the 2-fold symmetry axis?). I remember this from refining the structure of high pressure FeTiO3 which had space group R3c. - Kurt yes, i do think this centric space group does not need any origin fixing. And this first atom is not in special position at all. Thank a lot. stephen
Re: gsas reflection listings
Sorry if I recall what has been discussed before, but I cannot find it in the archives. I don't use apparantly the proper search terms. Try this in the old archive (90 emails !) : http://sdpd.univ-lemans.fr/cgi-bin/searchrietveld.pl?Range=AllFormat=StandardTerms=bail+gsas or this in the new archive (54 emails !) : http://www.mail-archive.com/cgi-bin/htsearch?method=andformat=shortconfig=rietveld_l_ill_frrestrict=exclude=words=bail+GSAS Try also that link : http://sdpd.univ-lemans.fr/iniref/lbm-story/ To summarize : The Rietveld decomposition formula which is applied at every refinement cycle for |Fobs| calculations needed for the Bragg R factor calculation in the Rietveld method, and iterated in the Le Bail method produces inherently independent structure factors for alpha1 and alpha2 components. In the original Le Bail method algorithm, the alpha1 and 2 components are reset at the 0.5 ratio after each iteration. The only way which would produce the correct ratio inherently would be to have a constrained unique profile shape taking account of both alpha1 and 2 components instead of 2 added peaks. If unhappy with GSAS, try FULLPROF, and vice versa, being able to use both of them is certainly the best. Armel
Re: gsas reflection listings
On 31 Mar 2004 at 11:34, Armel Le Bail wrote: Try this in the old archive (90 emails !) : http://sdpd.univ-lemans.fr/cgi-bin/searchrietveld.pl?Range=AllFormat=StandardTerms=bail+gsas or this in the new archive (54 emails !) : http://www.mail-archive.com/cgi-bin/htsearch?method=andformat=shortconfig=rietveld_l_ill_frrestrict=exclude=words=bail+GSAS It's because of your name: Le Bail. There are quite a few people that write LeBail and that was what I did erroneously: lebail+gsas. Only 7 hits in the new archive. You must encounter, as I do, indexing problems in journals: will they write lebail, le bail, or bail (lee, van der lee, vanderlee) :). Thanks for the links. Arie Try also that link : http://sdpd.univ-lemans.fr/iniref/lbm-story/ To summarize : The Rietveld decomposition formula which is applied at every refinement cycle for |Fobs| calculations needed for the Bragg R factor calculation in the Rietveld method, and iterated in the Le Bail method produces inherently independent structure factors for alpha1 and alpha2 components. In the original Le Bail method algorithm, the alpha1 and 2 components are reset at the 0.5 ratio after each iteration. The only way which would produce the correct ratio inherently would be to have a constrained unique profile shape taking account of both alpha1 and 2 components instead of 2 added peaks. If unhappy with GSAS, try FULLPROF, and vice versa, being able to use both of them is certainly the best. Armel *** A. van der Lee Institut Européen des Membranes (UMR 5635) Université de Montpellier II - cc 047 Place E. Bataillon 34095 Montpellier Cedex 5 FRANCE visiting address: 300 Av. Prof. E. Jeanbrau tél.: 00-33-(0)4.67.14.91.35 FAX.: 00-33-(0)4.67.14.91.19 ***
ICSD database updated to 76,480 inorganic structures
The ICSD-WWW database on http://icsdweb.fiz-karlsruhe.de/ or http://icsd.ill.fr/ has been updated to 76,480 inorganic structures for licensed users, with now over 6000 new entries being added each year. Unlicensed users have full-feature access to a demo 3000+ structure database. Notes and examples of how to produce photo-realistic crystal structure drawings from ICSD generated VRML files using textures or POV-Ray ray-tracing have been added on http://icsd.ill.fr/icsd/help/VRML-help.html Note that there are various ways of obtaining full access to ICSD-WWW, ranging from becoming a registered user of http://icsdweb.fiz-karlsruhe.de/ to a licence to operate your own ICSD-WWW server. See the above WWW-site for details. Armel will be pleased to know that the PHP-MySQL server software is available as open source (but copyright) code from http://icsd.ill.fr/icsd/install/ Alan. Alan Hewat, ILL Grenoble, FRANCE [EMAIL PROTECTED] fax (33) 4.76.20.76.48 (33) 4.76.20.72.13 (.26 Mme Guillermet) http://www.ill.fr/dif/AlanHewat.htm ___
