Re: [phenixbb] P43212 spacegroup change to C2221?

Dear Andreas 2009/8/28 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)

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 wrote:

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...

 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:

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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 :

...

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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-- ----------------------------------------------------------------- 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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