On second reading maybe I misunderstood what you were saying. If Phaser reads an MTZ file which doesn't conform to the convention (e.g. a<=b<=c NOT true in primitive orthorhombic) then it certainly should not by default permute the axes on output, I agree that that certainly would cause confusion.
However Phaser does accept an MTZ file which does conform (e.g. P22121 a<=b<=c) and doesn't (and shouldn't) permute the axes. So I vote for a default of preserving the input convention whatever it is, and I definitely vote against all axis permutations unless a) it's absolutely necessary (e.g. for consistency with other datasets), and b) the user specifically requests it (and really really means it!). -- 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