Re: ICSD database updated to 76,480 inorganic structures
Armel will be pleased to know that the PHP-MySQL server software is available as open source (but copyright) code from http://icsd.ill.fr/icsd/install/ Not enough Alan, I want not only the butter but also the money for the butter. The complete stuff fully open. 500 more CIFs in COD that week, coming from the AMCSD (the American Mineralogy Crystal Structure Database has now more than 5000 fully open entries, and the COD has 12000). AMCSD : http://www.geo.arizona.edu/AMS/amcsd.php COD : http://www.crystallography.net/ Armel
Re: ICSD database updated to 76,480 inorganic structures
At 15:56 31/03/2004, Armel Le Bail wrote: Not enough Alan, I want not only the butter but also the money for the butter. And the milkmaid as well I suppose Armel ? ICSD also contains papers from the American Mineralogist, and even provides direct links to the original paper in electronic form where that is available. (Bob Downs is working on making more back issues available on-line). Alan. Alan Hewat, ILL Grenoble, FRANCE [EMAIL PROTECTED] fax (33) 4.76.20.76.48 (33) 4.76.20.72.13 (.26 Mme Guillermet) http://www.ill.fr/dif/AlanHewat.htm ___
Re: gsas reflection listings
Arie, Your suggestion is the best way to handle this. Just sort the data by hkl to put Ka1 with Ka2 and then sum them pairwise. Some day I'll put that into REFLIST, but you can do that with the help of the MS-DOS comand sort (it is still there in the console for Win 2K, XP, etc.). Bob From: A. van der Lee [mailto:[EMAIL PROTECTED] Sent: Wed 3/31/2004 2:05 AM To: [EMAIL PROTECTED] Dear Bob, Sorry if I recall what has been discussed before, but I cannot find it in the archives. I don't use apparantly the proper search terms. Thanks anyhow for the rapid answer. Isn't it strange that in the LeBail refinement the Ka1 and Ka2 reflections are treated independently and that the 0.5 intensity ratio is not used? It is a purely physical phenomenon, independent of the structural model, that doesnot exist anyhow in the LeBail refinement. Ka1 and Ka2 are physically dependent, not? I can imagine that the correct partitioning is computationally difficult for independent reflections that are very close, but in case of dependent reflections it seems to me at first sight relatively easy. Would it be wrong from a methodological point of view if I attribute the Ka2 contribution to the Ka1 intensity for use in Direct Methods? That would be better than using only the Ka1 intensity when the partitioning is likely to be incorrect. A new cycle started by POWPREF indeed improves the partitioning, but is still rather far from correct. Arie On 30 Mar 2004 at 8:44, Von Dreele, Robert B. wrote: Dear Arie, Some of this has been discussed earlier but in a LeBail refinement in GSAS the Ka1 and Ka2 reflections are treated as independent and the 2:1 intensity ratio is not used. This arises because of the severe computational difficulty of connecting the intensities of these paired reflections together in a LeBail context. (Note: RATIO is not refinable in a LeBail refinement). The REFLIST reflection output (separate file) takes only the Ka1 set of reflections so that occasionally (as you observed) the reflection partitioning in the LeBail refinement has slighted a Ka1 reflection. This can occur especially for low angle reflections where Ka1 and Ka2 virtually overlap. You might get a better partitioning if you now restarted the LeBail refinement by running POWPREF to clear the results and then doing GENLES to convergence. The improved lattice parameters profile coefficients should give better reflection positions widths and hence better partitioning. Bob Von Dreele *** A. van der Lee Institut Européen des Membranes (UMR 5635) Université de Montpellier II - cc 047 Place E. Bataillon 34095 Montpellier Cedex 5 FRANCE visiting address: 300 Av. Prof. E. Jeanbrau tél.: 00-33-(0)4.67.14.91.35 FAX.: 00-33-(0)4.67.14.91.19 ***
Defining the origin of P2/n
