Re: [ccp4bb] Rmergicide Through Programming

[Graeme Winter]

Frank,

you are asking me to remove features that I like, so I would feel that the 
challenge is for you to prove that this is harmful however:

 - at the minimum, I find it a useful check sum that the stats are internally 
consistent (though I interpret it for lots of other reasons too)
 - it is faulty I agree, but (with caveats) still useful IMHO

Sorry for being terse, but I remain to be convinced that removing it increases 
the amount of information

CC’ing BB as requested

Best wishes Graeme


> On 5 Jul 2017, at 17:17, Frank von Delft  wrote:
> 
> You keep not answering the challenge.
> 
> It's really simple:  what information does Rmerge provide that Rmeas doesn't.
> 
> (If you answer, email to the BB.)
> 
> 
> On 05/07/2017 16:04, graeme.win...@diamond.ac.uk wrote:
>> Dear Frank,
>> 
>> You are forcefully arguing essentially that others are wrong if we feel an 
>> existing statistic continues to be useful, and instead insist that it be 
>> outlawed so that we may not make use of it, just in case someone 
>> misinterprets it.
>> 
>> Very well
>> 
>> I do however express disquiet that we as software developers feel browbeaten 
>> to remove the output we find useful because “the community” feel that it is 
>> obsolete.
>> 
>> I feel that Jacob’s short story on this thread illustrates that educating 
>> the next generation of crystallographers to understand what all of the 
>> numbers mean is critical, and that a numerological approach of trying to 
>> optimise any one statistic is essentially doomed. Precisely the same 
>> argument could be made for people cutting the “resolution” at the wrong 
>> place in order to improve the average I/sig(I) of the data set.
>> 
>> Denying access to information is not a solution to misinterpretation, from 
>> where I am sat, however I acknowledge that other points of view exist.
>> 
>> Best wishes Graeme
>> 
>> 
>> On 5 Jul 2017, at 12:11, Frank von Delft 
>> > wrote:
>> 
>> 
>> Graeme, Andrew
>> 
>> Jacob is not arguing against an R-based statistic;  he's pointing out that 
>> leaving out the multiplicity-weighting is prehistoric (Diederichs & Karplus 
>> published it 20 years ago!).
>> 
>> So indeed:   Rmerge, Rpim and I/sigI give different information.  As you say.
>> 
>> But no:   Rmerge and Rmeas and Rcryst do NOT give different information.  
>> Except:
>> 
>>   * Rmerge is a (potentially) misleading version of Rmeas.
>> 
>>   * Rcryst and Rmerge and Rsym are terms that no longer have significance in 
>> the single cryo-dataset world.
>> 
>> phx.
>> 
>> 
>> 
>> On 05/07/2017 09:43, Andrew Leslie wrote:
>> 
>> I would like to support Graeme in his wish to retain Rmerge in Table 1, 
>> essentially for exactly the same reasons.
>> 
>> I also strongly support Francis Reyes comment about the usefulness of Rmerge 
>> at low resolution, and I would add to his list that it can also, in some 
>> circumstances, be more indicative of the wrong choice of symmetry (too high) 
>> than the statistics that come from POINTLESS (excellent though that program 
>> is!).
>> 
>> Andrew
>> On 5 Jul 2017, at 05:44, Graeme Winter 
>> > wrote:
>> 
>> HI Jacob
>> 
>> Yes, I got this - and I appreciate the benefit of Rmeas for dealing with 
>> measuring agreement for small-multiplicity observations. Having this *as 
>> well* is very useful and I agree Rmeas / Rpim / CC-half should be the 
>> primary “quality” statistics.
>> 
>> However, you asked if there is any reason to *keep* rather than *eliminate* 
>> Rmerge, and I offered one :o)
>> 
>> I do not see what harm there is reporting Rmerge, even if it is just used in 
>> the inner shell or just used to capture a flavour of the data set overall. I 
>> also appreciate that Rmeas converges to the same value for large 
>> multiplicity i.e.:
>> 
>>Overall  InnerShell  OuterShell
>> Low resolution limit   39.02 39.02  1.39
>> High resolution limit   1.35  6.04  1.35
>> 
>> Rmerge  (within I+/I-) 0.080 0.057 2.871
>> Rmerge  (all I+ and I-)0.081 0.059 2.922
>> Rmeas (within I+/I-)   0.081 0.058 2.940
>> Rmeas (all I+ & I-)0.082 0.059 2.958
>> Rpim (within I+/I-)0.013 0.009 0.628
>> Rpim (all I+ & I-) 0.009 0.007 0.453
>> Rmerge in top intensity bin0.050- -
>> Total number of observations 1265512 16212 53490
>> Total number unique17515   224  1280
>> Mean((I)/sd(I)) 29.7 104.3   1.5
>> Mn(I) half-set correlation CC(1/2) 1.000 1.000 0.778
>> Completeness   100.0  

