Re: [ccp4bb] Question about losing reflections when refining in PHENIX

[Boaz Shaanan]

Hi, following Jonathan's reply, unless you specify "no anomalous" in the input file, Phenix will refine by default against the anomalous data in your input mtz, even if the signal is weak. You should also check how you define the type of mtz
 columns to be used in the refinement. There are several options in the data input part of the gui.
  Boaz

Boaz Shaanan, Ph.D.
Department of Life Sciences
Ben Gurion University of the Negev
Beer Sheva
Israel



On Oct 29, 2019 00:05, Jonathan Cooper <0c2488af9525-dmarc-requ...@jiscmail.ac.uk> wrote:





Hello, it looks as though the No observations that phenix is reporting is exactly twice the number of unique reflections. Perhaps phenix is reporting the merging statistics for the Friedel pairs (i.e. F(+) and F(-)) within your merged dataset.
 Hence the stats look much better than those for the raw data fed to Aimless. I think you should be able to make a perfectly respectable Table 1 with the merging stats from Mosflm/Aimless and the refinement stats from phenix but others will know how to do it
 properly.





On Monday, 28 October 2019, 20:05:52 GMT, Nemanja Vuksanovic  wrote:









Dear All,


I need a bit of help with an issue I am encountering with one of my datasets when using phenix.refine. After processing data with Mosflm I get the following parameters:




Overall InnerShell OuterShell
Low resolution limit   65.69 65.69  2.55
High resolution limit   2.45  8.83  2.45
Rmerge  (within I+/I-) 0.127 0.057 0.817

Rmerge  (all I+ and I-)0.130 0.058 0.848
Rmeas (within I+/I-)0.140 0.063 0.898
Rmeas (all I+ & I-)  0.136 0.061 0.888
Rpim (within I+/I-)   0.058 0.027 0.373
Rpim (all I+ & I-) 0.040 0.019 0.263
Rmerge in top intensity bin 0.062- - 
Total number of observations 288903  5972 32430
Total number unique25576   592  2857
Mean((I)/sd(I))  13.1  23.6   3.5
Mn(I) half-set correlation CC(1/2) 0.998 0.998 0.874
Completeness   100.0  99.7 100.0
Multiplicity11.3  10.1  11.4
Mean(Chi^2) 1.08  0.72  0.96
Anomalous completeness 100.0  99.9 100.0

Anomalous multiplicity   5.8   5.6   5.8
DelAnom correlation between half-sets -0.270-0.466-0.055
Mid-Slope of Anom Normal Probability   0.788   - -  



After molecular replacement with PHASER and then refinement with Phenix.refine, (defauIt settings in both) I generated a TABLE 1 in PHENIX and noticed that the total number of observations has dropped, significantly lowering multiplicity and R factors.
 Could you perhaps give me your opinion on what might be causing this discrepancy?I'd be happy to provide the mtz file and any other information if needed.

Table 1.  Data collection and refinement statistics.
Wavelength 
Resolution range 56.89  - 2.451 (2.539  - 2.451)
Space group I 2 3
Unit cell 160.9 160.9 160.9 90 90 90
Total reflections 51076 (5030)
Unique reflections 25538 (2515)
Multiplicity 2.0 (2.0)
Completeness (%) 99.96 (100.00)
Mean I/sigma(I) 13.37 (3.56)
Wilson B-factor 41.08
R-merge 0.0263 (0.1879)
R-meas 0.03719 (0.2657)
R-pim 0.0263 (0.1879)
CC1/2 0.999 (0.895)
CC* 1 (0.972)
Reflections used in refinement 25532 (2515)
Reflections used for R-free 1300 (121)
R-work 0.2698 (0.3589)
R-free 0.3115 (0.3897)
CC(work) 0.908 (0.679)
CC(free) 0.885 (0.444)
Number of non-hydrogen atoms 2310
  macromolecules 2310
Protein residues 286
RMS(bonds) 0.010
RMS(angles) 1.01
Ramachandran favored (%) 96.40
Ramachandran allowed (%) 2.52
Ramachandran outliers (%) 1.08
Rotamer outliers (%) 0.00
Clashscore 8.47
Average B-factor 43.55
  


Best Regards,
Nemanja Vuksanovic


-- 







Graduate Student
Department of Chemistry and Biochemistry
University of Wisconsin-Milwaukee


















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[ccp4bb] November 1, 2019 Deadline for S2C2 Proposals

[Dunn, Lisa B.]

