[phenixbb] LABIN labels for Autosol/resolve NCS scores

Florian Schmitzberger schmitzberger at crystal.harvard.edu
Thu Sep 16 07:23:44 PDT 2010


Dear All,

I would have a number of Phenix related questions:

Firstly, I used the anisotropy server ( to anisotropically truncate my  
mtz file with anomalous signal (SAD data). My question is if the  
labels (for F+/F- and SIGF+/SIGF- are correctly recognized by Phenix  
(Autosol).

The columns labels are: F_ref  for FP; QSIGF_ref for SIGFP; GF(+)pk  
for F(+); LSIGF(+)pk for SIGF(+), GF(-)pk for F(-); LSIGF(-)pk for  
SIGF(-).

It seems QSIGF and GF(+)pk/LSIGF(+)pk etc. are , but I am uncertain if  
it recognizes F_ref, because for the LABIN INPUT LABELS it says "NONE"  
for"F".

Phenix does not seem to detect the anistropy ("Not using aniso- 
corrected data files as the range of aniso b  is only  19.52  and  
'correct_aniso' is not set); so I suppose I should use the  
correct_aniso=True keyword.

Secondly, what are good values for the evaluation of the NCS mask and  
NCS averaging Resolve is using in Phenix;  NCS overlap values (e.g. in  
my case 1.1) and NCS_CORR (in my case 0.52) in the "resolve.scores"  
file. Does an NCS overlap value of greater than 1 make sense?

I am working with a (anisotropic) dataset with 4.1/4.5 A resolution,  
78 % solvent content, 2-fold NCS;  Perhaps a naive question: It is not  
possible to use B-factor sharpened maps for autobuilding with Phenix  
Autobuild is it?

Thank you for any comments!

Regards,

Florian
-----------------------------------------------------------
Florian Schmitzberger
Biological Chemistry and Molecular Pharmacology
Harvard Medical School
250 Longwood Avenue, SGM 130
Boston, MA 02115, US
Tel: 001 617 432 5602













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