[phenixbb] detwin data

Pavel Afonine PAfonine at lbl.gov
Mon Oct 13 10:35:02 PDT 2008


Hi Hua,

I presume there is nothing wrong here... phenix.xtriage gives you an 
estimate for twin fraction while phenix.refine refines it. So I would be 
rather surprised if didn't change.

Pavel.


On 10/13/2008 6:11 AM, HUA YUAN wrote:
> My concern is about the twin fraction refined in phenix.refine, which 
> is indicated as 0.50, in contract to 0.36 suggested by phenix.xtriage. 
>   Therefore, I'd like to get a detwinned data and then subject it to 
> phenix.refine.
>
> The twin las I'm using is "h, -k,-l" in C2 space group.
>
> Thanks,
>
> Hua
>
> On Wed, Oct 8, 2008 at 5:13 PM, Peter Zwart <PHZwart at lbl.gov 
> <mailto:PHZwart at lbl.gov>> wrote:
>
>     Hi,
>
>     For what do you need detwinned data? What is your twin fraction / law?
>     When twin fraction is above 45%, algebraic detwinning will give
>     weird results.
>
>
>     Phase info with twinned refinement is not possible with phenix.refine.
>
>     P
>
>
>
>     2008/10/8 Ralf W. Grosse-Kunstleve <rwgk at cci.lbl.gov
>     <mailto:rwgk at cci.lbl.gov>>:
>     >> I've used the phenix.refine with its detwin function.  Is there
>     any way to
>     >> have a detwinned data output so that I can use it for other things.
>     >> I tried use CCP4 detwin with the same twin law and twin
>     fraction obtained
>     >> from Phenix.  However, this didn't work.
>     >
>     > I hope Peter will comment on this.
>     >
>     >> Another question is whether I can use "some" phase information,
>     say from DM
>     >> into Phenix?  I tried to include the PHIDM but Phenix
>     complained about it
>     >> saying "wrong array".
>     >
>     > phenix.refine needs Hendrickson-Lattman coefficients. Often they are
>     > called HA,HB,HC,HD. I'm not sure if DM produces Hendrickson-Lattman
>     > coefficients, but it seems highly likely. You should be able to
>     > simply give the DM file with the Hendrickson-Lattman coefficients to
>     > phenix.refine; it should pick the arrays automatically. If your Fobs
>     > and R-free flags are also in the DM file (in addition to the
>     original
>     > data file), phenix.refine may prompt you to specify which copy
>     > you want. Then add one of the phenix.refine suggestions to the
>     > phenix.refine command line.
>     >
>     > Ralf
>     > _______________________________________________
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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
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