 November 1 is the next deadline for submitting proposals to the Stanford-SLAC 
Cryo-EM Center (S2C2).

 The missions of the Stanford-SLAC Cryo-EM Center (S2C2) are:

  1.  to provide access to state-of-the-art cryo-EM instruments for data 
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Best regards,

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Re: [ccp4bb] Question about losing reflections when refining in PHENIX

[Jonathan Cooper]

 Hello, it looks as though the No observations that phenix is reporting is 
exactly twice the number of unique reflections. Perhaps phenix is reporting the 
merging statistics for the Friedel pairs (i.e. F(+) and F(-)) within your 
merged dataset. Hence the stats look much better than those for the raw data 
fed to Aimless. I think you should be able to make a perfectly respectable 
Table 1 with the merging stats from Mosflm/Aimless and the refinement stats 
from phenix but others will know how to do it properly.
On Monday, 28 October 2019, 20:05:52 GMT, Nemanja Vuksanovic 
 wrote:  
 
  Dear All,
I need a bit of help with an issue I am encountering with one of my datasets 
when using phenix.refine. After processing data with Mosflm I get the following 
parameters:

Overall InnerShell OuterShell
Low resolution limit   65.69 65.69  2.55High 
resolution limit   2.45  8.83  2.45Rmerge  (within 
I+/I-) 0.127 0.057 0.817
Rmerge  (all I+ and I-)0.130 0.058 0.848Rmeas 
(within I+/I-)0.140 0.063 0.898Rmeas (all I+ & 
I-)  0.136 0.061 0.888Rpim (within I+/I-)   
0.058 0.027 0.373Rpim (all I+ & I-) 
0.040 0.019 0.263Rmerge in top intensity bin 
0.062- - Total number of observations 288903  5972  
   32430Total number unique25576   592  
2857Mean((I)/sd(I))  13.1  23.6   
3.5Mn(I) half-set correlation CC(1/2) 0.998 0.998 0.874Completeness 
  100.0  99.7 100.0Multiplicity 
   11.3  10.1  11.4Mean(Chi^2)  
   1.08  0.72  0.96Anomalous completeness   
  100.0  99.9 100.0
Anomalous multiplicity   5.8   5.6   5.8DelAnom 
correlation between half-sets -0.270-0.466-0.055Mid-Slope of Anom 
Normal Probability   0.788   - -  
After molecular replacement with PHASER and then refinement with Phenix.refine, 
(defauIt settings in both) I generated a TABLE 1 in PHENIX and noticed that the 
total number of observations has dropped, significantly lowering multiplicity 
and R factors. Could you perhaps give me your opinion on what might be causing 
this discrepancy?I'd be happy to provide the mtz file and any other information 
if needed.
Table 1.  Data collection and refinement statistics.
Wavelength 
Resolution range 56.89  - 2.451 (2.539  - 2.451)
Space group I 2 3
Unit cell 160.9 160.9 160.9 90 90 90
Total reflections 51076 (5030)
Unique reflections 25538 (2515)
Multiplicity 2.0 (2.0)
Completeness (%) 99.96 (100.00)
Mean I/sigma(I) 13.37 (3.56)
Wilson B-factor 41.08
R-merge 0.0263 (0.1879)
R-meas 0.03719 (0.2657)
R-pim 0.0263 (0.1879)
CC1/2 0.999 (0.895)
CC* 1 (0.972)
Reflections used in refinement 25532 (2515)
Reflections used for R-free 1300 (121)
R-work 0.2698 (0.3589)
R-free 0.3115 (0.3897)
CC(work) 0.908 (0.679)
CC(free) 0.885 (0.444)
Number of non-hydrogen atoms 2310
  macromolecules 2310
Protein residues 286
RMS(bonds) 0.010
RMS(angles) 1.01
Ramachandran favored (%) 96.40
Ramachandran allowed (%) 2.52
Ramachandran outliers (%) 1.08
Rotamer outliers (%) 0.00
Clashscore 8.47
Average B-factor 43.55
  

