Subject: | | Re: Merohedral twining for P212121. - |
From: | | Colin Nave <[log in to unmask]> |
Reply-To: | | [log in to unmask][log in to unmask], 8 Jun 2010 22:04:48 +0200572_us-ascii Hi Sean,
do the ligand and the Thr belong to the same chain, and did you check that the distance between the bonding atoms is not beyond coot's cut-off?
Tim
On Tue, Jun 08, 2010 at 11:16:03AM -0700, Sean Gay wrote: > I have used JLigand v 0.2.1 to create a link between a Thr residues and > a covalent adduct. The adduct refines well and shows up as a covalent > bond in PyMOL. However, when I'm in Coot there is no bond present > between the Thr OG1 and the ligand. I've loaded the Jligand link.lib > file [...][log in to unmask] |
Date: | | Tue, 22 Jun 2010 23:09:26 +0100 |
Content-Type: | | text/plain |
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Ian
Thanks - I did get my terminology wrong and terminology IS important.
The merohedral is incorrect for this case but I then confused things
further.
My interest was really what happened in the observed diffraction
pattern. With the large difference in the orthorhombic cell dimensions,
the spots will gradually separate for the higher orders. The point I
really wanted to discuss was whether there would be an advantage if one
could distinguish the spots and measure the intensity of each component.
I am sure one could do this - the question I had was whether it would be
useful.
Any comments appreciated.
Cheers
Colin
> -----Original Message-----
> From: CCP4 bulletin board [mailto:[log in to unmask]] On
> Behalf Of Ian Tickle
> Sent: 22 June 2010 17:35
> To: [log in to unmask]
> Subject: Re: [ccp4bb] Merohedral twining for P212121.
>
> On Tue, Jun 22, 2010 at 4:32 PM, Colin Nave
> <[log in to unmask]> wrote:
> > Secondly, the difference in the cell dimensions (b=123.92 and
> > c=128.89A) appears to be quite large and should lead to split spots
> > which (I think) corresponds to non merohedral twinning. Did you
> > observe these but integrated them as one?
>
> The distinction between merohedry (incl. pseudo-merohedry)
> and non-merohedral twinning is not whether the spots are
> split: splitting to a greater or lesser degree is often
> observed in the pseudo-merohedral case since the pseudo-twin
> law is never perfect.
> Rather the defining feature is whether the overlap of the
> twin-related lattices occurs in 3 dimensions (i.e. exact
> overlap for merohedry, or approximate for pseudo-merohedry)
> or only 2 in the non-merohedral case. In the latter case
> this means that there's no obvious relationship between the
> spot positions for the components of the twin (except
> possibly in the zone related to the plane of 2-D overlap).
>
> Cases where 3-D overlap occurs only for some integer fraction
> of the spots are often mistakenly termed 'non-merohedral'
> even though overlap occurs in 3-D and so there's a clear
> relationship for the fraction of spots that are twin-related.
> The correct term for this case is 'reticular merohedry' (or
> 'reticular pseudo-merohedry'). A nice site where all the
> twinning terminology is clearly defined is:
>
> http://www.lcm3b.uhp-nancy.fr/mathcryst/twins.htm
>
> > (Regarding what to call the twinning I have some sympathies with
> > Humpty Dumpty's view "When I use a word... it means just
> what I choose
> > it to mean-neither more nor less" As important a philosopher as
> > Wittgenstein.)
>
> But it helps a lot if everyone can agree on the terminology
> (e.g. on the precise definition of 'non-merohedral') - most
> of the arguments on the BB seem to stem from the use of
> conflicting definitions!
>
> Cheers
>
> -- Ian
>
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