Re: [ccp4bb] Careless and negative Wilson B-factor

2023-01-08 Thread 조규혁 
Dear Doeke,Thank you for developing such excellent software! I will try the options you suggested and post any additional issues to GitHub.Regarding the R-merge, R-meas, and R-pim values, I used the XDS CORRECT output (XDS_ASCII.HKL) as the "Unmerged data" and an mtz file obtained from each of the merging software as the "MTZ file" input in Phenix.table_one to calculate these values.For the Aimless-refined model, I ran phenix.refine with the "Update waters" option, using the structure factor obtained from Aimless and a model previously refined with the Careless output structure factor. However, the refined electron density with the Aimless output was weaker than that with the Careless output, which resulted in the removal of most of the water during the phenix.refine cycles.Thank you,Gyuhyeok- Original Mail -Sender : "Hekstra, Doeke Romke" Recipient :  Received Date : 2023/Jan/9(Mon) 12:21:46Subject : Re: [ccp4bb] Careless and negative Wilson B-factor






Dear Gyuhyeok,
 
Please feel free to describe any challenges with settings for Careless at
https://github.com/rs-station/careless/issues
We will be happy to help and improve our online documentation accordingly.

I assume some of the statistics you report below are simply duplicated from Aimless? We did not implement calculations for R-merge, R-meas, and R-pim. Careless can currently report CC1/2, CCanom (if Friedel mates were kept apart), Rsplit, and a new quantity,
 CCpred, based on prediction of expected intensities for a heldout test set of integrated intensities. To do so, make sure you use the “--merge-half-datasets” and “--half-dataset-repeats N” (with N some number of repeats) when running Careless. You can then
 use “careless.cchalf your_output_xval.mtz” to obtain CC1/2.
There are some curious differences between your refinements (for example, 203 versus 13 solvent molecules) that may or may not be directly related to Careless. If you are willing to share your PDB and MTZ files, we’d be very interested.
 
Thanks,
Doeke
 
 

From: CCP4 bulletin board  
On Behalf Of "???"
Sent: Sunday, January 8, 2023 9:45 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Careless and negative Wilson B-factor

 
Dear Eleanor, 

 
I agree that the decrease in the B-factor is likely due to "Careless."
The author of this article seems to recognize Wilson B-factor issues during the peer review process (https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-022-35280-8/MediaObjects/41467_2022_35280_MOESM2_ESM.pdf)
 and offers some options for addressing them (such as the --wilson-prior-b WILSON_PRIOR_B option).
It may take some time for me to get the software running correctly.
 
Gyuhyeok
 
P.S. I have attached some preliminary statistics using datasets from Careless or Aimless. Please note that both the Atomic B-factor and the Wilson B-factor are significantly reduced in Careless
 data. 
 




Merging tool


Carelss


Aimless




Wavelength


1.


1.




Resolution range


37.98 - 2.60
(2.69 - 2.60)


43.06 - 2.60
(2.69 - 2.60)




Space group


I 2 3


I 2 3




Unit cell


161.128 161.128 161.128
90 90 90


161.128 161.128 161.128
90 90 90




Total reflections


886846 (79364)


886852 (79364)




Unique reflections


21520 (2135)


21522 (2135)




Multiplicity


41.2 (37.2)


41.2 (37.2)




Completeness (%)


99.95 (100.00)


99.94 (99.95)




Mean I/sigma(I)


14.2 (0.8)


14.2 (0.8)




Wilson B-factor


-0.91


74.5




R-merge


0.240 (4.566)


0.240 (4.566)




R-meas


0.243 (4.629)


0.243 (4.629)




R-pim


0.038 (0.757)


0.038 (0.757)




CC1/2


0.998 (0.362)


0.997 (0.362)




CC*


0.999 (0.729)


0.999 (0.729)




Reflections used in refinement


21520 (2135)


21519 (2134)




Reflections used for R-free


1118 (112)


1118 (112)




R-work


0.2027 (0.2547)


0.2093 (0.3422)




R-free


0.2601 (0.3282)


0.2564 (0.3634)




CC(work)


0.664 (0.708)


0.919 (0.622)




CC(free)


0.622 (0.569)


