[ccp4bb] Workshop on image processing of electron crystallography data: Aug. 19-25, 2012
Workshop on Image Processing with 2dx August 19-25, 2012, in Basel, Switzerland. We invite for applications to participate in the fourth international workshop on electron crystallography of membrane proteins. This workshop will focus on data processing, with emphasis on 3D reconstructions from images of tilted 2D crystals. The hand-on workshop on the processing of images from cryo-electron microscopy of 2D crystals of membrane proteins (electron crystallography) will provide the theoretical background and practical applications in advanced image processing algorithms. The workshop will use the 2dx software system, which is based on the MRC programs. Theoretical morning lectures will be followed by practical exercises in the afternoon. Although we will provide iMacs for every participant, you are encouraged to bring your own laptop (Linux or OSX), or at least a portable hard-drive (USB2.0), onto which we will install the relevant software systems and test data during the workshop. You are also welcome to bring your own dataset. Speakers and instructors include: Marcel Arheit, C-CINA, Biozentrum, University of Basel, Switzerland. Daniel Castano-Diez, C-CINA, Biozentrum, University of Basel, Switzerland Anchi Cheng, Scripps, CA, USA. Hans Hebert, Karolinska, Stockholm, Sweden. Cristina Paulino, MPI for Biophysics, Frankfurt, Germany. Sebastian Scherer, C-CINA, Biozentrum, University of Basel, Switzerland Henning Stahlberg, C-CINA, Biozentrum, University of Basel, Switzerland. Xiangyan Zeng, FVSU, GA, USA The detailed program is available here: http://www.2dx.unibas.ch/workshop/2012 A registration fee of 300 CHF (approx. $340) for participants from non-profit organizations includes lunch and snacks. Registration is open here: http://www.2dx.unibas.ch/workshop/2012/registration-for-the-workshop Oganizers: Marcel Arheit, Karen Bergmann, and Henning Stahlberg. All the best, Henning Stahlberg. 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
Re: [ccp4bb] Expanding p4212 coordinates to p1
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 1 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 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 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 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
>>>> 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
[ccp4bb] Expanding p4212 coordinates to p1
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
