But that only means that the SF contribution from that pair of molecules in the
unit cell is zero for (00l) l=odd reflections. Depending on the
crystallographic symmetry (e.g. if it were 3-fold or higher order) there may be
other pairs for which the SF contribution is non-zero for all (00l) (but zero
for the the odd orders in some other line that is symmetry-equivalent to (00l)).
So for example I did a test with 2 mols in the a.u. related by an exact
(0,0,1/2) NCS translation in P222:
h k l Fcalc phicalc
0 0 1 0.00 180.00
0 0 2 5120.88 180.00
0 0 3 0.00 180.00
0 0 4 1273.09 0.00
0 0 5 0.01 0.00
0 0 6 260.21 180.00
0 0 7 0.00 180.00
0 0 8 39.42 180.00
0 0 9 0.01 0.00
0 0 10 43.19 0.00
0 0 11 0.00 180.00
0 0 12 118.59 180.00
0 0 13 0.01 0.00
0 0 14 120.89 180.00
0 0 15 0.01 0.00
(00l) l odd are definitely absent here! - because none of the crystallographic
2-folds affect the (0,0,1/2) translation.
Then I generated 2 mols in the a.u. related by the (1/2,0,0) NCS translation in
P4 to get the (h00) line (note that the 4-fold along c would not affect a
c-axis translation):
1 0 0 25189.10 0.00
2 0 0 200.09 0.00
3 0 0 14404.46 180.00
4 0 0 12608.60 180.00
5 0 0 4669.64 180.00
6 0 0 748.81 0.00
7 0 0 3184.06 0.00
8 0 0 3858.87 0.00
9 0 0 2578.38 0.00
10 0 0 382.61 0.00
11 0 0 683.43 180.00
12 0 0 444.89 180.00
13 0 0 236.65 180.00
14 0 0 352.46 180.00
15 0 0 5.62 0.00
No absences! The 4-fold generates a pair of molecules related by the
(0,1/2,0), not the (1/2,0,0) translation. So Eleanor is right only in specific
cases, Ronald is right in the general case.
As an aside, while I was verifying this, I think I found a problem with the P3
specific SF calculation in SFALL. Here's what I get for 2 mols in the a.u.
related by an exact (0,0,1/2) NCS translation in P3 using the default P3
specific routine:
0 0 1 8.24 -175.63
0 0 2 7339.05 121.46
0 0 3 27.32 125.92
0 0 4 949.76 -10.37
0 0 5 39.10 -103.39
0 0 6 461.79 -115.99
0 0 7 19.18 61.53
0 0 8 219.72 -96.80
0 0 9 66.51 -174.45
0 0 10 288.25 -86.65
Now if I use the P1 routine (SFSG 1):
0 0 1 0.00 165.96
0 0 2 7343.28 121.51
0 0 3 0.00 -24.58
0 0 4 974.19 -13.35
0 0 5 0.00 -155.29
0 0 6 438.79 -115.60
0 0 7 0.01 133.49
0 0 8 226.07 -97.44
0 0 9 0.01 -101.82
0 0 10 291.15 -83.96
The 3-fold along c should not generate any pairs not related by the (0,0,1/2)
NCS translation, so there should be (00l) l odd absences in this case. So
something wrong here! Personally I always use the P1 routines, why take a
chance just to shave a few secs off the run time? (note that ccp4i uses the
default, i.e. the space-group specific routines).
Cheers
-- Ian
> -----Original Message-----
> From: owner-ccp...@jiscmail.ac.uk
> [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Eleanor Dodson
> Sent: 15 December 2008 09:56
> To: Ronald E Stenkamp
> Cc: CCP4BB@jiscmail.ac.uk
> Subject: Re: [ccp4bb] About system absence in P4222?
>
> Plug the coordinates (x,y,z) and x+tx, Y+ty, z+tz) into the
> SF equation.
> If the translation component along c is 0.5 say, then all the 00l
> reflections for l=2n+1 will be absent.
>
> Eleanor
>
>
> Ronald E Stenkamp wrote:
> > Hi.
> >
> > Non-crystallographic symmetry (NCS) doesn't apply to the entire
> > crystal, so how can it give rise to systematic absences? I know it
> > can give rise to systematically weak classes of
> reflections, but they
> > aren't entirely absent.
> >
> > Ron
> >
> > On Thu, 11 Dec 2008, Winter, G (Graeme) wrote:
> >
> >> One of the many facilities in pointless is to search for
> absences and
> >> provide a list of likely spacegroup choices based on the
> results. It
> >> includes adjustments for neighbouring spots to address one of
> >> Eleanor's concerns. NCS can cause reflections to be systematically
> >> absent too.
> >>
> >> The program can be found on the ccp4 prerelease pages or on the
> >> pointless ftp site.
> >>
> >> Cheers,
> >>
> >> Graeme
> >>
> >> -----Original Message-----
> >> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk]
> On Behalf Of
> >> Eleanor Dodson
> >> Sent: 11 December 2008 09:41
> >> To: CCP4BB@JISCMAIL.AC.UK
> >> Subject: Re: [ccp4bb] About system absence in P4222?
> >>
> >> 劉家欣(NTHU) wrote:
> >>> Dear All:
> >>>
> >>> We have a crystl with P4222 sg.
> >>> All statistics look fine.
> >>> However, there is a system absense in l axis.
> >>> Any body have experiences on that?
> >>> Any suggestions would be high appreciated.
> >>>
> >>> jaishin
> >>>
> >> can you give more details, eg all reflections along the particular
> >> axis..
> >> Things like ice rings or overlapping intensity from a next
> neighbour
> >> getting integrated inapropriately can cause anomalies..
> >> Eleanor
> >>
> >
> >
> >
>
>
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