Dear Stephen ( others), I know there have been a number of replies to this since P2/n does have an inversion center which is positioned at the unit cell origin. However, if the space group is Pn (or P2) then the location of the origin is arbitrary on one or more axes. GSAS does automatically handle this by forcing the first and second atoms to have the opposite shifts for each of the arbitrary axes. So in Pn the shifts for atom #1 will be sx,sy,sz and for atom #2 they will be -sx,sy',-sz, i.e. the sx sz shifts will be opposite but identical for these two atoms while each will have it's own sy. Beware, different damping applied to these atoms will make it drift as the applied shifts won't be equal opposite. If you do not want this to happen then put in your own hold on the appropriate coordinates for one atom or else put in your own constraint. Bob Von Dreele From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Sent: Wed 3/31/2004 12:02 AM To: [EMAIL PROTECTED] Dear Rietvelders, I used GSAS to refine my structure in P2/n, however the program automatically fixed the the XYZ positions of the first atom during refinement. To my surprise, this atom is not seen in the fixed atom list in the atom parameters menu of GSAS. Please advise and many thanks, stephen
Re: Defining the origin of P2/n
[EMAIL PROTECTED] wrote: Dear Rietvelders, I used GSAS to refine my structure in P2/n, however the program automatically fixed the the XYZ positions of the first atom during refinement. To my surprise, this atom is not seen in the fixed atom list in the atom parameters menu of GSAS. Please advise and many thanks, stephen I am amazed by the flow of miss information that flows on this list whenever an apparent problem with a space group comes up. I am forced to wonder if the correspondents in these exchanges have ever looked at 'The International Tables, Volume A(1983)' or Volume 1(1969) or the earlier volume which dates in the 1930's. Or any of the several other treatises that can also serve as a source for this information. The GSAS package contains a program, SpcGroup, that can be used to list the symmetry operations of any possible string defining a possible space group. In general the space group symbol consists of 2 or more groups of characters delimited by spaces. Please note that the spaces separating axial operations are required in the GSAS interpretation of the space group symbol. Thus 'R3c' must be written as 'R 3 c' or taking advantage of the fact that the lattice type can only occupy one character, 'R3 c', is accepted, but not recommended. I might also note that all of this is based on the use of keyboards in general use in English speaking countries. And I did have no information concerning what you might get using other keyboards. Now for P2/n is a centric space group for which there, in my mind, there exists no reasonable origin choice that the 1bar site. Therefore the software would always choose that for the origin of the unit cell. Allen C. Larson
Defining the origin of P2/n
Bob, Thank you for the clarification. I never had doubts that GSAS handles fixed origin issue properly but also never understand how it is done. This way has one big advantage over user fixed origin -- it yields standard uncertainties for all atoms and therefore for all distances, etc. Peter Zavalij -Original Message- From: Von Dreele, Robert B. [mailto:[EMAIL PROTECTED] Sent: Wednesday, March 31, 2004 10:17 AM To: [EMAIL PROTECTED] Dear Stephen ( others), I know there have been a number of replies to this since P2/n does have an inversion center which is positioned at the unit cell origin. However, if the space group is Pn (or P2) then the location of the origin is arbitrary on one or more axes. GSAS does automatically handle this by forcing the first and second atoms to have the opposite shifts for each of the arbitrary axes. So in Pn the shifts for atom #1 will be sx,sy,sz and for atom #2 they will be -sx,sy',-sz, i.e. the sx sz shifts will be opposite but identical for these two atoms while each will have it's own sy. Beware, different damping applied to these atoms will make it drift as the applied shifts won't be equal opposite. If you do not want this to happen then put in your own hold on the appropriate coordinates for one atom or else put in your own constraint. Bob Von Dreele From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Sent: Wed 3/31/2004 12:02 AM To: [EMAIL PROTECTED] Dear Rietvelders, I used GSAS to refine my structure in P2/n, however the program automatically fixed the the XYZ positions of the first atom during refinement. To my surprise, this atom is not seen in the fixed atom list in the atom parameters menu of GSAS. Please advise and many thanks, stephen
Re: Defining the origin of P2/n
