Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

. From: James Foadi [mailto:james_fo...@yahoo.co.uk] Sent: Tuesday, July 11, 2017 10:03 AM To: Vellieux Frédéric ; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming Hello Frederic. Interesting. Have you got some reference on this to share? James Dr James Foadi PhD

Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

ubject: Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming What is the difference between Rmerge and Rsym - I thought they were the same? Rrim == Rmeas I think Phil > On 10 Jul 2017, at 15:18, John Berrisford wrote: > > Dear Herman > > The new PDB deposition system (OneDep) a

Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

ers, Fred. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Phil Evans Sent: Monday, July 10, 2017 5:43 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming What is the difference between Rmerge and Rsym - I th

Re: [ccp4bb] [ccp4bb] Rmergicide Through Programming

> > (2) Rsym has just: > >> R sym value in percent. > > see > . > To be honest, if that is the official definition it does make me wonder what > it is doing in the dictionary at all. > > Reg

Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

-Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Edward A. Berry Gesendet: Samstag, 8. Juli 2017 22:31 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Rmergicide Through Programming But R-merge is not really narrower as a fraction of the mea

Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

the 1960's to be used with punch cards. >> >> My 2 cents. >> Herman >> >> >> >> -Ursprüngliche Nachricht- >> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von >> Edward A. Berry >> Gesendet: Samstag, 8. Juli 2017

Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Edward A. Berry Gesendet: Samstag, 8. Juli 2017 22:31 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Rmergicide Through Programming But R-merge is not really narrower as a fraction of the mean value- it just gets smaller proportionantly

[ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

.AC.UK] Im Auftrag von Edward A. Berry Gesendet: Samstag, 8. Juli 2017 22:31 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Rmergicide Through Programming But R-merge is not really narrower as a fraction of the mean value- it just gets smaller proportionantly as all the numbers get smaller: RMS

Re: [ccp4bb] Rmergicide Through Programming

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> [mailto:graeme.win...@diamond.ac.uk] Sent: Tue

Re: [ccp4bb] Rmergicide Through Programming

icity 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> [mailto:graeme.win...@diamond.ac.uk] Sent: Tuesday, July 04, 2017 4:37 PM To: Keller, Jacob mailto:

Re: [ccp4bb] Rmergicide Through Programming

--- From: graeme.win...@diamond.ac.uk<mailto:graeme.win...@diamond.ac.uk> [mailto:graeme.win...@diamond.ac.uk] Sent: Tuesday, July 04, 2017 4:37 PM To: Keller, Jacob mailto:kell...@janelia.hhmi.org>> Cc: ccp4bb@jiscmail.ac.uk<mailto:ccp4bb@jiscmail.ac.uk> Subject: Re: [ccp4bb] Rmer

Re: [ccp4bb] Rmergicide Through Programming

icity 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> [mailto:graeme.win...@diamond.ac.uk] Sent: Tuesday, July 04, 2017 4:37 PM To: Keller, Jacob mailto:kell...

Re: [ccp4bb] Rmergicide Through Programming

cal 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

Re: [ccp4bb] Rmergicide Through Programming

out! JPK -Original Message- From: graeme.win...@diamond.ac.uk<mailto:graeme.win...@diamond.ac.uk> [mailto:graeme.win...@diamond.ac.uk] Sent: Tuesday, July 04, 2017 4:37 PM To: Keller, Jacob mailto:kell...@janelia.hhmi.org>> Cc: ccp4bb@jiscmail.ac.uk<mailto:ccp4bb@jisc

Re: [ccp4bb] Rmergicide Through Programming

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> [mailto:graeme.win...@diamond.ac.uk] Sent: Tuesday, July 04, 2017 4:37 PM To: Keller, Jacob ma

Re: [ccp4bb] Rmergicide Through Programming

and suspect perhaps the Rmeas folks can/will answer better than I. All the best, Jacob From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frank von Delft Sent: Friday, July 07, 2017 2:26 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Rmergicide Through Programming Okay, that

