[phenixbb] Xtriage problem

[Ralf Grosse-Kunstleve]

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 <abhinavk at slac.stanford.edu>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 at SSRL, SLAC
> (650) 926-2992
>
>
> -------- Original Message --------  Subject: RE: SP16569N-180314  Date: Tue,
> 1 May 2012 15:09:00 -0700  From: Miller, Mitchell D.
> <mmiller at slac.stanford.edu> <mmiller at slac.stanford.edu>  To: Kumar,
> Abhinav <abhinavk at slac.stanford.edu> <abhinavk at slac.stanford.edu>
>
> 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 at 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.
>
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20120501/62d1773e/attachment-0001.htm>