Hi Mirek, I have absolutely loved this discussion of other options for comparing datasets! But to your original problem:
To tell CCP4 where r is installed, you need to add this to your $PATH. You will want to figure out where r is installed on your computer and then add it to your .bashrc file or .zshrc file if you are using a newer Mac. These instructions might be helpful: https://gist.github.com/nex3/c395b2f8fd4b02068be37c961301caa7 . You can follow the instructions for Mac Os or for Linux. You can tell that you have done this correctly by opening a new terminal window and typing "which r" (no quotes) into the command prompt. It should return a path to where you have r installed. You can then launch ccp4 by typing "ccp4i2" into the command prompt. Clicking on the icon might also work, but I generally launch CCP4 from a terminal window. Also, if you have problems launching ccp4 from terminal, add this to your .bashrc/.zshrc, making sure that the path you are listing is correct for your installation of ccp4 and that you re-start your terminal after doing this: #ccp4 source /Applications/ccp4-7.1/bin/ccp4.setup-sh Good luck! Kind regards, Jessica On Tue, Jul 26, 2022 at 8:10 AM Clemens Vonrhein <vonrh...@globalphasing.com> wrote: > Dear all, > > [just to add some caveats in case future students see this thread and > start cut-n-pasting commands to successfully create some kind of MTZ > file of dubious content] > > Unless we're talking about some really old datasets (of historical > interest) or a disastrous situation (all backups lost), by far the > best approach would be to go back to the original data in the form of > the (unscaled) unmerged intensities - in order to do the > scaling+merging of the two datasets then, right? > > One can do all kind of things with amplitudes (F) in MTZ files using > various fabulous CCP4 programs (SFTOOLS, SCALEIT, RSTATS, CAD, > POINTLESS, COMBAT), but be careful that it is not just some > simple/brainless arithmetic on numerical values that happen to be > called F/SIGF. Been there, done that, got the T-shirt ... > > The important thing is to understand what the OP is trying to achive > here. As others mentioned: > > ... calculate R-merge for Fs from two datasets processed from two > different crystals ... > > sounds to like a confusion between > > (1) comparing two sets of amplitudes via an R-factor (not R-merge!) > > * can be done with e.g. SCALEIT or RSTATS > > * with or without scaling? > > * what scale parametrisation (k, k/B, anisotropic)? > > * overall or in bins? What binning? > > (2) getting a "R-merge" value for some kind of "Table-1" (paper or > deposition): > > * can't be done "correctly" from amplitudes > > * go back to original data and (re)processing > > And > > ... would take two mtz files and merge the Fs ... > > might just ask for a method to "average" two sets of amplitudes: > > * inverse-variance weighted? > > * unweighted? > > * for what purpose - and why not go back to the original data to do > proper scaling/merging there? > > The subject line "Comparing two datasets" seems to ask for something > different again: a way of comparing (R-factor? CC?) datasets, not > necessarily combining/merging them? > > Cheers > > Clemens > > > On Tue, Jul 26, 2022 at 02:11:17PM +0100, Phil Evans wrote: > > If you want to merge them then you can use Pointless/Aimless/ctruncate, > with the warning that the conversion from F to I is not ideal, and > ctruncate should be set to regenerate F from I just as sqrt ie not apply > the truncate procedure again. > > Pointless supersedes combat for this conversion > > Again, just for comparison use scaleit > > > > Phil > > > > Sent from my iPhone > > > > > On 26 Jul 2022, at 13:33, Jon Cooper < > 0000488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote: > > > > > > Hello again, as far as I can tell, the question is about two already > merged/unique datasets which Mirek wishes to merge into one. As far as I > can tell/remember, Scaleit is for scaling datasets side-by-side to get > isomorphous differences, etc, and I don't know of a way that you could get > it to merge 2 datasets as Mirek requested. Probably I am wrong but Scaleit > R-factors are different from R-merge, although the latter might be a bit > dubious in the circumstances. Anyway, I think the Combat route is a viable > way of achieving what the questioner wants to achieve ;-0 > > > > > > > > > Sent from ProtonMail mobile > > > > > > > > > > > > -------- Original Message -------- > > > On 26 Jul 2022, 12:25, John R Helliwell < jrhelliw...