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.
