Phil, For the record, the program XPREP - widely used by small molecule crystallographers but also useful for macromoleculess - always makes the conventional cell (in this example P 21 21 2) the default (i.e. what you get if you always hit <Enter>), and writes out new .hkl and .ins files in this setting unless the user forces it to do otherwise (the .ins file is used for solving the structure with direct methods and contains the cell corresponding to the new .hkl file). There are three cases where it is intentionally made less awkward for the user to choose an alternative setting if she/he so wishes:
1. Primitive rhombohedral rather than the hexagonal cell with three times the volume. Unlike the situation for macromolecules, where some older programs do not work with the primitive rhombohedral cell, the primitive cell is quite often chosen for small molecules. 2. The space group I2 rather than C2 if it results in a beta angle much closer to 90 degrees (or when it is desired to compare the structure with a structure - possibly another crystalline phase of the same compound - in say I222). The same applies to other C-centred monoclinic cells, e.g. Cc <-> Ia etc. (but Fd is discouraged). 3. The setting P21/n rather than P21/c if it results in a beta angles much closer to 90 etc. These three 'unconventional' settings are also generally accepted by the checking software, databases and journals. To cover all reasonable non-standard settings, XPREP actually understands 413 different space groups! Best wishes, 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, 24 Sep 2007, Phil Evans wrote: > I think this is only a problem in the primitive orthorhombic system (at least > I assume people don't want hexagonal axes along a, A & B centred lattices etc, > although there is no reason in principle why not). > > Following some earlier discussions with Ian, Pointless now honours (and > preserves) a reference file (HKLREF) in eg P 2 21 21, and also explicit > reindex operations, but an initial indexing will still enforce the "standard" > setting eg P 21 21 2, because I accept the "reference" setting from the cctbx > library > > ie suppose you have a crystal which when indexed with a <= b <= c and > Pointless decides unambiguously for the sake of argument) that the axis along > a is a 2-fold and the other two are 2(1) screws, ie space group P 2 21 21. > > At present this will be reindexed to the "standard" setting P 21 21 2, but is > that what you want, or should it be left as a<b<c? Which criterion takes > precedence? > > Phil > > > On 19 Sep 2007, at 17:54, Ian Tickle wrote: > > > Hi Sue > > > > It's certainly true that the convention in the 1935 and 1952 editions of > > IT Volume 1 *appeared* to be the 'standard setting' convention that you > > describe because only the 'standard' settings were listed, and this was > > the way that many crystallographers interpreted it (actually only > > macromolecular crystallographers, the small molecule people stick to the > > IUCr convention), so this is probably where you're coming from. However > > the 1983 edition of Volume A clarified the situation and made it clear > > that this was never the intention, so all the conventional settings are > > now shown on the SG diagram pages. P22121 & P21221 certainly are > > defined in IT Vol. A - look on the diagram page for SG no. 18 & you'll > > see them. > > > > The 'standard symbol' for a space group is merely the heading on the > > page used only for indexing purposes, so space groups P22121, P21221 and > > P21212 all have the same standard symbol P21212; hence the standard > > symbol is not unique and can't be used to unambiguously define the space > > group. The 'standard setting' is merely the space group setting that > > has the same name as the standard symbol. Even if that weren't true do > > we really want to be still sticking to a convention that was abandoned > > 25 years ago and doesn't a later convention override an earlier one > > anyway? > > > > Actually the convention in use is not the issue anyway, I don't care > > which convention is used as long as all programs use the same > > convention! - then I'll never need to permute axes (just as > > fundamentally I don't care which co-ordinate format is used as long as > > all programs use the same one, then I'll never need to reformat). So > > Mosflm uses the IUCr convention (i.e. a<=b<=c for primitive > > orthorhombic), and therefore any program which doesn't support that > > convention for any space group forces you to permute the axes completely > > unnecessarily. > > > > -- Ian > > > > > -----Original Message----- > > > From: Sue Roberts [mailto:[EMAIL PROTECTED] > > > Sent: 19 September 2007 16:38 > > > To: Ian Tickle > > > Subject: Re: [ccp4bb] arp/warp in p22121 > > > > > > Hi Ian > > > > > > But there's an older convention, which is to use the space groups > > > settings defined in the International Tables - and P22121 is not a > > > standard setting. > > > > > > Sue > > > > > > > > > On Sep 19, 2007, at 8:18 AM, Ian Tickle wrote: > > > > > > > I'm confused now, sticking to the IUCr convention should not > > > > require any > > > > axis permutation. My beef is specifically