[phenixbb] P43212 spacegroup change to C2221?

[Peter Zwart]

> Because it's a cool way for getting your head around the twinning
> problems...
> Cheers
> phx


Indeed, that is what it was written for.

try something like

phenix.python $somedriectory/cctbx/examples/sub_group_graphy.py  P432 > tmp.com
chmod +x tmp.com
tmp.com
display sg_graph.png

you need to have dot installed (comes with ccp4)

HTH

Peter






>
>
> Peter Zwart wrote:
>> Can you send the exact unit cell parameters? The number you give now
>> are to rough to make a fair comparison.
>>
>> In any case, C2221 does lie directly below P43212 (see attached
>> figure), so you have a good chance that is a possibility.
>> On the other hand, so are P43 and P212121.
>> It is fairly straightforwadr to try all, just cumbersome.
>> I suggest however you get your data in P1, and solve it in that spacegroup.
>> Subsequently, run
>>
>> phenix.xtriage p1data.mtz reference.structure.file=MR.1.pdb
>>
>> and start interpreting the RvsR tables.
>> Contact me directly if you have difficulties with this, or share with
>> the bb as this is a very instructive exercise.
>>
>> Cheers
>>
>> Peter
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> 2009/8/25 Leigh Allen <c.leigh.allen at gmail.com>:
>>
>>> Hello Phenix users.
>>>
>>> I recently solved the structure of my enzyme using SAD to a resolution of
>>> 1.9A.  The R values were 0.19/0.25 and the space group was P43212 with a
>>> unit cell ~80, 80, 220.
>>>
>>> I then starting collecting datasets cocrystallized with ATP analogs and
>>> noticed that a lot of my datasets have a different unit cell when scaled in
>>> P43212.  It comes out to be ~60, 60, 220 and I can NOT get a solution in
>>> Phaser with this data.  If I scale it in C2221, then the unit cell is the
>>> same (80, 80, 220), but upon refinement, the R factors don't go much below
>>> 0.26/0.32.  Has anyone ever seen something like this happen?  I'm unsure if
>>> I should feel like the solution is C2221 since there are space groups of
>>> higher symmetry with similar residuals that seem plausible in indexing just
>>> the smaller unit cell. Should I keep trying to get a solution out of the
>>> data that leads to different unit cell parameters, but has higher symmetry?
>>>
>>> Xtriage seems to find twinning, but I think it's from NCS since my ASU
>>> contains a homodimer.  I could also be wrong about this...
>>>
>>> Thanks in advance for any advice!
>>>
>>> *******
>>> Leigh Allen
>>> Ph.D Candidate
>>> McCafferty Lab
>>> Duke University
>>> Department of Chemistry
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>>
>>>
>>>
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>



-- 
-----------------------------------------------------------------
P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB:     http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
CCTBX:  http://cctbx.sf.net
-----------------------------------------------------------------