I'm coming in late here, having only now found time to look at the images. 
It's facinating, isn't it?

Since the lines are not arcs centered on the origin, this isn't mosaic 
spread.

For those who haven't seen the image and the zoom, the diffraction pattern 
clearly shows one very long axis and a couple of much shorter ones.  The 
rotation image is taken rotating around the long one.  The small lines are 
perpendicular to the long axis, and run fairly continuously, narrowly and 
evenly spaced at the intervals of the reflections along this axis, 
throughout the diffraction pattern. They're all faint and about the same 
intensity, and modulated along their length only slightly.  Also it 
appears that this is a rotation of about one degree; Margriet doesn't give 
us clues for any of this.

I'm guessing that whoever said it's a diffuse scatter effect is close to 
the mark.  I think diffuse scatter comes from the contents of each unit 
cell being essentially identical, but that within the molecule things are 
waving around a bit (where are Don Caspar and George Phillips when we need 
them?), that is, different in each unit cell. I'll go a touch farther and 
suggest that it's really disorder -- each unit cell is well aligned to the 
others, but each one is different in a more significant way.  I'll guess 
that the RNA decamer is aligned along this long unit cell axis, but in 
some way either there's an opportunity for the register along the RNA axis 
to slip from one unit cell to the other or each is rotated slightly.

On the other hand, the fact that there's a wide distribution of 
intensities in the Bragg spots, which are quite sharp, is confusing -- 
there must be a lot of contrast in the averaged structure for this to be 
true.

Ok, it's interesting, but I have no idea.

Bob


On Wed, 28 Jan 2009, Jacob Keller wrote:

> There is something in the unit cell, aligned with the long axis of the cell, 
> with a periodicity corresponding to ~1/5 of the long axis. This can be seen 
> as greater intensities along the long axis every fifth spot. Without knowing 
> the unit cell parameters, I would guess it is either the interplanar spacings 
> of the nucleotides (probably this is too small) or the periodic twist of the 
> helix itself. Interesting that the RNA is a decamer ( = 2 x 5). I would be 
> curious to know what the unit cell parameters are, or more generally, what is 
> causing that noticeable periodicity...
>
> Jacob
>
> *******************************************
> Jacob Pearson Keller
> Northwestern University
> Medical Scientist Training Program
> Dallos Laboratory
> F. Searle 1-240
> 2240 Campus Drive
> Evanston IL 60208
> lab: 847.491.2438
> cel: 773.608.9185
> email: [log in to unmask]
> *******************************************
>
> ----- Original Message ----- From: "James Holton" <[log in to unmask]>
> To: <[log in to unmask]>
> Sent: Wednesday, January 28, 2009 12:20 PM
> Subject: Re: [ccp4bb] small lines in diffraction pattern
>
>
>> Hmm.  I don't remember that thread.  However, I personally think it is a 
>> good idea to keep the "mosaic crystal" as Ewald and Darwin defined it. Just 
>> because current integration software lumps things together into a 
>> "mosaicity" does not mean that every mechanism contributing to the rocking 
>> width of a spot should be given the same name.  Especially when it is 
>> difficult to describe the mosaic crystal using any other words.  Perhaps 
>> Colin could come up with a cool word for unit cell non-uniformity?  Or is 
>> he waiting for us to name it after him?  "Nonuniform Anisotropic Variance 
>> of Elasticity"?  or "Cells Of Loose INdex"?
>> 
>> Comments and suggestions are welcome.
>> 
>> -James Holton
>> MAD Scientist
>> 
>> Jacob Keller wrote:
>>> I had thought that in a previous thread, we had all come to a consensus 
>>> that actually the largest source of what is normally explained as 
>>> "mosaicity" is really differences in unit cell size, due perhaps to uneven 
>>> shrinkage in crystals upon freezing or otherwise. I believe that there was 
>>> actually an acta cryst paper which investigated all of the various 
>>> ingredients of "mosaicity" which supports this (this is why I said it.)
>>>  Jacob
>>>  *******************************************
>>> Jacob Pearson Keller
>>> Northwestern University
>>> Medical Scientist Training Program
>>> Dallos Laboratory
>>> F. Searle 1-240
>>> 2240 Campus Drive
>>> Evanston IL 60208
>>> lab: 847.491.2438
>>> cel: 773.608.9185
>>> email: [log in to unmask] <mailto:[log in to unmask]>
>>> *******************************************
>> 
>