0.766 (0.478)




Number of non-hydrogen atoms


3930


3740




macromolecules


3655


3655




ligands


72


72




solvent


203


13




Protein residues


443


443




RMS(bonds)


0.008


0.009




RMS(angles)


1.030


1.110




Ramachandran favored (%)


95.4


93.2




Ramachandran allowed (%)


4.3


6.4




Ramachandran outliers (%)


0.2


0.5




Rotamer outliers (%)


2.0


3.3




Clashscore


8.95


8.41




Average B-factor


19.9


70.2




macromolecules


19.7


70.0




ligands


31.1


81.5

Re: [ccp4bb] Careless and negative Wilson B-factor

2023-01-08 Thread Hekstra, Doeke Romke 
Dear Gyuhyeok,

Please feel free to describe any challenges with settings for Careless at 
https://github.com/rs-station/careless/issues
We will be happy to help and improve our online documentation accordingly.

I assume some of the statistics you report below are simply duplicated from 
Aimless? We did not implement calculations for R-merge, R-meas, and R-pim. 
Careless can currently report CC1/2, CCanom (if Friedel mates were kept apart), 
Rsplit, and a new quantity, CCpred, based on prediction of expected intensities 
for a heldout test set of integrated intensities. To do so, make sure you use 
the “--merge-half-datasets” and “--half-dataset-repeats N” (with N some number 
of repeats) when running Careless. You can then use “careless.cchalf 
your_output_xval.mtz” to obtain CC1/2.
There are some curious differences between your refinements (for example, 203 
versus 13 solvent molecules) that may or may not be directly related to 
Careless. If you are willing to share your PDB and MTZ files, we’d be very 
interested.

Thanks,
Doeke


From: CCP4 bulletin board  On Behalf Of "???"
Sent: Sunday, January 8, 2023 9:45 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Careless and negative Wilson B-factor


Dear Eleanor,



I agree that the decrease in the B-factor is likely due to "Careless."

The author of this article seems to recognize Wilson B-factor issues during the 
peer review process 
(https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-022-35280-8/MediaObjects/41467_2022_35280_MOESM2_ESM.pdf)
 and offers some options for addressing them (such as the --wilson-prior-b 
WILSON_PRIOR_B option).

It may take some time for me to get the software running correctly.



Gyuhyeok



P.S. I have attached some preliminary statistics using datasets from Careless 
or Aimless. Please note that both the Atomic B-factor and the Wilson B-factor 
are significantly reduced in Careless data.


Merging tool
Carelss
Aimless
Wavelength
1.
1.
Resolution range

37.98 - 2.60
(2.69 - 2.60)

43.06 - 2.60
(2.69 - 2.60)
Space group
I 2 3
I 2 3
Unit cell
161.128 161.128 161.128
90 90 90
161.128 161.128 161.128
90 90 90
Total reflections
886846 (79364)
886852 (79364)
Unique reflections
21520 (2135)
21522 (2135)
Multiplicity
41.2 (37.2)
41.2 (37.2)
Completeness (%)
99.95 (100.00)
99.94 (99.95)
Mean I/sigma(I)
14.2 (0.8)
14.2 (0.8)
Wilson B-factor
-0.91
74.5
R-merge
0.240 (4.566)
0.240 (4.566)
R-meas
0.243 (4.629)
0.243 (4.629)
R-pim
0.038 (0.757)
0.038 (0.757)
CC1/2
0.998 (0.362)
0.997 (0.362)
CC*
0.999 (0.729)
0.999 (0.729)
Reflections used in refinement
21520 (2135)
21519 (2134)
Reflections used for R-free
1118 (112)
1118 (112)
R-work
0.2027 (0.2547)
0.2093 (0.3422)
R-free
0.2601 (0.3282)
0.2564 (0.3634)
CC(work)
0.664 (0.708)
0.919 (0.622)
CC(free)
0.622 (0.569)
0.766 (0.478)
Number of non-hydrogen atoms
3930
3740
macromolecules
3655
3655
ligands
72
72
solvent
203
13
Protein residues
443
443
RMS(bonds)
0.008
0.009
RMS(angles)
1.030
1.110
Ramachandran favored (%)
95.4
93.2
Ramachandran allowed (%)
4.3
6.4
Ramachandran outliers (%)
0.2
0.5
Rotamer outliers (%)
2.0
3.3
Clashscore
8.95
8.41
Average B-factor
19.9
70.2
macromolecules
19.7
70.0
ligands
31.1
81.5
solvent
20.1
61.5

