[phenixbb] Xtriage problem

Abhinav Kumar abhinavk at slac.stanford.edu
Tue May 1 15:22:25 PDT 2012


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


(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>
To: 	Kumar, Abhinav <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

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

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

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:


(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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