Hi Eleanor
According to the peak search the 3 highest peaks on the chi=180 section are
at:
| 3 90.00 -52.26 180.00 0.49 |
| 4 90.00 -73.73 180.00 0.47 |
| 5 90.00 -66.55 180.00 0.44 |
plus a lot of lower peaks on that section which are clearly in the noise.
However eyeballing that contoured section that's clearly not right: there
are no clear peaks at those positions and I bet the ones above would vanish
with higher contour levels.
The highest peaks are elsewhere on the contoured chi=180 section, i.e. due
to the 3 crystallographic 2-folds at:
90 0 180 (2_x)
90 90 180 (2_y)
0 0 180 (2_z)
The other peaks in the peak search could be similarly in error: it would
probably work better with a noise threshold. I would have more confidence
in the results if I saw the contoured sections for myself !
A peak on the chi=90 section doesn't necessarily imply a 4-fold axis (i.e.
a closed group). It could simply be 2 (or even 3) subunits related by a 90
deg. rotation (i.e. not a closed group). A 4-fold axis gives rise to
multiple overlapping peaks on the chi=90 and chi=180 sections (so the peak
heights would be greater).
Cheers
-- Ian
On Sat, 22 May 2021 at 18:14, Eleanor Dodson <eleanor.dod...@york.ac.uk>
wrote:
> Ian - I read the log file - agree, you cant get much from the pictures..
> But the peak heat of the translation vector is 50% od the origin - ie
> pretty strong..
> And ditto for the rotation angles - all 50% of origin too
> But of course any set of rotation angles does not have to generate a
> closed rotation system - they could be relating distant monomers..
> Cheers Eleanor
>
>
>
> On Sat, 22 May 2021 at 17:50, Ian Tickle <ianj...@gmail.com> wrote:
>
>>
>> Hi Eleanor
>>
>> On Sat, 22 May 2021 at 14:55, Eleanor Dodson <
>> 0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>>> And several strong rotations
>>> 180 0 90. - ie a 4 fold round the c axis?
>>> 0 0 60 - ie a 6 fold round the c axis?
>>>
>>
>> How can you tell that from the meagre information provided by MOLREP? An
>> NCS point group doesn't have to be a crystallographic one: it could be
>> 5-fold, 7-fold, 19-fold or indeed anything-fold and we're not given the
>> relevant sections to make a decision on that. MOLREP has an option to
>> choose a different angle for the 60 deg. section, but to sample the chi
>> angle at 5 deg. intervals would require running 32 jobs! It's much easier
>> to run POLARRFN once and get all the sections in one job.
>>
>> Also NCS doesn't even have to form a closed group, i.e. assuming there
>> are 2 subunits they don't have to be related by a 180 deg rotation (or 90
>> deg for 4 subunits, or 60 deg for 6). It could be any angle of rotation
>> relating 2 (or more) subunits.
>>
>> Then numerous two folds in the a b plane.
>>>
>>
>> Isn't that just noise because MOLREP has used a contour level that's much
>> too low? If you raise the contour levels that noise will disappear, and
>> maybe the c axis rotations as well (though I doubt that: the c axis peaks
>> look quite strong). I couldn't see how to change the contour levels in
>> MOLREP: again POLARRFN allows you to do that.
>>
>> Cheers
>>
>> -- Ian
>>
>>
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