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font-size:x-small }a.comment-indicator:hover + comment { background:#ffd; 
position:absolute; display:block; border:1px solid black; padding:0.5em; 
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black; width:0.5em; height:0.5em; }comment { display:none; }
- 원본 메일 -
보낸사람 : Eleanor Dodson 
mailto:eleanor.dod...@york.ac.uk>>
받는사람 : mailto:gyuhyeok...@gist.ac.kr>>
받은날짜 : 2023/Jan/8(Sun) 10:39:39
제목 : Re: [ccp4bb] Careless and negative Wilson B-factor
I suppose so, but I would refine your final model against the initial data too, 
and see what R factors you get..
Eleanor

On Fri, 6 Jan 2023 at 14:46, "조규혁" 
mailto:gyuhyeok...@gist.ac.kr>> wrote:

Dear Eleanor,



I was wondering if the model and structure factors with the negative Wilson 
B-factor can be deposited in the PDB or made interpretable for biochemical 
experiments.

The data were initially processed in XDS and the CORRECT output (XDS_ASCII.HKL) 
was provided to Careless.



Sincerely,



Gyuhyeok
- 원본 메일 -
보낸사람 : Eleanor Dodson 
mailto:eleanor.dod...@york.ac.uk>>
받는사람 : mailto:gyuhyeok...@gist.ac.kr>>
참조 : mailto:CCP4BB@jiscmail.ac.uk>>
받은날짜 : 2023/Jan/6(Fri) 20:09:57
제목 : Re: [ccp4bb] Careless and negative Wilson B-factor
The tool must have sharpened your data - sometimes enhancing the outer data 
does improve the electron density..
So I wouldnt worry about that "negative" B factor - it is doubtless a result of 
the "careless" run, and not presumably the one you got at the data processing 
step..
Eleanor


On Fri, 6 Jan 2023 at 08:27,

Re: [ccp4bb] Careless and negative Wilson B-factor

2023-01-08 Thread Hekstra, Doeke Romke 
Hi Gyuhyeok and everyone,

Thank you. We developed Careless to  support scaling and merging of data from a 
wide range of diffraction experiments, including Laue, XFEL, 
time-resolved/serial, etc. Nice to hear that your electron density maps look 
promising. This is new software and we will continue to learn from all user 
feedback!

In Careless, the observations are scaled using the assumption that overall the 
amplitudes of the corresponding structure factors follow the Wilson 
distribution (see, for example, 
https://www-structmed.cimr.cam.ac.uk/Course/Statistics/statistics.html). By 
default, this means that the average structure factor amplitude does not fall 
off with resolution (a global B = 0). In this sense, the Careless output is 
normalized, as Kay observed. (there is a subtle difference with 'official' 
normalized structure factors, as described, for example, in section 7.10 of 
Rupp's textbook, Biomolecular Crystallography).

Real data, of course, show a decrease in diffraction intensity with 
resolution-something that usually gets worse with radiation dose. Scaling 
algorithms attempt to correct integrated intensities to all follow the same 
scaling behavior, for example matching the first frame. In Careless, you can 
specify an expected overall B factor by adding a flag, for example

--wilson-prior-b 17.0

specifies the expectation of an overall B factor of 17 A^2, rather than 0. It 
should make Xtriage's error go away.

So far, we have found that the default typically works just fine for molecular 
replacement and structure refinement. We have also successfully used Careless 
output for phasing with SHELX* and Phaser.

The PDB is aware of Careless and you can specify it as the scaling program 
used. Please let us know if you encounter any difficulties with deposition.

As a reminder, Careless is free, open-source software. We encourage everyone to 
file "issues", including bugs and feature requests, on the GitHub repo. If 
you'd like to extend the capabilities of Careless for your own purposes, you 
can do so yourself too!