Re: [ccp4bb] Rmergicide Through Programming

[Graeme Winter]

Dear Frank,

You are forcefully arguing essentially that others are wrong if we feel an 
existing statistic continues to be useful, and instead insist that it be 
outlawed so that we may not make use of it, just in case someone misinterprets 
it.

Very well

I do however express disquiet that we as software developers feel browbeaten to 
remove the output we find useful because “the community” feel that it is 
obsolete.

I feel that Jacob’s short story on this thread illustrates that educating the 
next generation of crystallographers to understand what all of the numbers mean 
is critical, and that a numerological approach of trying to optimise any one 
statistic is essentially doomed. Precisely the same argument could be made for 
people cutting the “resolution” at the wrong place in order to improve the 
average I/sig(I) of the data set.

Denying access to information is not a solution to misinterpretation, from 
where I am sat, however I acknowledge that other points of view exist.

Best wishes Graeme


On 5 Jul 2017, at 12:11, Frank von Delft 
> wrote:


Graeme, Andrew

Jacob is not arguing against an R-based statistic;  he's pointing out that 
leaving out the multiplicity-weighting is prehistoric (Diederichs & Karplus 
published it 20 years ago!).

So indeed:   Rmerge, Rpim and I/sigI give different information.  As you say.

But no:   Rmerge and Rmeas and Rcryst do NOT give different information.  
Except:

  * Rmerge is a (potentially) misleading version of Rmeas.

  * Rcryst and Rmerge and Rsym are terms that no longer have significance in 
the single cryo-dataset world.

phx.



On 05/07/2017 09:43, Andrew Leslie wrote:

I would like to support Graeme in his wish to retain Rmerge in Table 1, 
essentially for exactly the same reasons.

I also strongly support Francis Reyes comment about the usefulness of Rmerge at 
low resolution, and I would add to his list that it can also, in some 
circumstances, be more indicative of the wrong choice of symmetry (too high) 
than the statistics that come from POINTLESS (excellent though that program 
is!).

Andrew
On 5 Jul 2017, at 05:44, Graeme Winter 
> wrote:

HI Jacob

Yes, I got this - and I appreciate the benefit of Rmeas for dealing with 
measuring agreement for small-multiplicity observations. Having this *as well* 
is very useful and I agree Rmeas / Rpim / CC-half should be the primary 
“quality” statistics.

However, you asked if there is any reason to *keep* rather than *eliminate* 
Rmerge, and I offered one :o)

I do not see what harm there is reporting Rmerge, even if it is just used in 
the inner shell or just used to capture a flavour of the data set overall. I 
also appreciate that Rmeas converges to the same value for large multiplicity 
i.e.:

   Overall  InnerShell  OuterShell
Low resolution limit   39.02 39.02  1.39
High resolution limit   1.35  6.04  1.35

Rmerge  (within I+/I-) 0.080 0.057 2.871
Rmerge  (all I+ and I-)0.081 0.059 2.922
Rmeas (within I+/I-)   0.081 0.058 2.940
Rmeas (all I+ & I-)0.082 0.059 2.958
Rpim (within I+/I-)0.013 0.009 0.628
Rpim (all I+ & I-) 0.009 0.007 0.453
Rmerge in top intensity bin0.050- -
Total number of observations 1265512 16212 53490
Total number unique17515   224  1280
Mean((I)/sd(I)) 29.7 104.3   1.5
Mn(I) half-set correlation CC(1/2) 1.000 1.000 0.778
Completeness   100.0  99.7 100.0
Multiplicity72.3  72.4  41.8

