Hi,
I was referring to P42(1)2, which is the CCP4 symmetry number 90.
I am working on 2D membrane protein crystals and cryo-electron microscopy
images of these, where I initially deal with two-dimensional projection images,
which are eventually merged into a 3D dataset. Therefore my sloppy formulation.
Thanks for the suggestions from several people on this list.
What I am doing now, and what works well, is:
\rm -f SCRATCH/merge3Dref-clean.mtz
#
${bin_ccp4}/sftools << eof
read SCRATCH/merge3Dref.mtz
sort h k l
set spacegroup
${CCP4_SYM}
select phaerr
select invert
purge
y
write SCRATCH/merge3Dref-clean.mtz
quit
eof
#
\rm -f SCRATCH/merge3Dref-clean-p1.mtz
#
${bin_ccp4}/cad hklin1 SCRATCH/merge3Dref-clean.mtz hklout
SCRATCH/merge3Dref-clean-p1.mtz << eof
reso overall 10000 1
outlim spacegroup 1
labin file 1 all
end
eof
#
\rm -f merge3Dref.mtz
#
${bin_ccp4}/sftools << eof
read SCRATCH/merge3Dref-clean-p1.mtz
sort h k l
set spacegroup
1
reduce matrix 1 0 0 0 1 0 0 0 1
write merge3Dref.mtz
quit
eof
#
All the best,
Henning.
On Apr 12, 2012, at 6:10 PM, Ian Tickle wrote:
> Yes I was also confused by the fact that P4212 is obviously a space
> group (upper case 'P') whereas p4 and p1 are plane groups (lower case
> 'p'), as stated. Not sure what 'p2121' is though, I assumed it was
> somehow related to the p2gg plane group (no 8). Also there's no plane
> group 'p6212', but then there's no space group 'P6212' either.
>
> Perhaps the original poster could clarify and take care with his P's and p's?
>
> Cheers
>
> -- Ian
>
> On 12 April 2012 16:51, Bart Hazes <bha...@ualberta.ca> wrote:
>> I am confused by the discussion on this message. Although it says plane
>> group I assume it really is a normal 3D tetragonal space group, P42(1)2
>>
>> So Eleanor's suggestion should work and sftools expand command will do the
>> job as well.
>>
>> Bart
>>
>>
>> On 12-04-12 05:03 AM, Eleanor Dodson wrote:
>>
>> Apologies - I didn't notice the plane group..
>> Although I think if the sym ops are correctly listed in the P4121 file they
>> will just be applied as given..
>> Eleanor
>>
>> On 12 April 2012 11:58, Ian Tickle <ianj...@gmail.com> wrote:
>>>
>>> I didn't realise the CCP4 suite could handle the plane groups: where
>>> are they listed (they're not in symop.lib or syminfo.lib)? Or are
>>> they doing some clever projections of the space groups?
>>>
>>> Cheers
>>>
>>> -- Ian
>>>
>>> On 12 April 2012 11:48, Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote:
>>>> Cad will do this correctly
>>>> Reflection utilitied - merge mtz ( rather confusing job title - sorry..)
>>>> mtz in - the P4121.mtz data
>>>> Output - P41212-ext.mtz
>>>>
>>>> Defne mtz output
>>>>
>>>> Select define limit for refl;action by Laue code select P1
>>>>
>>>> then you will get a list of all P1 reflections with phases correctly
>>>> modified.
>>>>
>>>> If you really want to work in P1 you will need to change the space group
>>>> in
>>>> P41212-ext.mtz
>>>> Easiest way is
>>>> mtzutils hklin1 P4121-ext.mtz hklout P41212-ext-symP1.mtz
>>>> SYMM P1
>>>> end
>>>>
>>>> DONT change the G of P41212.mtz before doing the extension - the program
>>>> needs the P41212 sym ops to change the phases correctly..
>>>>
>>>> If you want the coordinates extended too
>>>> use pdbset to get a P1 set of cds.. (Coordinate utilities
>>>> Edit pdb
>>>> select pdbset and "generate chains by symmetry operators"
>>>> eleanor
>>>> Eleanor
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On 12 April 2012 06:51, Henning Stahlberg <henning.stahlb...@unibas.ch>
>>>> wrote:
>>>>>
>>>>> Hi Everybody,
>>>>>
>>>>> I am working in a P4212 plane group, which is a p4 symmetric structure
>>>>> with a screw axis in addition. My map has in the unit cell two 4-fold
>>>>> symmetric structures, one if which is upside-down with respect to the
>>>>> other
>>>>> one. If using expand in sftools, then the resulting map is p4
>>>>> symmetrized
>>>>> in the center between two p4-symmetric structures, which is wrong. This
>>>>> is
>>>>> probably the phase origin problem referred to here:
>>>>> http://www.ccp4.ac.uk/dist/html/sftools.html#expand
>>>>>
>>>>> Would anybody have a suggestion how I can expand the p4212 MTZ file to
>>>>> full p1, but with properly respecting the symmetry phase origin?
>>>>>
>>>>> My illiterate guess would be to either
>>>>> 1) shift the phase origin in the p4212 MTZ file by (180.0;0.0); then
>>>>> use
>>>>> sftools with "expand 1" to create the full reflection sets in p1; then
>>>>> shift
>>>>> back by (180.0;0.0); or
>>>>> 2) use sftools with the command "expand 1", and then modify (invert?)
>>>>> the
>>>>> phases of the reflections in the quadrants that have wrong phases.
>>>>>
>>>>> In option 1) I am not sure if it is possible to shift phase origin,
>>>>> while
>>>>> staying in p4212 symmetry. How could I do that?
>>>>> In option 2) I would probably get into deep water the next time I work
>>>>> with another symmetry, like p6212, or p2121, where I would have to deal
>>>>> not
>>>>> with quadrants but with triangles of 60deg angle?
>>>>>
>>>>> Any suggestions would be highly appreciated.
>>>>>
>>>>> All the best,
>>>>>
>>>>> Henning.
>>>>>
>>>>> Henning Stahlberg, PhD
>>>>> Prof. for Structural Biology, C-CINA, Biozentrum, University Basel
>>>>> Mattenstrasse 26 | D-BSSE | WRO-1058 | CH-4058 Basel | Switzerland
>>>>> http://c-cina.org | Tel. +41-61-387 32 62
>>>>
>>>>
>>
>>