Code & Installation instructions: https://github.com/rs-station/careless

Usage examples: https://github.com/rs-station/careless-examples

Publication: https://www.nature.com/articles/s41467-022-35280-8



-- Doeke



Dear all,

I recently tested a novel merging tool for crystallography data called Careless 
(https://github.com/rs-station/careless).

When I used it on our 2.6 A-resolution structure in the I23 space group with a 
lipid bound structure, I noticed that the electron density surrounding the acyl 
chain was significantly improved.

However, I am concerned about the Wilson B-factor. The Phenix.table_one tool 
reports that the Wilson B-factor of the merged mtz file is -0.91. 
Phenix.Xtriage warns that a negative Wilson B-factor can be an indication of 
unusual pathology or artificial manipulation.

Has anyone else encountered similar conditions? Are there any circumstances in 
which a negative Wilson B-factor can be rationalized?

Thank you,
Gyuhyeok



P.S. Here is the part of the output of Phenix.table_one.


Wavelength
1.
Resolution range
37.98 - 2.60
(2.69 - 2.60)
Space group
I 2 3
Unit cell
161.128 161.128 161.128
90 90 90
Total reflections
886846 (79364)
Unique reflections
21520 (2135)
Multiplicity
41.2 (37.2)
Completeness (%)
99.95 (100.00)
Mean I/sigma(I)

14.2 (0.8)
Wilson B-factor
-0.91
R-merge
0.240 (4.566)
R-meas
0.243 (4.629)
R-pim
0.038 (0.757)
CC1/2
0.998 (0.362)
CC*
0.999 (0.729)

PhD student

Department of Chemistry

Gwangju Institute of Science and Technology (GIST)
123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005

Republic of Korea

Tel. +82 62-715-4633

e-mail: [log in to 
unmask]



[cid:image002.jpg@01D92396.2A1F4820]


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Re: [ccp4bb] Careless and negative Wilson B-factor

2023-01-08 Thread 조규혁 
Dear Eleanor, I agree that the decrease in the B-factor is likely due to "Careless."The author of this article seems to recognize Wilson B-factor issues during the peer review process (https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-022-35280-8/MediaObjects/41467_2022_35280_MOESM2_ESM.pdf) and offers some options for addressing them (such as the --wilson-prior-b WILSON_PRIOR_B option).It may take some time for me to get the software running correctly.GyuhyeokP.S. I have attached some preliminary statistics using datasets from Careless or Aimless. Please note that both the Atomic B-factor and the Wilson B-factor are significantly reduced in Careless data.



	
	
	
	
	
	




	
	
	
	
		Merging tool
		Carelss
		Aimless
	
	
		Wavelength
		1.
		1.
	
	
		  Resolution range
		   37.98  - 2.60(2.69  - 2.60)
		  43.06  - 2.60(2.69  - 2.60)
	
	
		   Space group
		 I 2 3
		I 2 3
	
	
		 Unit cell
		  161.128 161.128 161.12890 90 90
		 161.128 161.128 161.12890 90 90
	
	
		 Total reflections
		886846 (79364)
		   886852 (79364)
	
	
		Unique reflections
		  21520 (2135)
		 21522 (2135)
	
	
		  Multiplicity
		   41.2 (37.2)
		  41.2 (37.2)
	
	
		  Completeness (%)
		99.95 (100.00)
		99.94 (99.95)
	
	
		   Mean I/sigma(I)
		  14.2 (0.8)
		 14.2 (0.8)
	
	
		   Wilson B-factor
		-0.91
		74.5
	
	
		   R-merge
		 0.240 (4.566)
		0.240 (4.566)
	
	
		R-meas
		 0.243 (4.629)
		0.243 (4.629)
	
	
		 R-pim
		 0.038 (0.757)
		0.038 (0.757)
	
	
		 CC1/2
		 0.998 (0.362)
		0.997 (0.362)
	
	
		   CC*
		 0.999 (0.729)
		0.999 (0.729)
	
	
		Reflections used in refinement
		  21520 (2135)
		 21519 (2134)
	
	
		   Reflections used for R-free
		1118 (112)
		   1118 (112)
	
