[phenixbb] Xtriage problem
Abhinav Kumar
abhinavk at slac.stanford.edu
Wed May 2 08:07:17 PDT 2012
Hi Ralf,
The log files are attached.
They are same regardless of the version of phenix.
Thanks,
Abhinav
JCSG at SSRL, SLAC
(650) 926-2992
On 05/01/2012 10:31 PM, Ralf Grosse-Kunstleve wrote:
> 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 <mailto: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 <tel:%28650%29%20926-2992>
>
>
>
> -------- Original Message --------
> Subject: RE: SP16569N-180314
> Date: Tue, 1 May 2012 15:09:00 -0700
> From: Miller, Mitchell D. <mmiller at slac.stanford.edu>
> <mailto:mmiller at slac.stanford.edu>
> To: Kumar, Abhinav <abhinavk at slac.stanford.edu>
> <mailto: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 <tel:%28650%29%20926-2992>
>
>
>
> 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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>
>
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