[phenixbb] P43212 spacegroup change to C2221?

Folmer Fredslund folmerf at gmail.com
Fri Aug 28 05:05:46 PDT 2009


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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>>>>
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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
>> PHENIX: http://www.phenix-online.org
>> CCTBX:  http://cctbx.sf.net
>> -----------------------------------------------------------------
>>
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