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 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 :

...

...

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 [email protected] 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 [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

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 :

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 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 :

...

...

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 [email protected] 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 [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

________________________________ _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] 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 -----------------------------------------------------------------