@gmail.com> > wrote: > > > > > > Dear Colleagues, > > > Scaleit is a terrific program. > > > Amongst its strengths already listed I would also mention its > breakdown table with F so that in the strongest F reflections bin any > systematic errors between the two data sets can show up if the Rfactor is > greater than about 1%. > > > Greetings, > > > John > > > Emeritus Professor John R Helliwell DSc > > > > > > > > > > > > > > >> On 26 Jul 2022, at 11:40, Eleanor Dodson < > 0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > > >> > > >> > > >> Not only does SCALEIT do the job - it presented useful plots and an > informative log file.. > > >> Eleanor > > >> (You need to run CAD hklin1 Xtal1.mtz hklin2 Xtal2.mtz ...and > obviously the columns from each Xtal will need different labels..) > > >> > > >> On Tue, 26 Jul 2022 at 09:45, Phil Evans <p...@mrc-lmb.cam.ac.uk> > wrote: > > >>> If you give Pointless Fs, it squares them to Is (not correct if the > Fs have been derived from the truncate procedure, but not too bad). It will > then give you a comparison. If you give the two datasets to Pointless, > labelling them as different datasets, you can use Aimless to compare them > > >>> > > >>> But as Andrew said, the appropriate CCP4 program is Scaleit: it’s > old but still works and gives lots of statistics > > >>> > > >>> Phil > > >>> > > >>> Sent from my iPhone > > >>> > > >>>> On 26 Jul 2022, at 09:37, Andrew Leslie - MRC LMB < > and...@mrc-lmb.cam.ac.uk> wrote: > > >>>> > > >>>> I think that POINTLESS works with intensities rather than > structure factors (I’m not sure if this can be changed). Also, SCALEIT > gives a much more detailed breakdown (R factors as a function of resolution > and differences in terms of sigmas etc) than POINTLESS WILL. > > >>>> > > >>>> Cheers, > > >>>> > > >>>> Andrew > > >>>> > > >>>>> On 26 Jul 2022, at 09:24, LEGRAND Pierre < > pierre.legr...@synchrotron-soleil.fr> wrote: > > >>>>> > > >>>>> Hello Mirek, > > >>>>> > > >>>>> A very quick approach for that is offered by pointless: > > >>>>> > > >>>>> pointless HKLREF 1_1_aimless.mtz HKLIN 2_1_aimless.mtz > > >>>>> or > > >>>>> pointless HKLREF 1_1_aimless.mtz XDSIN XDS_ASCII.HK > > >>>>> > > >>>>> You will obtain a table looking like that, taking into account to > possible reindexing: > > >>>>> > > >>>>> Alternative indexing scores relative to reference > > >>>>> Alternative reindexing Lklhd CC R(E^2) > Number Cell_deviation > > >>>>> 1 [h,k,l] 0.993 0.962 0.118 > 19150 0.08 > > >>>>> 2 [-k,h,l] 0.007 0.078 0.512 > 19150 0.87 > > >>>>> > > >>>>> > > >>>>> Best wishes, > > >>>>> > > >>>>> Pierre Legrand > > >>>>> PROXIMA-1 Beamline > > >>>>> Synchrotron SOLEIL > > >>>>> > > >>>>> De: "Nicolas Foos" <nicf...@embl.fr> > > >>>>> À: CCP4BB@JISCMAIL.AC.UK > > >>>>> Envoyé: Mardi 26 Juillet 2022 08:36:35 > > >>>>> Objet: Re: [ccp4bb] Comparing two datasets > > >>>>> > > >>>>> Hi Mirek, > > >>>>> > > >>>>> I am pretty sure XSCALE will do that for you : > https://xds.mr.mpg.de/html_doc/xscale_program.html > > >>>>> > > >>>>> If not, maybe have a look on SHELXC in SIR mode. > > >>>>> > > >>>>> Hope this help. > > >>>>> > > >>>>> Nicolas > > >>>>> > > >>>>> On 25/07/2022 21:52, Cygler, Miroslaw wrote: > > >>>>> Hi, > > >>>>> I would like to calculate the R-merge for Fs from two datasets > processed from two different crystals. Tried to use Blend but got the > message that Blend requires R. Downloaded R but do not know how to tell > CCP4 where it is located on my Mac. Is there another program that would > take two mtg files and merge the Fs? > > >>>>> Any help would be greatly appreciated. > > >>>>> > > >>>>> > > >>>>> Mirek > > >>>>> > > >>>>> > > >>>>> > > >>>>> > > >>>>> > > >>>>> To unsubscribe from the CCP4BB list, click the following link: > > >>>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > >>>>> > > >>>>> -- > > >>>>> Nicolas Foos PhD - ARISE fellow > > >>>>> https://orcid.org/0000-0003-2331-8399 > > >>>>> > > >>>>> EMBL Grenoble, McCarthy Team > > >>>>> 71 av. des Martyrs, > > >>>>> 38000 Grenoble FRANCE > > >>>>> > > >>>>> +33 4 57 42 84 67 > > >>>>> > > >>>>> To unsubscribe from the CCP4BB list, click the following link: > > >>>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > >>>>> > > >>>>> > > >>>>> > > >>>>> To unsubscribe from the CCP4BB list, click the following link: > > >>>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > >>>>> > > >>>> > > >>>> > > >>>> To unsubscribe from the CCP4BB list, click the following link: > > >>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > >>>> > > >>> > > >>> To unsubscribe from the CCP4BB list, click the following link: > > >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > >>> > > >> > > >> To unsubscribe from the CCP4BB list, click the following link: > > >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > >> > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > ######################################################################## > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > > -- > > *-------------------------------------------------------------- > * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com > * Global Phasing Ltd., Sheraton House, Castle Park > * Cambridge CB3 0AX, UK www.globalphasing.com > *-------------------------------------------------------------- > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