Dear Peter, the most correct constraint would be to fix a sum of coordinates of all atoms along polar axis, but not only of the first two. It gives the best estimation of the standard uncertainties. Yaroslav Filinchuk PZ Bob, PZ Thank you for the clarification. I never had doubts that GSAS handles fixed origin issue properly but also never understand how it PZ is done. This way has one big advantage over user fixed origin -- it yields standard uncertainties for all atoms and therefore for PZ all distances, etc. PZ Peter Zavalij PZ -Original Message- PZ From: Von Dreele, Robert B. [mailto:[EMAIL PROTECTED] PZ Sent: Wednesday, March 31, 2004 10:17 AM PZ To: [EMAIL PROTECTED] PZ Dear Stephen ( others), PZ I know there have been a number of replies to this since P2/n does have an inversion center which is positioned at the unit cell PZ origin. However, if the space group is Pn (or P2) then the location of the origin is arbitrary on one or more axes. GSAS does PZ automatically handle this by forcing the first and second atoms to have the opposite shifts for each of the arbitrary axes. So in PZ Pn the shifts for atom #1 will be sx,sy,sz and for atom #2 they will be -sx,sy',-sz, i.e. the sx sz shifts will be opposite but PZ identical for these two atoms while each will have it's own sy. Beware, different damping applied to these atoms will make it drift PZ as the applied shifts won't be equal opposite. If you do not want this to happen then put in your own hold on the appropriate PZ coordinates for one atom or else put in your own constraint. PZ Bob Von Dreele PZ PZ From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] PZ Sent: Wed 3/31/2004 12:02 AM PZ To: [EMAIL PROTECTED] PZ Dear Rietvelders, PZ I used GSAS to refine my structure in P2/n, however the program automatically PZ fixed the the XYZ positions of the first atom during refinement. To my PZ surprise, this atom is not seen in the fixed atom list in the atom parameters PZ menu of GSAS. PZ Please advise and many thanks, PZ stephen
Re: Defining the origin of P2/n
Peter Zavalij wrote: Bob, Thank you for the clarification. I never had doubts that GSAS handles fixed origin issue properly but also never understand how it is done. This way has one big advantage over user fixed origin -- it yields standard uncertainties for all atoms and therefore for all distances, etc. Peter Zavalij When there is a 1bar site it is automatically chosen as the origin of the unit cell. Any other choice would require adding a extra shift parameter to the X, Y and Z notation in generation the matrices which perform the symmetry operations. Allen
Re: Defining the origin of P2/n
Obviously. I was talking about fixing the origin when it is not fixed by symmetry. By the way, GSAS when generate symmetry from space group symbol provide information about the origin. If the origin is not fixed by symmetry is it clearly stated: For example for P2 The location of the origin is arbitrary in y Note that GSAS can handle symbols w/o spaces but not in all cases; e.g. both P2/n and P 2/n results correct symmetry. HOWEVER P 2 2 2 and P222 do not. The later symbol give P2 symmetry! Anyway before making any conclusions correct space group symbol with properly placed spaces has to be used. Peter Zavalij -Original Message- From: Allen Larson [mailto:[EMAIL PROTECTED] Sent: Wednesday, March 31, 2004 11:58 AM To: [EMAIL PROTECTED] Peter Zavalij wrote: Bob, Thank you for the clarification. I never had doubts that GSAS handles fixed origin issue properly but also never understand how it is done. This way has one big advantage over user fixed origin -- it yields standard uncertainties for all atoms and therefore for all distances, etc. Peter Zavalij When there is a 1bar site it is automatically chosen as the origin of the unit cell. Any other choice would require adding a extra shift parameter to the X, Y and Z notation in generation the matrices which perform the symmetry operations. Allen
Re: Defining the origin of P2/n