Best Regards,Nemanja Vuksanovic
-- 
Graduate StudentDepartment of Chemistry and BiochemistryUniversity of 
Wisconsin-Milwaukee




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[ccp4bb] Question about losing reflections when refining in PHENIX

[Nemanja Vuksanovic]

Dear All,

I need a bit of help with an issue I am encountering with one of my datasets 
when using phenix.refine. After processing data with Mosflm I get the following 
parameters:


Overall InnerShell OuterShell

Low resolution limit   65.69 65.69  2.55

High resolution limit   2.45  8.83  2.45

Rmerge  (within I+/I-) 0.127 0.057 0.817


Rmerge  (all I+ and I-)0.130 0.058 0.848

Rmeas (within I+/I-)0.140 0.063 0.898

Rmeas (all I+ & I-)  0.136 0.061 0.888

Rpim (within I+/I-)   0.058 0.027 0.373

Rpim (all I+ & I-) 0.040 0.019 0.263

Rmerge in top intensity bin 0.062- -

Total number of observations 288903  5972 32430

Total number unique25576   592  2857

Mean((I)/sd(I))  13.1  23.6   3.5

Mn(I) half-set correlation CC(1/2) 0.998 0.998 0.874

Completeness   100.0  99.7 100.0

Multiplicity11.3  10.1  11.4

Mean(Chi^2) 1.08  0.72  0.96

Anomalous completeness 100.0  99.9 100.0


Anomalous multiplicity   5.8   5.6   5.8

DelAnom correlation between half-sets -0.270-0.466-0.055

Mid-Slope of Anom Normal Probability   0.788   - -

After molecular replacement with PHASER and then refinement with Phenix.refine, 
(defauIt settings in both) I generated a TABLE 1 in PHENIX and noticed that the 
total number of observations has dropped, significantly lowering multiplicity 
and R factors. Could you perhaps give me your opinion on what might be causing 
this discrepancy?I'd be happy to provide the mtz file and any other information 
if needed.

Table 1.  Data collection and refinement statistics.
Wavelength
Resolution range 56.89  - 2.451 (2.539  - 2.451)
Space group I 2 3
Unit cell 160.9 160.9 160.9 90 90 90
Total reflections 51076 (5030)
Unique reflections 25538 (2515)
Multiplicity 2.0 (2.0)
Completeness (%) 99.96 (100.00)
Mean I/sigma(I) 13.37 (3.56)
Wilson B-factor 41.08
R-merge 0.0263 (0.1879)
R-meas 0.03719 (0.2657)
R-pim 0.0263 (0.1879)
CC1/2 0.999 (0.895)
CC* 1 (0.972)
Reflections used in refinement 25532 (2515)
Reflections used for R-free 1300 (121)
R-work 0.2698 (0.3589)
R-free 0.3115 (0.3897)
CC(work) 0.908 (0.679)
CC(free) 0.885 (0.444)
Number of non-hydrogen atoms 2310
  macromolecules 2310
Protein residues 286
RMS(bonds) 0.010
RMS(angles) 1.01
Ramachandran favored (%) 96.40
Ramachandran allowed (%) 2.52
Ramachandran outliers (%) 1.08
Rotamer outliers (%) 0.00
Clashscore 8.47
Average B-factor 43.55


Best Regards,
Nemanja Vuksanovic

--
Graduate Student
Department of Chemistry and Biochemistry
University of Wisconsin-Milwaukee






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Published   28.Oct.2019
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