Re: [ccp4bb] Rmergicide Through Programming

> 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

Re: [ccp4bb] Rmergicide Through Programming

d.ac.uk> [mailto:graeme.win...@diamond.ac.uk] Sent: Tuesday, July 04, 2017 4:37 PM To: Keller, Jacob mailto:kell...@janelia.hhmi.org>> Cc: ccp4bb@jiscmail.ac.uk<mailto:ccp4bb@jiscmail.ac.uk> Subject: Re: [ccp4bb] Rmergicide Through Programming HI Jacob Unbiased estimate of the

Re: [ccp4bb] Rmergicide Through Programming

s 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> [mailto:graeme.win...@diamond.ac.uk] Sent: Tuesday, July 04, 2017 4:37 PM To: Keller, Jacob mailto:kell

Re: [ccp4bb] Rmergicide Through Programming

hich 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 al

Re: [ccp4bb] Rmergicide Through Programming

t comment it out! JPK -Original Message- From: graeme.win...@diamond.ac.uk<mailto:graeme.win...@diamond.ac.uk> [mailto:graeme.win...@diamond.ac.uk] Sent: Tuesday, July 04, 2017 4:37 PM To: Keller, Jacob mailto:kell...@janelia.hhmi.org>> Cc: ccp4bb@jiscmail.ac.uk<mailto:ccp4bb@jiscm

Re: [ccp4bb] Rmergicide Through Programming

, developers, just comment it out! JPK -Original Message- From: graeme.win...@diamond.ac.uk <mailto:graeme.win...@diamond.ac.uk> [mailto:graeme.win...@diamond.ac.uk] Sent: Tuesday, July 04, 2017 4:37 PM To: Keller, Jacob <mailto:kell...@janelia.hhmi.org>> Cc: ccp4bb@jiscm

Re: [ccp4bb] Rmergicide Through Programming

>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 beleag

Re: [ccp4bb] Rmergicide Through Programming

us 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:

Re: [ccp4bb] Rmergicide Through Programming

rom: 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/si

Re: [ccp4bb] Rmergicide Through Programming

crystallographers? Or…it really doesn’t matter that much? JPK From: Eleanor Dodson [mailto:eleanor.dod...@york.ac.uk] Sent: Tuesday, July 04, 2017 5:37 PM To: Keller, Jacob Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Rmergicide Through Programming Agree although i usually look to CC1/2. Rmeas makes

Re: [ccp4bb] Rmergicide Through Programming

I find the lack of reporting statistics of the low resolution bins unfortunate! Most statistics in Table 1 report the average across all resolutions or just the high resolution reflection shell. With respect to Rmerge, the agreement between the most intense (low resolution) symmetry related

Re: [ccp4bb] Rmergicide Through Programming

n...@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 usefu

Re: [ccp4bb] Rmergicide Through Programming

y 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] Rme

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 sensib

Re: [ccp4bb] Rmergicide Through Programming

>Rmerge does contain information which complements the others. What information? I was trying to think of a counterargument to what I proposed, but could not think of a reason in the world to keep reporting it. JPK On 4 Jul 2017, at 12:00, Keller, Jacob mailto:kell...@janelia.hhmi.org>> wrot

Re: [ccp4bb] Rmergicide Through Programming

Jacob Rmerge does contain information which complements the others. I'd prefer it remains but agree it needs to be properly understood alongside the others you mention Cheers Graeme On 4 Jul 2017, at 12:00, Keller, Jacob mailto:kell...@janelia.hhmi.org>> wrote: Dear Crystallographers, Havin

[ccp4bb] Rmergicide Through Programming

Dear Crystallographers, Having been repeatedly chagrinned about the continued use and reporting of Rmerge rather than Rmeas or similar, I thought of a potential way to promote the change: what if merging programs would completely omit Rmerge/cryst/sym? Is there some reason to continue to report