Hi Jiamu,

We don't want to do that because we already have some near-isomorphous
datasets for native and protein-ligand complexes indexed according to
the conventional orthorhombic setting (a<=b<=c); we don't want to have
to revisit those since they are finished structures, and obviously it's
very desirable for all near-isomorphous structures to be indexed in the
same way - for one thing it makes MR so much easier because you need
only do a limited search around the starting positions of each monomer,
which eliminates all false solutions and also saves a lot of time.

In fact Garib already confirmed that Refmac is equally happy whether the
setting is P22121 or P21212 (AFAIK this is or will soon be true of all
CCP4 software, however I'm aware of at least a few non-CCP4 programs
that currently restrict the user to the 'standard' settings!).

In any case, the fact that P21212 is the 'standard' form of the
Hermann-Mauguin symbol P22121 is completely irrelevant.  The "standard
H-M symbol" is only of interest in theoretical crystallography, for
example in categorising space-group symbols, e.g. if you want to decide
in software whether P22121, P21221 & P21212 are just rotated settings of
the same space group, you reduce each symbol to the standardised
symbolic form, in this case P21212, then do a string comparison and hey
presto you discover they're identical, whereas say P2122 reduced to
standard form (P2221) clearly isn't.  This is made clear in Int. Tab.
Cryst. Vol. A (5th ed., 2002) Section 12.3.4. "Standardization rules for
short symbols" (p. 832 in my ed.); see also Table 12.3.4.1. "Standard
space-group symbols" (p. 824).

But this is just about theoretical symbol manipulation, it has nothing
whatsoever to do with the practical aspects of choosing the
*conventional* settings of the space groups.  These are defined in Table
9.3.4.1. "Conventional cells" (p. 758).  For all orthorhombic space
groups (except end-centred ones) the convention is a <= b <= c, and the
conventional space-group symbol follows from that convention and the
observed systematic absences, hence in my case with a=63.968, b=66.886,
c=93.360 and sys. abs. on 0k0 and 00l the conventional symbol is P22121.

I think this situation arose in the 70's and 80's because software
writers saw that limiting users to the 'standard settings' was a way of
reducing the amount of work they needed to do to code the space-group
information, ignoring established conventions in the process, so the
convention became re-defined by the programmers - but in my view
software should always follow the science, it should never lead or limit
it.

Ralf Grosse-Kunstleve has done an excellent job of tabulating the
properties of all space groups (in $CLIBD/syminfo.lib) in
machine-readable form, so there's no longer any excuse for not doing it
properly!

Cheers

-- Ian
 

> -----Original Message-----
> From: Jiamu Du [mailto:[log in to unmask]] 
> Sent: 21 March 2007 01:45
> To: Ian Tickle
> Subject: Re: [ccp4bb] Warning messages from Refmac.
> 
> You can reindex you data to SG P21212. This is the standard SG.
> I have met this case just a week before.
>  
> On 3/20/07, Ian Tickle <[log in to unmask]> wrote: 
> 
> 
> 	All - I'm refining some structures in SG P22121 and I 
> lots of warning
> 	msgs from Refmac: "===> Warning: No such space group in 
> ASYLIM". 
> 	
> 	The job seems to run fine & I can't see anything 
> untoward with the
> 	results or the output files, so I was just wondering 
> whether I need be
> 	concerned about the messages?  It would be a pain to 
> have to re-index 
> 	everything to P21212, particularly if it's not necessary!
> 	
> 	Thanks a lot in advance.
> 	
> 	-- Ian
> 	
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> Astex Therapeutics Ltd by emailing 
> [log in to unmask] and destroy all copies of the 
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> 	
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> all its messaging traffic in compliance with its corporate 
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> -- 
> Jiamu Du
> State Key Laboratory of Molecular Biology
> Institute of Biochemistry and Cell Biology Shanghai 
> Institutes for Biological Sciences
> Chinese Academy of Sciences (CAS) 
> 

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 [log in to unmask] 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.