	
		R-work
		   0.2027 (0.2547)
		  0.2093 (0.3422)
	
	
		R-free
		   0.2601 (0.3282)
		  0.2564 (0.3634)
	
	
		  CC(work)
		 0.664 (0.708)
		0.919 (0.622)
	
	
		  CC(free)
		 0.622 (0.569)
		0.766 (0.478)
	
	
		  Number of non-hydrogen atoms
		3930
		3740
	
	
		macromolecules
		3655
		3655
	
	
		   ligands
		72
		72
	
	
		   solvent
		203
		13
	
	
		  Protein residues
		443
		443
	
	
		RMS(bonds)
		0.008
		0.009
	
	
		   RMS(angles)
		1.030
		1.110
	
	
		  Ramachandran favored (%)
		95.4
		93.2
	
	
		  Ramachandran allowed (%)
		4.3
		6.4
	
	
		 Ramachandran outliers (%)
		0.2
		0.5
	
	
		  Rotamer outliers (%)
		2.0
		3.3
	
	
		Clashscore
		8.95
		8.41
	
	
		  Average B-factor
		19.9
		70.2
	
	
		macromolecules
		19.7
		70.0
	
	
		   ligands
		31.1
		81.5
	
	
		   solvent
		20.1
		61.5
	




- 원본 메일 -보낸사람 : Eleanor Dodson 받는사람 :  받은날짜 : 2023/Jan/8(Sun) 10:39:39제목 : Re: [ccp4bb] Careless and negative Wilson B-factorI suppose so, but I would refine your final model against the initial data too, and see what R factors you get..EleanorOn Fri, 6 Jan 2023 at 14:46, "조규혁"  wrote:Dear Eleanor,I was wondering if the model and structure factors with the negative Wilson B-factor can be deposited in the PDB or made interpretable for biochemical experiments.The data were initially processed in XDS and the CORRECT output (XDS_ASCII.HKL) was provided to Careless.Sincerely,Gyuhyeok- 원본 메일 -보낸사람 : Eleanor Dodson 받는사람 :  참조 :  받은날짜 : 2023/Jan/6(Fri) 20:09:57제목 : Re: [ccp4bb] Careless and negative Wilson B-factorThe tool must have sharpened your data - sometimes enhancing the outer data does improve the electron density..So I wouldnt worry

Re: [ccp4bb] Careless and negative Wilson B-factor

2023-01-06 Thread Kay Diederichs 
Dear Gyuhyeok,

I have no first-hand experience with CARELESS.

But my understanding is that CARELESS gives you normalized structure factor 
amplitudes; this "normalization" roughly corresponds to a removal (subtraction) 
of the Wilson B-factor from conventionally processed structure factor 
amplitudes.

As a result, you'd expect maps that appear sharpened relative to what we 
normally look at, and a Wilson B-factor around 0. So this is all consistent 
with what you report.

It is unclear to me whether one can or should refine against data from CARELESS 
without taking extra measures, and whether and how the data can be deposited 
with the PDB. At least they should be suitably flagged.

HTH,
Kay



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Re: [ccp4bb] Careless and negative Wilson B-factor

2023-01-06 Thread 조규혁 
Dear Eleanor,I was wondering if the model and structure factors with the negative Wilson B-factor can be deposited in the PDB or made interpretable for biochemical experiments.The data were initially processed in XDS and the CORRECT output (XDS_ASCII.HKL) was provided to Careless.Sincerely,Gyuhyeok- 원본 메일 -보낸사람 : Eleanor Dodson 받는사람 :  참조 :  받은날짜 : 2023/Jan/6(Fri) 20:09:57제목 : Re: [ccp4bb] Careless and negative Wilson B-factorThe tool must have sharpened your data - sometimes enhancing the outer data does improve the electron density..So I wouldnt worry about that "negative" B factor - it is doubtless a result of the "careless" run, and not presumably the one you got at the data processing step..EleanorOn Fri, 6 Jan 2023 at 08:27, "조규혁"  wrote:Dear all,I recently tested a novel merging tool for crystallography data called Careless (https://github.com/rs-station/careless).When I used it on our 2.6 A-resolution structure in the I23 space group with a lipid bound structure, I noticed that the electron density surrounding the acyl chain was significantly improved.However, I am concerned about the Wilson B-factor. The Phenix.table_one tool reports that the Wilson B-factor of the merged mtz file is -0.91. Phenix.Xtriage warns that a negative Wilson B-factor can be an indication of unusual pathology or artificial manipulation.Has anyone else encountered similar conditions? Are there any circumstances in which a negative Wilson B-factor can be rationalized?Thank you,GyuhyeokP.S. Here is the part of the output of Phenix.table_one.