Anomalous completeness 100.0 100.0 100.0
Anomalous multiplicity  37.2  42.7  21.0
DelAnom correlation between half-sets  0.497 0.766-0.026
Mid-Slope of Anom Normal Probability   1.039   - -

(this is a good case for Rpim & CC-half as resolution limit criteria)

If the statistics you want to use are there & some others also, what is the 
pressure to remove them? Surely we want to educate on how best to interpret the 
entire table above to get a fuller picture of the overall quality of the data? 
My 0th-order request would be to publish the three shells as above ;o)

Cheers Graeme



On 4 Jul 2017, at 22:09, Keller, Jacob 
> wrote:

I suggested replacing Rmerge/sym/cryst with Rmeas, not Rpim. Rmeas is simply 
(Rmerge * sqrt(n/n-1)) where n is the number of measurements of that 
reflection. It's merely a way of correcting for the multiplicity-related 
artifact 

Re: [ccp4bb] long loop

[mesters]

Do you have an inactive variant of the protein? If yes, use limited 
proteolysis in the presence of methylated histones to find out which 
flexible parts are really important and or protected by complex 
formation. Further, try to crystallize a complex of inactive demethylase 
and methylated histones, a long shot but a good way to combat the 
apparent flexibility


Good luck,

Jeroen


Am 04.07.17 um 17:22 schrieb dongxiaofei:

Dear ALL,
I want to make a protein crystal,but there is a long loop between 
domains of protein , which contains two small domains owning about 40 
amino acids respectively and a loop about 70 amino acids.
Loop is so long and flexible ,but I don't want to delete some 
fragments,because it may be  important for protein's function of a 
histone demethylase.

Besides, the  surface charge of  protein is whole negative .
I have tried a long time but it is hard to me to get crystal.

Would be very grateful for any advice!

Thanks

Dong Xiao






--
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Deputy, Senior Researcher & Lecturer
Program Coordinator /Infection Biology/ 



Institute of Biochemistry, University of Lübeck
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Hence, in most cases, a high-resolution crystal structure (< 2.0 Å)will 
provide a better description of the structure in solution than the 
corresponding NMR structure  (Kuszewski, Gronenborn & Clore, 1996, 
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[ccp4bb] Research Technician Position in Structural Biology in Vienna

[Kristina Djinovic Carugo]

Dear Colleagues

I would really appreciate if you could share the following info 
regarding this available position.

Best regards and thanks
Kristina


We are looking for a highly motivated research technician to join the 
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 and 
Kristina Djinovic Carugo 
, to 
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The Max F. Perutz Laboratories are equipped with state of the art 
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--
Department of Structural and Computational Biology
Max F. Perutz Laboratories
University of Vienna
Vienna Biocenter (VBC), Campus Vienna Biocenter 5
A-1030 Vienna
Austria


e-mail: kristina.djino...@univie.ac.at
Phone: +43-1-4277-52203
Phone: +43-1-4277-52201 (secretary)
Mobile A: +43-664-602 77-522 03
Fax: +43-1-4277-9522

Re: [ccp4bb] long loop

[Briggs, David C]

I know that this might be considered heresy on a crystallography mailing list, 
but do you have any friendly NMRists at your institution?


D


Dr David C Briggs

Hohenester Lab

Department of Life Sciences

Imperial College London

UK

http://about.me/david_briggs


From: CCP4 bulletin board  on behalf of dongxiaofei 
<18811070...@163.com>
Sent: 04 July 2017 16:22:39
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] long loop

Dear ALL,
I want to make a protein crystal,but there is a long loop between domains of 
protein , which contains two small domains owning about 40 amino acids 
respectively and a loop about 70 amino acids.
Loop is so long and flexible ,but I don't want to delete some fragments,because 
it may be  important for protein's function of a histone demethylase.
Besides, the  surface charge of  protein is whole negative .
I have tried a long time but it is hard to me to get crystal.

