[phenixbb] P43212 spacegroup change to C2221?

Fri Aug 28 06:00:14 PDT 2009

Thanks, Folmer, that did the trick.  So obvious, I should have tried
it myself...

Andreas

On Fri, Aug 28, 2009 at 1:05 PM, Folmer Fredslund<folmerf at gmail.com> wrote:
> Dear Andreas
>
>
> 2009/8/28 Andreas Forster <docandreas at gmail.com>:
>> 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)
>
> I just checked this myself and what I found worked perfectly was to
> actually read some of the output that are in the tmp.com file.
>
> I get something like the following in the end of the tmp.com file:
>
> dot -Tpng > sg_graph.png << EOF
>  digraph f { rankdir=LR"P 1" -> "P 65" ;"P 1" -> "P 32" ;"P 1" -> "P 1
> 1 21" ;"P 1 1 21" -> "P 65" ;"P 32" -> "P 65" ;}
> EOF
>
> Simply pasting this in a terminal seems to work perfectly.
>
> Best regards,
> Folmer Fredslund
>
>
>
>
>>
>>
>> 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
>>>>>>
>>>>>> _______________________________________________
>>>>>> phenixbb mailing list
>>>>>> phenixbb at phenix-online.org
>>>>>> 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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