	
	
	
	
	
	




	
	
	
		Wavelength
		1.
	
	
		  Resolution range
		   37.98  - 2.60(2.69 - 2.60)
	
	
		   Space group
		 I 2 3
	
	
		 Unit cell
		  161.128 161.128 161.12890 90 90
	
	
		 Total reflections
		886846 (79364)
	
	
		Unique reflections
		  21520 (2135)
	
	
		  Multiplicity
		   41.2 (37.2)
	
	
		  Completeness (%)
		99.95 (100.00)
	
	
		   Mean I/sigma(I)
		  14.2 (0.8)
	
	
		   Wilson B-factor
		-0.91
	
	
		   R-merge
		  0.240 (4.566)
	
	
		R-meas
		 0.243 (4.629)
	
	
		 R-pim
		  0.038 (0.757)
	
	
		 CC1/2
		 0.998 (0.362)
	
	
		   CC*
		 0.999 (0.729)
	




	
		PhD studentDepartment of ChemistryGwangju Institute of Science and Technology (GIST)123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005Republic of KoreaTel. +82 62-715-4633e-mail: gyuhyeok...@gist.ac.kr
	




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		PhD studentDepartment of ChemistryGwangju Institute of Science and Technology (GIST)123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005Republic of KoreaTel. +82 62-715-4633e-mail: gyuhyeok...@gist.ac.kr
	




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Re: [ccp4bb] Careless and negative Wilson B-factor

2023-01-06 Thread 조규혁 
Dear Jon,The data were obtained from a single crystal.Gyuhyeok- 원본 메일 -보낸사람 : Jon Cooper <488a26d62010-dmarc-requ...@jiscmail.ac.uk>받는사람 :  받은날짜 : 2023/Jan/6(Fri) 21:48:21제목 : Re: [ccp4bb] Careless and negative Wilson B-factorHello, are the data from serial crystallography? The redundancy and the CC's are very good but the R-merge (an unpopular metric these days) is quite high? Cheers, Jon Cooper2Sent from ProtonMail mobile Original Message On 6 Jan 2023, 08:17, 조규혁 < gyuhyeok...@gist.ac.kr> wrote:Dear all,I recently tested a novel merging tool for crystallography data called Careless (https://github.com/rs-station/careless).When I used it on our 2.6 A-resolution structure in the I23 space group with a lipid bound structure, I noticed that the electron density surrounding the acyl chain was significantly improved.However, I am concerned about the Wilson B-factor. The Phenix.table_one tool reports that the Wilson B-factor of the merged mtz file is -0.91. Phenix.Xtriage warns that a negative Wilson B-factor can be an indication of unusual pathology or artificial manipulation.Has anyone else encountered similar conditions? Are there any circumstances in which a negative Wilson B-factor can be rationalized?Thank you,GyuhyeokP.S. Here is the part of the output of Phenix.table_one.




	
	
	
	





	
	
	
		Wavelength
		1.
	
	
		  Resolution range
		   37.98  - 2.60(2.69 - 2.60)
	
	
		   Space group
		 I 2 3
	
	
		 Unit cell
		  161.128 161.128 161.12890 90 90
	
	
		 Total reflections
		886846 (79364)
	
	
		Unique reflections
		  21520 (2135)
	
	
		  Multiplicity
		   41.2 (37.2)
	
	
		  Completeness (%)
		99.95 (100.00)
	
	
		   Mean I/sigma(I)
		  14.2 (0.8)
	
	
		   Wilson B-factor
		-0.91
	
	
		   R-merge
		  0.240 (4.566)
	
	
		R-meas
		 0.243 (4.629)
	
