[phenixbb] P43212 spacegroup change to C2221?

[Andreas Forster]

Ah, Peter, cool stuff indeed.  I tried to follow your procedure with P65:

phenix.python $somedriectory/cctbx/examples/sub_group_graphy.py  P66 > tmp.com
chmod +x tmp.com
tmp.com  # fails:  bash:  tmp.com:  command not found
./tmp.com
# also fails with the following error message

./tmp.com: line 2: ----------------------------: command not found
./tmp.com: line 4: Outgoing: command not found
./tmp.com: line 5: P: command not found
./tmp.com: line 6: P: command not found
./tmp.com: line 7: P: command not found
./tmp.com: line 8: P: command not found
./tmp.com: line 10: syntax error near unexpected token `('
./tmp.com: line 10: `P 1  --->  P 65  ::    using: (x-y,x,z+5/6)
(y,-x+y,z+1/6)  (-y,x-y,z+2/3)  (-x+y,-x,z+1/3)  (-x,-y,z+1/2)
symops left: 0'

Three empty files are generated: [], [P 65, and [P 65].

Any suggestions?  Dot is installed.  OS is RHEL 5.4.  Phenix is 1.4-3
(cctbx tag: 2008_12_07_1353)


Andreas


On Wed, Aug 26, 2009 at 11:36 PM, Peter Zwart<phzwart at gmail.com> wrote:
>> 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
>>>>
>>>> _______________________________________________
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>>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>>
>>>
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>
>
>
> --
> -----------------------------------------------------------------
> 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
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