Yes, but the atom doesn't have to sit there, unlike in the case of 2/m. So, GSAS has to fix z for one atom... I don't have my International Tables with me, please correct me if I'm wrong (there should be no sites with a fixed z parameter in P2/n). - Kurt --- Kurt Leinenweber Department of Chemistry Arizona State University Tempe, AZ 85287-1604 Phone: (480)-965-8853 Fax: (480)-965-2747 --- -Original Message- From: Magnus H. Sørby [mailto:[EMAIL PROTECTED] Sent: Wednesday, March 31, 2004 12:24 AM To: [EMAIL PROTECTED] Stephen and Kurt, P2/n has a 2-fold axis perpendicular to a glide plane, so it does have fixed points (unlike e.g. R3c). Best regards, Magnus H. Sørby -Opprinnelig melding- Fra: Kurt Leinenweber [mailto:[EMAIL PROTECTED] Sendt: 31. mars 2004 08:55 Til: [EMAIL PROTECTED] Emne: Defining the origin of P2/n Stephen, I think that P2/n has no fixed points, and in order to keep the whole structure from shifting along the c-axis, one of the atoms has to be arbitrarily fixed. GSAS automatically fixes the first atom z-parameter (was your atom on the 2-fold symmetry axis?). I remember this from refining the structure of high pressure FeTiO3 which had space group R3c. - Kurt --- Kurt Leinenweber Department of Chemistry Arizona State University Tempe, AZ 85287-1604 Phone: (480)-965-8853 Fax: (480)-965-2747 --- -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Sent: Tuesday, March 30, 2004 11:03 PM To: [EMAIL PROTECTED] Dear Rietvelders, I used GSAS to refine my structure in P2/n, however the program automatically fixed the the XYZ positions of the first atom during refinement. To my surprise, this atom is not seen in the fixed atom list in the atom parameters menu of GSAS. Please advise and many thanks, stephen
Re: Defining the origin of P2/n
This problem can actually quite simply be solved without tables: There is the old rule (which crystrallographers a definitely able to prove) to obtain the crystal class: 1.delete the Bravais type symbol (delete P in case of P2/n) 2.substitute screw axes by the correspondingly oriented simple rotations (we already have a rotation, 2(1) becomes 2) 3.substitute glide planes by mirror planes with the same orientation. (2/n becomes 2/m) This gives you the symbol of the crystal class/crystallographic point group. Thus you can see that P2/n belongs to the crystal class 2/m, which has a centre of inversion. All space group types belonging to a centrosymmetric crystal class have one or several Wyckoff sites with centre of inversion. Therefore, there must be a position (there are several ones) with fixed z coordinate. Andreas Leineweber Kurt Leinenweber wrote: Yes, but the atom doesn't have to sit there, unlike in the case of 2/m. So, GSAS has to fix z for one atom... I don't have my International Tables with me, please correct me if I'm wrong (there should be no sites with a fixed z parameter in P2/n). - Kurt --- Kurt Leinenweber Department of Chemistry Arizona State University Tempe, AZ 85287-1604 Phone: (480)-965-8853 Fax: (480)-965-2747 --- -Original Message- From: Magnus H. Srby [mailto:[EMAIL PROTECTED]] Sent: Wednesday, March 31, 2004 12:24 AM To: [EMAIL PROTECTED] Stephen and Kurt, P2/n has a 2-fold axis perpendicular to a glide plane, so it does have fixed points (unlike e.g. R3c). Best regards, Magnus H. Srby -Opprinnelig melding- Fra: Kurt Leinenweber [mailto:[EMAIL PROTECTED]] Sendt: 31. mars 2004 08:55 Til: [EMAIL PROTECTED] Emne: Defining the origin of P2/n Stephen, I think that P2/n has no fixed points, and in order to keep the whole structure from shifting along the c-axis, one of the atoms has to be arbitrarily fixed. GSAS automatically fixes the first atom z-parameter (was your atom on the 2-fold symmetry axis?). I remember this from refining the structure of high pressure FeTiO3 which had space group R3c. - Kurt --- Kurt Leinenweber Department of Chemistry Arizona State University Tempe, AZ 85287-1604 Phone: (480)-965-8853 Fax: (480)-965-2747 --- -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]] Sent: Tuesday, March 30, 2004 11:03 PM To: [EMAIL PROTECTED] Dear Rietvelders, I used GSAS to refine my structure in P2/n, however the program automatically fixed the the XYZ positions of the first atom during refinement. To my surprise, this atom is not seen in the "fixed atom list" in the atom parameters menu of GSAS. Please advise and many thanks, stephen
Re: Defining the origin of P2/n