	
		 R-pim
		  0.038 (0.757)
	
	
		 CC1/2
		 0.998 (0.362)
	
	
		   CC*
		 0.999 (0.729)
	





		PhD studentDepartment of ChemistryGwangju Institute of Science and Technology (GIST)123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005Republic of KoreaTel. +82 62-715-4633e-mail: gyuhyeok...@gist.ac.kr





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		PhD studentDepartment of ChemistryGwangju Institute of Science and Technology (GIST)123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005Republic of KoreaTel. +82 62-715-4633e-mail: gyuhyeok...@gist.ac.kr
	




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Re: [ccp4bb] Careless and negative Wilson B-factor

2023-01-06 Thread Alejandro Buschiazzo 
Dear Jon and Gyuhyeok

the real connaisseurs (e.g. Kay Diedrichs, et al) will certainly respond much 
better to this!
Redundancy is really high here (which is good of course), likely explaining the 
high-ish Rmerge. 
Indeed, “redundancy-aware“ indices, like Rpim, are much better, and actually 
quite good overall :)

It is true that Rmeas (with also integrates multiplicity), does diverge quite a 
bit from Rpim. As far as I recall the difference between these two being that 
the former reports on individual measurements, whilst Rpim uses merged data. 
Why that difference among them? Kay?

In any case, with >40 multiplicity, Rpim looks pretty good (and, consistent 
with CCs, makes sense)

Best, Alejandro




> On 6 Jan 2023, at 09:47, Jon Cooper 
> <488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hello, are the data from serial crystallography? The redundancy and the CC's 
> are very good but the R-merge (an unpopular metric these days) is quite high? 
> 
> Cheers, Jon Cooper2
> 
> 
> Sent from ProtonMail mobile
> 
> 
> 
>  Original Message 
> On 6 Jan 2023, 08:17, 조규혁 < gyuhyeok...@gist.ac.kr> wrote:
> 
> Dear all,
> 
> I recently tested a novel merging tool for crystallography data called 
> Careless (https://github.com/rs-station/careless).
> 
> When I used it on our 2.6 A-resolution structure in the I23 space group with 
> a lipid bound structure, I noticed that the electron density surrounding the 
> acyl chain was significantly improved.
> 
> However, I am concerned about the Wilson B-factor. The Phenix.table_one tool 
> reports that the Wilson B-factor of the merged mtz file is -0.91. 
> Phenix.Xtriage warns that a negative Wilson B-factor can be an indication of 
> unusual pathology or artificial manipulation.
> 
> Has anyone else encountered similar conditions? Are there any circumstances 
> in which a negative Wilson B-factor can be rationalized?
> 
> Thank you,
> Gyuhyeok
> 
> 
> 
> P.S. Here is the part of the output of Phenix.table_one.
> 
> 
> 
> Wavelength1.
> Resolution range  37.98 - 2.60
> (2.69 - 2.60)
> Space group   I 2 3
> Unit cell 161.128 161.128 161.128
> 90 90 90
> Total reflections 886846 (79364)
> Unique reflections21520 (2135)
> Multiplicity  41.2 (37.2)
> Completeness (%)  99.95 (100.00)
> Mean I/sigma(I)   
> 14.2 (0.8)
> 
> Wilson B-factor   -0.91
> R-merge   0.240 (4.566)
> R-meas0.243 (4.629)
> R-pim 0.038 (0.757)
> CC1/2 0.998 (0.362)
> CC*   0.999 (0.729)
> 
> 
> 
> 
> 
> 
> 
> 
> PhD student
> 
> Department of Chemistry
> 
> Gwangju Institute of Science and Technology (GIST)
> 
> 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005
> Republic of Korea
> 
> Tel. +82 62-715-4633
> 
> e-mail: gyuhyeok...@gist.ac.kr
> 
> 
> 
> 
>  
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Careless and negative Wilson B-factor

2023-01-06 Thread Jon Cooper 
Hello, are the data from serial crystallography? The redundancy and the CC's 
are very good but the R-merge (an unpopular metric these days) is quite high?

