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<b<c, CELL-BASED in Pointless), and the alternative
(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