Sorry Allen - I guess this new generation of crystallographers really is as bad as you think! - Kurt --- Kurt Leinenweber Department of Chemistry Arizona State University Tempe, AZ 85287-1604 Phone: (480)-965-8853 Fax: (480)-965-2747 --- -Original Message- From: Allen Larson [mailto:[EMAIL PROTECTED] Sent: Wednesday, March 31, 2004 9:33 AM To: [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Dear Rietvelders, I used GSAS to refine my structure in P2/n, however the program automatically fixed the the XYZ positions of the first atom during refinement. To my surprise, this atom is not seen in the fixed atom list in the atom parameters menu of GSAS. Please advise and many thanks, stephen I am amazed by the flow of miss information that flows on this list whenever an apparent problem with a space group comes up. I am forced to wonder if the correspondents in these exchanges have ever looked at 'The International Tables, Volume A(1983)' or Volume 1(1969) or the earlier volume which dates in the 1930's. Or any of the several other treatises that can also serve as a source for this information. The GSAS package contains a program, SpcGroup, that can be used to list the symmetry operations of any possible string defining a possible space group. In general the space group symbol consists of 2 or more groups of characters delimited by spaces. Please note that the spaces separating axial operations are required in the GSAS interpretation of the space group symbol. Thus 'R3c' must be written as 'R 3 c' or taking advantage of the fact that the lattice type can only occupy one character, 'R3 c', is accepted, but not recommended. I might also note that all of this is based on the use of keyboards in general use in English speaking countries. And I did have no information concerning what you might get using other keyboards. Now for P2/n is a centric space group for which there, in my mind, there exists no reasonable origin choice that the 1bar site. Therefore the software would always choose that for the origin of the unit cell. Allen C. Larson
Re: Defining the origin of P2/n
Thanks Andreas. I realized I was wrong when I drew a picture of how the glide plane and the 2-fold axis interact with the translational symmetry. They make 4 points at +x +y +z, -x -y +z, +x +y -z, -x -y -z (2 pairs definitely related by a center of symmetry). I should have done that before I posted tothe list! I am at home with newborn twins and have not had my hands on the blue book for several days. - Kurt ---Kurt LeinenweberDepartment of ChemistryArizona State UniversityTempe, AZ 85287-1604Phone: (480)-965-8853Fax: (480)-965-2747--- -Original Message-From: Andreas Leineweber [mailto:[EMAIL PROTECTED]Sent: Wednesday, March 31, 2004 11:09 AMTo: [EMAIL PROTECTED]Subject: Re: Defining the origin of P2/nThis problem can actually quite simply be solved without tables:There is the old rule (which crystrallographers a definitely able to prove) to obtain the crystal class:1.delete the Bravais type symbol (delete P in case of P2/n)2.substitute screw axes by the correspondingly oriented simple rotations (we already have a rotation, 2(1) becomes 2)3.substitute glide planes by mirror planes with the same orientation. (2/n becomes 2/m)This gives you the symbol of the crystal class/crystallographic point group.Thus you can see that P2/n belongs to the crystal class 2/m, which has a centre of inversion. All space group types belonging to a centrosymmetric crystal class have one or several Wyckoff sites with centre of inversion. Therefore, there must be a position (there are several ones) with fixed z coordinate.Andreas LeineweberKurt Leinenweber wrote: Yes, but the atom doesn't have to sit there, unlike in the case of 2/m. So, GSAS has to fix z for one atom... I don't have my International Tables with me, please correct me if I'm wrong (there should be no sites with a fixed z parameter in P2/n). - Kurt --- Kurt Leinenweber Department of Chemistry Arizona State University Tempe, AZ 85287-1604 Phone: (480)-965-8853 Fax: (480)-965-2747 --- -Original Message- From: Magnus H. Sørby [mailto:[EMAIL PROTECTED]] Sent: Wednesday, March 31, 2004 12:24 AM To: [EMAIL PROTECTED] Stephen and Kurt, P2/n has a 2-fold axis perpendicular to a glide plane, so it does have fixed points (unlike e.g. R3c). Best regards, Magnus H. Sørby -Opprinnelig melding- Fra: Kurt Leinenweber [mailto:[EMAIL PROTECTED]] Sendt: 31. mars 2004 08:55 Til: [EMAIL PROTECTED] Emne: Defining the origin of P2/n Stephen, I think that P2/n has no fixed points, and in order to keep the whole structure from shifting along the c-axis, one of the atoms has to be arbitrarily fixed. GSAS automatically fixes the first atom z-parameter (was your atom on the 2-fold symmetry axis?). I remember this from refining the structure of high pressure FeTiO3 which had space group R3c. - Kurt --- Kurt Leinenweber Department of Chemistry Arizona State University Tempe, AZ 85287-1604 Phone: (480)-965-8853 Fax: (480)-965-2747 --- -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]] Sent: Tuesday, March 30, 2004 11:03 PM To: [EMAIL PROTECTED] Dear Rietvelders, I used GSAS to refine my structure in P2/n, however the program automatically fixed the the XYZ positions of the first atom during refinement. To my surprise, this atom is not seen in the "fixed atom list" in the atom parameters menu of GSAS. Please advise and many thanks, stephen