against unnecessary > > > > axis > > > > permutations! Surely it's when the program doesn't support the > > > > convention that you are forced to permute the axes? > > > > > > > > Besides I did solve a structure in P22121 with Phaser so > > > I'm even more > > > > confused! > > > > > > > > -- Ian > > > > > > > > > -----Original Message----- > > > > > From: [EMAIL PROTECTED] > > > > > [mailto:[EMAIL PROTECTED] On Behalf Of Airlie > > > > > McCoy > > > > > Sent: 19 September 2007 15:09 > > > > > To: CCP4BB@JISCMAIL.AC.UK > > > > > Subject: Re: [ccp4bb] arp/warp in p22121 > > > > > > > > > > > The problem is specifically that ARP/wARP *doesn't* > > > support the IUCr > > > > > > convention as given in IT (Vol. A, >= 1983 edition, Table > > > > > 9.3.4.1, p.758 > > > > > > in 5th ed.) regarding choice of cell in primitive > > > orthorhombic space > > > > > > groups, and I suspect in centred monoclinic ones also. > > > > > AFAIK ARP/wARP > > > > > > and pointless are the only two CCP4 programs that > > > > > > currently > > > > > don't fully > > > > > > support the IUCr convention > > > > > > > > > > Phaser doesn't "support" the IUCr convention, and if it was > > > > > used for the > > > > > original MR in this case (I don't know whether it was or > > > > > not), then it > > > > > would have caused the "problem". We have had user requests to > > > > > change the > > > > > output to the IUCr convention, but other people get confused > > > > > if the axes > > > > > are permuted. So the choice will be made an output option - > > > > > Frank von Delft > > > > > suggested the keyword "IUCR [ON/OFF]"! Vote for your choice > > > > > of default > > > > > now... > > > > > > > > > > Airlie McCoy > > > > > > > > > > > > > > > > > > > > > > Disclaimer > > > > This communication is confidential and may contain privileged > > > > information intended solely for the named addressee(s). It may > > > > not > > > > be used or disclosed except for the purpose for which it has been > > > > sent. If you are not the intended recipient you must not review, > > > > use, disclose, copy, distribute or take any action in > > > reliance upon > > > > it. If you have received this communication in error, > > > please notify > > > > Astex Therapeutics Ltd by emailing > > > > [EMAIL PROTECTED] > > > > and destroy all copies of the message and any attached documents. > > > > Astex Therapeutics Ltd monitors, controls and protects all its > > > > messaging traffic in compliance with its corporate email policy. > > > > The Company accepts no liability or responsibility for any onward > > > > transmission or use of emails and attachments having left > > > the Astex > > > > Therapeutics domain. Unless expressly stated, opinions in this > > > > message are those of the individual sender and not of Astex > > > > Therapeutics Ltd. The recipient should check this email and any > > > > attachments for the presence of computer viruses. Astex > > > > Therapeutics Ltd accepts no liability for damage caused by any > > > > virus transmitted by this email. E-mail is susceptible to data > > > > corruption, interception, unauthorized amendment, and tampering, > > > > Astex Therapeutics Ltd only send and receive e-mails on the basis > > > > that the Company is not liable for any such alteration or any > > > > consequences thereof. > > > > Astex Therapeutics Ltd., Registered in England at 436 Cambridge > > > > Science Park, Cambridge CB4 0QA under number 3751674 > > > > > > > > > > Sue Roberts > > > Biochemistry & Biophysics > > > University of Arizona > > > > > > [EMAIL PROTECTED] > > > > > > > > > > > > > > > > > > > > > Disclaimer > > This communication is confidential and may contain privileged information > > intended solely for the named addressee(s). It may not be used or > > disclosed except for the purpose for which it has been sent. If you are > > not the intended recipient you must not review, use, disclose, copy, > > distribute or take any action in reliance upon it. If you have received > > this communication in error, please notify Astex Therapeutics Ltd by > > emailing [EMAIL PROTECTED] and destroy all copies of the > > message and any attached documents. > > Astex Therapeutics Ltd monitors, controls and protects all its messaging > > traffic in compliance with its corporate email policy. The Company > > accepts no liability or responsibility for any onward transmission or use > > of emails and attachments having left the Astex Therapeutics domain. > > Unless expressly stated, opinions in this message are those of the > > individual sender and not of Astex Therapeutics Ltd. The recipient should > > check this email and any attachments for the presence of computer > > viruses. Astex Therapeutics Ltd accepts no liability for damage caused by > > any virus transmitted by this email. E-mail is susceptible to data > > corruption, interception, unauthorized amendment, and tampering, Astex > > Therapeutics Ltd only send and receive e-mails on the basis that the > > Company is not liable for any such alteration or any consequences > > thereof. > > Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science > > Park, Cambridge CB4 0QA under number 3751674 > >
