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: [log in to unmask]
[mailto:[log in to unmask]] On Behalf Of Eleanor Dodson
Sent: 15 December 2008 09:56
To: Ronald E Stenkamp
Cc: [log in to unmask]
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:[log in to unmask]]
On Behalf Of
Eleanor Dodson
Sent: 11 December 2008 09:41
To: [log in to unmask]
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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