Cheers, Jon Cooper2

Sent from ProtonMail mobile

 Original Message 
On 6 Jan 2023, 08:17, 조규혁 wrote:

> Dear all,
>
> I recently tested a novel merging tool for crystallography data called 
> Careless (https://github.com/rs-station/careless).
>
> When I used it on our 2.6 A-resolution structure in the I23 space group with 
> a lipid bound structure, I noticed that the electron density surrounding the 
> acyl chain was significantly improved.
>
> However, I am concerned about the Wilson B-factor. The Phenix.table_one tool 
> reports that the Wilson B-factor of the merged mtz file is -0.91. 
> Phenix.Xtriage warns that a negative Wilson B-factor can be an indication of 
> unusual pathology or artificial manipulation.
>
> Has anyone else encountered similar conditions? Are there any circumstances 
> in which a negative Wilson B-factor can be rationalized?
>
> Thank you,
> Gyuhyeok
>
> P.S. Here is the part of the output of Phenix.table_one.
>
> Wavelength1.
> Resolution range  37.98 - 2.60
> (2.69 - 2.60)
> Space group   I 2 3
> Unit cell 161.128 161.128 161.128
> 90 90 90
> Total reflections 886846 (79364)
> Unique reflections21520 (2135)
> Multiplicity  41.2 (37.2)
> Completeness (%)  99.95 (100.00)
> Mean I/sigma(I)
>
> 14.2 (0.8)
>
> Wilson B-factor   -0.91
> R-merge   0.240 (4.566)
> R-meas0.243 (4.629)
> R-pim 0.038 (0.757)
> CC1/2 0.998 (0.362)
> CC*   0.999 (0.729)
>
>>> PhD student
>>>
>>> Department of Chemistry
>>>
>>> Gwangju Institute of Science and Technology (GIST)
>>>
>>> 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005
>>>
>>> Republic of Korea
>>>
>>> Tel. +82 62-715-4633
>>>
>>> e-mail: gyuhyeok...@gist.ac.kr
>
> ---
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1



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Re: [ccp4bb] Careless and negative Wilson B-factor

2023-01-06 Thread Eleanor Dodson 
The tool must have sharpened your data - sometimes enhancing the outer data
does improve the electron density..
So I wouldnt worry about that "negative" B factor - it is doubtless a
result of the "careless" run, and not presumably the one you got at the
data processing step..
Eleanor


On Fri, 6 Jan 2023 at 08:27, "조규혁"  wrote:

> Dear all,
>
> I recently tested a novel merging tool for crystallography data called
> Careless (https://github.com/rs-station/careless).
>
> When I used it on our 2.6 A-resolution structure in the I23 space group
> with a lipid bound structure, I noticed that the electron density
> surrounding the acyl chain was significantly improved.
>
> However, I am concerned about the Wilson B-factor. The Phenix.table_one
> tool reports that the Wilson B-factor of the merged mtz file is -0.91.
> Phenix.Xtriage warns that a negative Wilson B-factor can be an indication
> of unusual pathology or artificial manipulation.
>
> Has anyone else encountered similar conditions? Are there any
> circumstances in which a negative Wilson B-factor can be rationalized?
>
> Thank you,
> Gyuhyeok
>
>
> P.S. Here is the part of the output of Phenix.table_one.
>
>
> Wavelength 1.
> Resolution range 37.98 - 2.60
> (2.69 - 2.60)
> Space group I 2 3
> Unit cell 161.128 161.128 161.128
> 90 90 90
> Total reflections 886846 (79364)
> Unique reflections 21520 (2135)
> Multiplicity 41.2 (37.2)
> Completeness (%) 99.95 (100.00)
> Mean I/sigma(I)
>
> 14.2 (0.8)
> * Wilson B-factor* *-0.91*
> R-merge 0.240 (4.566)
> R-meas 0.243 (4.629)
> R-pim 0.038 (0.757)
> CC1/2 0.998 (0.362)
> CC* 0.999 (0.729)
>
>
>
>
>
> PhD student
>
> Department of Chemistry
>
> Gwangju Institute of Science and Technology (GIST)
> 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005
>
> Republic of Korea
>
> Tel. +82 62-715-4633
>
> e-mail: gyuhyeok...@gist.ac.kr
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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