Choosing origins
I am amazed by the flow of miss information that flows on this list whenever an apparent problem with a space group comes up. I asked a related question on sci.techniques.xtallography a few weeks ago, but have yet to hear anything, misinformation or otherwise. If anyone here can give me some pointers, I'd be very grateful. I just want to find all the allowed equivalent origin choices for comparing structures, and I'm wondering if there is a way to choose a specific one (for example in terms of the phases of certain reflections?). Thanks, Jon Forwarded from sci.techniques.xtallography, with my apologies if you have seen it before. I was looking at models coming back from a molecular replacement program being run using various datasets and then trying to decide if the models are good or bad, and therefore if the data were good or bad. In a specific example with space group P212121, frequently the resulting model was found displaced by 1/2,0,0 from the ideal position (and invariably moved still further away by one of 21 axes). [All programs are using x,y,z; 1/2-x,-y,1/2+z; -x,1/2+y,1/2-z; 1/2+x,1/2-y,-z for P212121.] From looking at the space group diagrams in Int Tables, this seems to be a perfectly good origin shift, as the symmetry operators are arranged around [1/2,0,0] in the same way as [0,0,0]. So I wrote a little script which applies all the origin shifts and symmetry operators to a test model and tells me which origin shift and symmetry operator gives the closest fit a target model. All well and good for P212121, but now I was thinking that one day I might want to do this for another space group... The first attempt to generalise was to apply the space group symmetry to the point [0,0,0], which gives me three face centers, but misses the body center and points 1/2,0,0. Then it occurred to look at the Patterson symmetry (apparently Pmmm here) and from that I could probably have gotten a list of possible origin shifts, with a concern about sometimes flipping enantiomers. Now I'm scared that one day I'll meet a trigonal thing which has hexagonal Patterson symmetry and could come back rotated by 60 degrees, but still be the same structure! So the question is: How can the full list coordinate transformations be generated which leave a structure invarient? For P212121 it seems that add [0.5,0,0] is allowed, but I didn't see how I should figure that out from the info in Int tables, or algorithmically. There's a followup: How should the transformation be chosen in order to end up at a unique and reproducible representation of the structure? Would something like platon just do all this? At least one pair of structures in the PDB database seem to represent different choices about this origin shifting, but they represent the same packing and structure... realising that was not as straightforward as it would have been had both structures been recorded in a standardised way. Thanks in advance, Jon
Choosing origins
Hi Jon, A lot of what you'll need is in the back of the International Tables Vol. A in Chapter 15 which goes under the snappy title of Euclidean and affine normalisers of space groups and their use in crystallography. From memory, earlier incarnations of Vol. A do not have this chapter. Bill -Original Message- From: Jon Wright [mailto:[EMAIL PROTECTED] Sent: 31 March 2004 21:14 To: [EMAIL PROTECTED] I am amazed by the flow of miss information that flows on this list whenever an apparent problem with a space group comes up. I asked a related question on sci.techniques.xtallography a few weeks ago, but have yet to hear anything, misinformation or otherwise. If anyone here can give me some pointers, I'd be very grateful. I just want to find all the allowed equivalent origin choices for comparing structures, and I'm