Would be very grateful for any advice!
Thanks
Dong Xiao

Re: [ccp4bb] Rmergicide Through Programming

[Frank von Delft]

Graeme, Andrew

Jacob is not arguing against an R-based statistic;  he's pointing out 
that leaving out the multiplicity-weighting is prehistoric (Diederichs & 
Karplus published it 20 years ago!).


So indeed:   Rmerge, Rpim and I/sigI give different information. As you say.

But no:   Rmerge and Rmeas and Rcryst do NOT give different 
information.  Except:


  * Rmerge is a (potentially) misleading version of Rmeas.

  * Rcryst and Rmerge and Rsym are terms that no longer have 
significance in the single cryo-dataset world.


phx.



On 05/07/2017 09:43, Andrew Leslie wrote:


I would like to support Graeme in his wish to retain Rmerge in Table 
1, essentially for exactly the same reasons.


I also strongly support Francis Reyes comment about the usefulness of 
Rmerge at low resolution, and I would add to his list that it can 
also, in some circumstances, be more indicative of the wrong choice of 
symmetry (too high) than the statistics that come from POINTLESS 
(excellent though that program is!).


Andrew
On 5 Jul 2017, at 05:44, Graeme Winter > wrote:


HI Jacob

Yes, I got this - and I appreciate the benefit of Rmeas for dealing 
with measuring agreement for small-multiplicity observations. Having 
this *as well* is very useful and I agree Rmeas / Rpim / CC-half 
should be the primary “quality” statistics.


However, you asked if there is any reason to *keep* rather than 
*eliminate* Rmerge, and I offered one :o)


I do not see what harm there is reporting Rmerge, even if it is just 
used in the inner shell or just used to capture a flavour of the data 
set overall. I also appreciate that Rmeas converges to the same value 
for large multiplicity i.e.:


   Overall InnerShell  OuterShell
Low resolution limit   39.02 39.02   1.39
High resolution limit   1.35  6.04   1.35

Rmerge  (within I+/I-) 0.080 0.057 2.871
Rmerge  (all I+ and I-)0.081 0.059 2.922
Rmeas (within I+/I-)   0.081 0.058   2.940
Rmeas (all I+ & I-)0.082 0.059 2.958
Rpim (within I+/I-)0.013 0.009 0.628
Rpim (all I+ & I-) 0.009 0.007 0.453
Rmerge in top intensity bin0.050-   -
Total number of observations 1265512 16212 53490
Total number unique17515   224 1280
Mean((I)/sd(I)) 29.7 104.3   1.5
Mn(I) half-set correlation CC(1/2) 1.000 1.000   0.778
Completeness   100.0  99.7 100.0
Multiplicity 72.3  72.4   41.8

Anomalous completeness 100.0 100.0 100.0
Anomalous multiplicity  37.2 42.7  21.0
DelAnom correlation between half-sets  0.497 0.766-0.026
Mid-Slope of Anom Normal Probability   1.039   -   -

(this is a good case for Rpim & CC-half as resolution limit criteria)

If the statistics you want to use are there & some others also, what 
is the pressure to remove them? Surely we want to educate on how best 
to interpret the entire table above to get a fuller picture of the 
overall quality of the data? My 0th-order request would be to publish 
the three shells as above ;o)


Cheers Graeme



On 4 Jul 2017, at 22:09, Keller, Jacob > wrote:


I suggested replacing Rmerge/sym/cryst with Rmeas, not Rpim. Rmeas 
is simply (Rmerge * sqrt(n/n-1)) where n is the number of 
measurements of that reflection. It's merely a way of correcting for 
the multiplicity-related artifact of Rmerge, which is becoming even 
more of a problem with data sets of increasing variability in 
multiplicity. Consider the case of comparing a data set with a 
multiplicity of 2 versus one of 100: equivalent data quality would 
yield Rmerges diverging by a factor of ~1.4. But this has all been 
covered before in several papers. It can be and is reported in 
resolution bins, so can used exactly as you say. So, why not 
"disappear" Rmerge from the software?


