Re: [phenixbb] Xtriage problem

Could you send me (not the list) the outputs of: phenix.mtz.dump junk.mtz iotbx.reflection_file_reader junk.mtz from both versions of phenix? Ralf On Tue, May 1, 2012 at 3:22 PM, Abhinav Kumar wrote:

Hi,

When I try to do R vs R analysis for calculated data using xtriage, it has a problem accepting calc labels.

source /home/sw/rhel5/x86_64/phenix/phenix-1.7.3-928/phenix_env phenix.xtriage_1.7.3-928 junk.mtz calc_labels=FC

==> Sorry: No matching array: scaling.input.xray_data.calc_labels=FC

Howevere, it works fine with an earlier version:

source /home/sw/rhel5/x86_64/phenix/phenix-1.6.4-486/phenix_env phenix.xtriage_1.6.4-486 junk.mtz calc_labels=FC

Thanks, Abhinav

JCSG@SSRL, SLAC (650) 926-2992

-------- Original Message -------- Subject: RE: SP16569N-180314 Date: Tue, 1 May 2012 15:09:00 -0700 From: Miller, Mitchell D. To: Kumar, Abhinav

Hmm, it seems like it may be a bug introduced into phenix. (or else they changed they syntax and did not update the documentation)

Can you report it? I get it to do the RvR analysis for calculated data if I use source /home/sw/rhel5/x86_64/phenix/phenix-1.6.4-486/phenix_env phenix.xtriage_1.6.4-486 junk.mtz calc_labels=FC

but if I use source /home/sw/rhel5/x86_64/phenix/phenix-1.7.1-743/phenix_env phenix.xtriage_1.7.1-743 junk.mtz calc_labels=FC

or source /home/sw/rhel5/x86_64/phenix/phenix-1.7.3-928/phenix_env phenix.xtriage_1.7.3-928 junk.mtz calc_labels=FC then I get the error Sorry: No matching array: scaling.input.xray_data.calc_labels=FC

Thanks, Mitch P.S. the results I got were: R vs R statistic: R_abs_twin = <|I1-I2|>/<|I1+I2|> Lebedev, Vagin, Murshudov. Acta Cryst. (2006). D62, 83-95

R_abs_twin observed data : 0.451 R_abs_twin calculated data : 0.502

R_sq_twin = <(I1-I2)^2>/<(I1+I2)^2> R_sq_twin observed data : 0.279 R_sq_twin calculated data : 0.335

The analyses of the Patterson function reveals a significant off-origin peak that is 44.82 % of the origin peak, indicating pseudo translational symmetry. The chance of finding a peak of this or larger height by random in a structure without pseudo translational symmetry is equal to the 1.4447e-04. See the relevant section of the logfile for more details. The results of the L-test indicate that the intensity statistics behave as expected. No twinning is suspected. Even though no twinning is suspected, it might be worthwhile carrying out a refinement using a dedicated twin target anyway, as twinned structures with low twin fractions are difficult to distinguish from non-twinned structures.

-----Original Message----- From: Kumar, Abhinav Sent: Tuesday, May 01, 2012 1:30 PM To: Miller, Mitchell D. Subject: Re: SP16569N-180314

I am having trouble inputting Calc labels to xtriage: My mtz file has the following columns: FreeR_flag FP SIGFP FC PHIC FC_ALL PHIC_ALL FWT PHWT DELFWT PHDELWT FOM PHCOMB I tried "FC,PHIC" and "FC" for calc labels but xtriage does not like it. It writes: No matching array: scaling.input.xray_data.calc_labels=FC

Possible choices: /mnt/exdsstaff/abhinavk/Refine/SP16569N-180314/RESULTS/current.mtz:FP,SIGFP /mnt/exdsstaff/abhinavk/Refine/SP16569N-180314/RESULTS/current.mtz:FOM /mnt/exdsstaff/abhinavk/Refine/SP16569N-180314/RESULTS/current.mtz:PHCOMB

Thanks, Abhinav

JCSG@SSRL, SLAC (650) 926-2992

On 05/01/2012 12:51 PM, Miller, Mitchell D. wrote:

Also, you could try running xtriage with FC's from the untwined refinement to look at the R vs R stats for Fc vs Fobs.

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