wondering if there is a way to choose a specific one (for example in terms of the phases of certain reflections?). Thanks, Jon Forwarded from sci.techniques.xtallography, with my apologies if you have seen it before. I was looking at models coming back from a molecular replacement program being run using various datasets and then trying to decide if the models are good or bad, and therefore if the data were good or bad. In a specific example with space group P212121, frequently the resulting model was found displaced by 1/2,0,0 from the ideal position (and invariably moved still further away by one of 21 axes). [All programs are using x,y,z; 1/2-x,-y,1/2+z; -x,1/2+y,1/2-z; 1/2+x,1/2-y,-z for P212121.] From looking at the space group diagrams in Int Tables, this seems to be a perfectly good origin shift, as the symmetry operators are arranged around [1/2,0,0] in the same way as [0,0,0]. So I wrote a little script which applies all the origin shifts and symmetry operators to a test model and tells me which origin shift and symmetry operator gives the closest fit a target model. All well and good for P212121, but now I was thinking that one day I might want to do this for another space group... The first attempt to generalise was to apply the space group symmetry to the point [0,0,0], which gives me three face centers, but misses the body center and points 1/2,0,0. Then it occurred to look at the Patterson symmetry (apparently Pmmm here) and from that I could probably have gotten a list of possible origin shifts, with a concern about sometimes flipping enantiomers. Now I'm scared that one day I'll meet a trigonal thing which has hexagonal Patterson symmetry and could come back rotated by 60 degrees, but still be the same structure! So the question is: How can the full list coordinate transformations be generated which leave a structure invarient? For P212121 it seems that add [0.5,0,0] is allowed, but I didn't see how I should figure that out from the info in Int tables, or algorithmically. There's a followup: How should the transformation be chosen in order to end up at a unique and reproducible representation of the structure? Would something like platon just do all this? At least one pair of structures in the PDB database seem to represent different choices about this origin shifting, but they represent the same packing and structure... realising that was not as straightforward as it would have been had both structures been recorded in a standardised way. Thanks in advance, Jon
Re: Choosing origins
Bill, Thanks! Exactly what I was after and I'd never have guessed it from the title... Jon On Wed, 31 Mar 2004, David, WIF (Bill) wrote: Hi Jon, A lot of what you'll need is in the back of the International Tables Vol. A in Chapter 15 which goes under the snappy title of Euclidean and affine normalisers of space groups and their use in crystallography. From memory, earlier incarnations of Vol. A do not have this chapter. Bill
Re: Choosing origins
I'm just good at guessing! See you end of April en France. Bill -Original Message- From: Jonathan Wright [mailto:[EMAIL PROTECTED] Sent: 31 March 2004 23:05 To: [EMAIL PROTECTED] Bill, Thanks! Exactly what I was after and I'd never have guessed it from the title... Jon On Wed, 31 Mar 2004, David, WIF (Bill) wrote: Hi Jon, A lot of what you'll need is in the back of the International Tables Vol. A in Chapter 15 which goes under the snappy title of Euclidean and affine normalisers of space groups and their use in crystallography. From memory, earlier incarnations of Vol. A do not have this chapter. Bill
Re: Choosing origins
Apologies for sending the personal note to Jon to the whole mailing list - at least it didn't have gigabytes of attachments - and for the English and American members of the mailing list, 'en' is not a spelling mistake! Bill -Original Message- From: Jonathan Wright [mailto:[EMAIL PROTECTED] Sent: 31 March 2004 23:05 To: [EMAIL PROTECTED] Bill, Thanks! Exactly what I was after and I'd never have guessed it from the title... Jon On Wed, 31 Mar 2004, David, WIF (Bill) wrote: Hi Jon, A lot of what you'll need is in the back of the International Tables Vol. A in Chapter 15 which goes under the snappy title of Euclidean and affine normalisers of space groups and their use in crystallography. From memory, earlier incarnations of Vol. A do not have this chapter. Bill