The only reason I could come up with for keeping it is historical 
reasons or comparisons to previous datasets, but anyway those 
comparisons would be confounded by variabities in multiplicity and a 
hundred other things, so come on, developers, just comment it out!


JPK




-Original Message-
From: graeme.win...@diamond.ac.uk 
 
[mailto:graeme.win...@diamond.ac.uk]

Sent: Tuesday, July 04, 2017 4:37 PM
To: Keller, Jacob >

Cc: ccp4bb@jiscmail.ac.uk 
Subject: Re: [ccp4bb] Rmergicide Through Programming

HI Jacob

Unbiased estimate of the true unmerged I/sig(I) of your data (I find 
this particularly 

Re: [ccp4bb] Rmergicide Through Programming

[Keller, Jacob]

>I do not see what harm there is reporting Rmerge, even if it is just used in 
>the inner shell or just used to capture a flavour of the data set overall. I 
>also appreciate that Rmeas converges to the same value for large multiplicity

Consider a callow young grad student, David, who being beleaguered by his 
distant advisor and armchair crystallographer, Dr. Murdstone, into improving 
the statistics of his data, resorts to every option, including trying to 
collect a high-multiplicity data set (100-fold!). To his chagrin, Rmerge keeps 
rising even in spite of these heroic efforts. His exceedingly humble post-doc 
friend and confidant, Uriah, pecks out with his clammy hands a script for 
improving Rmerge, to which he subjects David’s, and indeed all of the lab’s, 
data. Cheers resound at the improved statistics (and smaller mtz files), 
especially from Murdstone, although only MR seems to work now for solving 
structures, and final model stats generally worsen. With the help of some other 
corrective scripts written by Uriah based on Murthy’s Law, there is a lovely 
spate of papers published at well-known journals, and Dr. Murdstone becomes Sir 
Murdstone. Unfortunately, David’s data set requires experimental phasing, so he 
remains in a tailspin with progressively nastier emails arriving from Murdstone 
daily. Observing the situation, the reticent lab manager Agnes opens up the 
merging code, and deletes all mention of Rmerge. Uriah’s great successes 
suddenly stop, but somehow David is now able to solve his data set, and he 
marries Agnes, while all of the recent MR-based structures are retracted, 
notwithstanding the hundreds of subsequent papers based on their conclusions. 
David becomes a noted crystallographer with Agnes helping him slightly in the 
background, while humble Uriah finally finds useful and vastly remunerative 
employment in a pharma marketing and lobbying firm in the New World.

Is this happening right now somewhere? O Britannia, reck ye the perils of 
Rmerge.

Re: [ccp4bb] long loop

[Smith Liu]

Fab fragment binding towards long loop



在2017年07月04日 23:22，dongxiaofei 写道：
Dear ALL,
I want to make a protein crystal,but there is a long loop between domains of 
protein , which contains two small domains owning about 40 amino acids 
respectively and a loop about 70 amino acids.
Loop is so long and flexible ,but I don't want to delete some fragments,because 
it may be  important for protein's function of a histone demethylase.
Besides, the  surface charge of  protein is whole negative .
I have tried a long time but it is hard to me to get crystal.
 

Would be very grateful for any advice!

Thanks

Dong Xiao

 

 





 

Re: [ccp4bb] Rmergicide Through Programming

[Andrew Leslie]

I would like to support Graeme in his wish to retain Rmerge in Table 1, 
essentially for exactly the same reasons. 

I also strongly support Francis Reyes comment about the usefulness of Rmerge at 
low resolution, and I would add to his list that it can also, in some 
circumstances, be more indicative of the wrong choice of symmetry (too high) 
than the statistics that come from POINTLESS (excellent though that program 
is!).

