Re: [ccp4bb] space groups not supported by Refmac5

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: Rfactor got stuck with a data having alternate strong and weak reflections.
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-09-02

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From: John Rose rose {- at -} BCL4 {- dot -} BMB {- dot -} UGA {- dot -} EDU
Date: 2009-09-02

Subject: Re: space groups not supported by Refmac5
From: Phil Evans pre {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2009-09-02

Just to clarify this again: the question of "standard" settings for
primitive orthorhombic space groups (& the I2/C2 choice) was raised by
Ian Tickle in earlier discussions. He pointed out that the IUCr
standard was to choose a < b < c for primitive orthorhombic
irrespective of which axes are 2 or 2(1), and to choose either I2 or
C2 to give the smaller beta angle

his references

http://nvl.nist.gov/pub/nistpubs/jres/106/6/j66mig.pdf
http://nvl.nist.gov/pub/nistpubs/jres/107/4/j74mig.pdf

This makes sense as you can generally make a < b < c at the indexing
stage (unless some lengths are equal) before you know which axes are 2
or 2(1), and then you don't have to reindex later. For the I2/C2
choice, it is somewhat more convenient to have a less oblique axis
system if you can.

I made POINTLESS follow these conventions by default, but you do have
a choice. These settings should then be referred to as the "standard"
settings (ie a(SYMMETRY-BASED in Pointless) may be called "reference" settings (eg
always P21 21 2 for space group 18).

Most crystallographic software that we use is happy with non-reference
space groups eg space group P2 21 2 : all CCP4 and Phenix programs
are, as far as I know. The exceptions which don't work (and that I
know about) are:-

1) Arp/warp: Victor Lamzin has I believe promised (Victor?) that the
imminent new released version will work for these settings

2) Sharp: Clemens Vonrhein told me that he hoped the next release of
Sharp would handle these cases

I know this is a bit inconvenient at present, but I thought it a Good
Thing to follow recognised conventions (and to force software
developers to make their programs more general :-))

Phil Evans

On 18 Aug 2009, at 12:48, Michele Lunelli wrote:

> Dear Arefeh,
>
> Arp/warp works with standard space groups, therefore you have to
> reindex P21221 to P21212. In this
> message from Anastassis Perrakis you can find some advice:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0709&L=CCP4BB&T=0&F=&S=&P=100954
>
>
> Michele
>
>
>
> Arefeh Seyedarabi wrote:
>> Hi,
>>
>> I have a question; recently I have encountered a few space groups
>> which are
>> not supported by Refmac5. Examples include I2 and P21221. Both
>> these space
>> groups have been identified as the best solutions for the two
>> different
>> datasets I am working on using Pointless. However, I am faced with
>> difficulties in Refmac5, and the program fails to complete when I
>> select
>> refinement cycles with Arp-waters...with the message saying 'space
>> group not
>> supported'.
>>
>> Any suggestions on how this problem could be overcome?
>>
>> Regards,
>>
>> Arefeh
>>

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999