Hi Sjors and Marin

Thanks for your symmetry tutoring, which helped a lot.
The fact that “T" already contains 12 asymmetric units explains the nice map I got from a fairly small number of particles ;)

Thanks and best,
Sebastian 

> On Mar 9, 2015, at 11:01 PM, Sjors Scheres <[log in to unmask]> wrote:
> 
> Thanks Marin! I mis-read Sebastian's message. So, Sebastian, in that case
> you've already done what you should do. :-)
> In general, when in doubt about symmetry operators, one could use:
> "relion_refine --sym T --print_symmetry_ops" to get a list of all of them.
> For T it gives 12 operators, for the 12 "monomers".
> HTH, S
> 
> 
> 
>> Hi Sebastian,
>> 
>> I think there is some misunderstanding here. The 'T' point-group
>> symmetry has a minimum of 12 asymmetric units; it has four 3-fold axes,
>> and six 2-fold axes. The orientation of the T point-group symmetry
>> within a Cartesian X-Y-Z co-ordinate system is normally along a set of
>> orthogonal 2-fold axes. The 222 (=D2) pointgroup symmetry is a subset of
>> the T (=23) pointgroup symmetry, the way the 222 pointgroup symmetry is
>> a subset of the the Icosahedral (=532) pointgroup symmetry. (See:
>> http://www.singleparticles.org/methodology/MvH_Pointgroup_Symmetry.pdf).
>> There thus always are 3 asymmetric units ('monomers') around each 3-fold
>> axis of the 'T' pointgroup symmetry (4x3 = 12 asymmetric units). There
>> is nothing to be gained when you relax the pointgroup symmetry to C3!
>> You then only average over 3 monomers rather than 12.  Thus the FSC
>> resolution (Harauz & van Heel 1986)  will only drop if you refine in
>> C3.  As a side note, when I programmed this point-group symmetry in
>> Imagic (together with all other possible point-group symmetries), some
>> thirty years ago, there were no known T-symmetric oligomers.  ;)
>> 
>> Hope this helps
>> 
>> Marin
>> 
>> ====================================================================================================
>> 
>> 
>> On 08/03/2015 09:15, Sjors Scheres wrote:
>>> Hi Sebastian,
>>> I guess that what you are describing is a case of "local" symmetry, i.e.
>>> it is not true symmetry in that it does not hold for the entire
>>> particle.
>>> If this is the case, then you should run a refinement in tetrameric
>>> symmetry (like you did), then cut out the 3 pseudo-symmetrical subunits
>>> from the unfil.mrc maps, and then use some 3D program to align and
>>> average
>>> over these 3 subunits. This will give you a further improvement in
>>> resolution for your subunits. Similar procedures are used frequently for
>>> T>1 icosahedrl viruses. One example that jumps to my mind is the
>>> rotavirus
>>> structure from Niko Grigorieff.
>>> BTW: Estimating a "gold-standard" FSC for the locally-averaged half-maps
>>> may become a bit more difficult due to the masks involved in the local
>>> averaging.
>>> HTH,
>>> S
>>> 
>>> 
>>>> Hi
>>>> 
>>>> I'm working on a protein that has a tetrameric symmetry (symmetry: T).
>>>> Each face of the tetramer features an additional C3 symmetry.
>>>> Thus each particle has 12 asymmetric units.
>>>> My initial runs with symmetry=T (4 asymmetric units per boxed particle)
>>>> where very successful, but now I'm interested in applying the
>>>> whole/right
>>>> symmetry during the refinement.
>>>> 
>>>> Is there a symmetry option (or hack) that fulfils my needs?
>>>> 
>>>> Thanks and best,
>>>> Sebastian
>>>> 
>>> 
>> 
>> 
>> --
>> ================================================================
>> 
>>     Prof Dr Ir Marin van Heel
>> 
>>     Professor of Cryo-EM Data Processing
>> 
>>     Leiden University
>>     NeCEN Building Room 05.27
>>     Einsteinweg 55
>>     2333 CC Leiden
>>     The Netherlands
>> 
>>     Tel. NL: +31(0)715271424 // Mobile NL: +31(0)652736618
>>     Skype:    Marin.van.Heel
>>     email:  marin.vanheel(A_T)gmail.com
>>     and:    mvh.office(A_T)gmail.com
>> 
>> ----------------------------------------------
>> 
>>     Emeritus Professor of Structural Biology
>> 
>>     Imperial College London
>>     Faculty of Natural Sciences
>>     Biochemistry Building (Room 512)
>>     South Kensington Campus
>>     London SW7 2AZ,  UK
>>     email:  m.vanheel(A_T)ic.ac.uk
>> 
>>     Tel. UK:   +44(0)2075945316 //Mobile: +44(0)7941540625
>> 
>> ----------------------------------------------
>>     Visiting Professor at:
>> 
>>     Laboratório Nacional de Nanotecnologia - LNNano
>>     CNPEM/ABTLuS, Campinas, Brazil
>>     Brazilian mobile phone  +55-19-99369051
>> 
>> ------------------------------------------------------------------
>> 
>> I receive many emails per day and, although I try,
>> there is no guarantee that I will actually read each incoming email.
>> Moreover, our Spam filters can be strikt and sometimes make
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>> 
>> 
>> 
> 
> 
> -- 
> Sjors Scheres
> MRC Laboratory of Molecular Biology
> Francis Crick Avenue, Cambridge Biomedical Campus
> Cambridge CB2 0QH, U.K.
> tel: +44 (0)1223 267061
> http://www2.mrc-lmb.cam.ac.uk/groups/scheres
>