[phenixbb] detwin data

Peter Zwart PHZwart at lbl.gov
Mon Oct 13 12:49:49 PDT 2008


well said.

Furthermore, refinement against  detwinned data is not advisable, not
a proper thing to do and most likely will make things worse as
compared to refinement with an appropriate twin target.

P


2008/10/13 Pavel Afonine <PAfonine at lbl.gov>:
> 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> 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>:
>> >> 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
>> > _______________________________________________
>> > phenixbb mailing list
>> > phenixbb at phenix-online.org
>> > http://www.phenix-online.org/mailman/listinfo/phenixbb
>> >
>>
>>
>>
>> --
>> -----------------------------------------------------------------
>> 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
>> -----------------------------------------------------------------
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>
> ________________________________
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>
>



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



More information about the phenixbb mailing list