Andrew
> On 5 Jul 2017, at 05:44, Graeme Winter  wrote:
> 
> HI Jacob
> 
> Yes, I got this - and I appreciate the benefit of Rmeas for dealing with 
> measuring agreement for small-multiplicity observations. Having this *as 
> well* is very useful and I agree Rmeas / Rpim / CC-half should be the primary 
> “quality” statistics.
> 
> However, you asked if there is any reason to *keep* rather than *eliminate* 
> Rmerge, and I offered one :o)
> 
> I do not see what harm there is reporting Rmerge, even if it is just used in 
> the inner shell or just used to capture a flavour of the data set overall. I 
> also appreciate that Rmeas converges to the same value for large multiplicity 
> i.e.:
> 
>Overall  InnerShell  OuterShell
> Low resolution limit   39.02 39.02  1.39
> High resolution limit   1.35  6.04  1.35
> 
> Rmerge  (within I+/I-) 0.080 0.057 2.871
> Rmerge  (all I+ and I-)0.081 0.059 2.922
> Rmeas (within I+/I-)   0.081 0.058 2.940
> Rmeas (all I+ & I-)0.082 0.059 2.958
> Rpim (within I+/I-)0.013 0.009 0.628
> Rpim (all I+ & I-) 0.009 0.007 0.453
> Rmerge in top intensity bin0.050- - 
> Total number of observations 1265512 16212 53490
> Total number unique17515   224  1280
> Mean((I)/sd(I)) 29.7 104.3   1.5
> Mn(I) half-set correlation CC(1/2) 1.000 1.000 0.778
> Completeness   100.0  99.7 100.0
> Multiplicity72.3  72.4  41.8
> 
> Anomalous completeness 100.0 100.0 100.0
> Anomalous multiplicity  37.2  42.7  21.0
> DelAnom correlation between half-sets  0.497 0.766-0.026
> Mid-Slope of Anom Normal Probability   1.039   - -  
> 
> (this is a good case for Rpim & CC-half as resolution limit criteria)
> 
> If the statistics you want to use are there & some others also, what is the 
> pressure to remove them? Surely we want to educate on how best to interpret 
> the entire table above to get a fuller picture of the overall quality of the 
> data? My 0th-order request would be to publish the three shells as above ;o)
> 
> Cheers Graeme
> 
> 
> 
>> On 4 Jul 2017, at 22:09, Keller, Jacob > > wrote:
>> 
>> I suggested replacing Rmerge/sym/cryst with Rmeas, not Rpim. Rmeas is simply 
>> (Rmerge * sqrt(n/n-1)) where n is the number of measurements of that 
>> reflection. It's merely a way of correcting for the multiplicity-related 
>> artifact of Rmerge, which is becoming even more of a problem with data sets 
>> of increasing variability in multiplicity. Consider the case of comparing a 
>> data set with a multiplicity of 2 versus one of 100: equivalent data quality 
>> would yield Rmerges diverging by a factor of ~1.4. But this has all been 
>> covered before in several papers. It can be and is reported in resolution 
>> bins, so can used exactly as you say. So, why not "disappear" Rmerge from 
>> the software?
>> 
>> The only reason I could come up with for keeping it is historical reasons or 
>> comparisons to previous datasets, but anyway those comparisons would be 
>> confounded by variabities in multiplicity and a hundred other things, so 
>> come on, developers, just comment it out!
>> 
>> JPK
>> 
>> 
>> 
>> 
>> -Original Message-
>> From: graeme.win...@diamond.ac.uk  
>> [mailto:graeme.win...@diamond.ac.uk ] 
>> Sent: Tuesday, July 04, 2017 4:37 PM
>> To: Keller, Jacob > >
>> Cc: ccp4bb@jiscmail.ac.uk 
>> Subject: Re: [ccp4bb] Rmergicide Through Programming
>> 
>> HI Jacob
>> 
>> Unbiased estimate of the true unmerged I/sig(I) of your data (I find this 
>> particularly useful at low resolution) i.e. if your inner shell Rmerge is 
>> 10% your data agree very poorly; if 2% says your data agree very well 
>> provided you have sensible multiplicity… obviously depends on sensible 
>> interpretation. Rpim hides this (though tells you more about the quality of 
>>