If you are using CCP4I2 and use the task "Import merged data" that sort of reprocesses that data through AIMLESS. You get all the usual graphsv resolution - completeness, I/SigI , Wilson plot, Second moments etc and from those can make a sensible decision on where the resolution limit should be set.. In my experience rescaling isnt usually necessary - the scales are weighted by SigI and very weak data has little effect.. Eleanor
On Thu, 18 Apr 2024 at 09:22, Harry Powell < 0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > Hi > > Only comment is that (surely) any decent refinement program these days > would down-weight any reflections with negligible I/sig(I) (for example, > those in the “unobserved” high resolution regions) so that they do not > contribute (significantly) to the refinement. Or am I wrong (I don’t mind > being wrong, and since I am a little rusty in these mattrers I would be > very happy to be educated)? > > Doesn’t Aimless produce a table with the cumulative statistics at various > resolution limits? So you don’t even need to re-scale & merge to get the > stats to whatever your chosen high resolution limit is (I’d choose CC -1/2 > = 0.30, as Doeke suggests)? Do HKL or XSCALE do the same (sorry, I haven’t > looked at their output for quite some time)? > > Just my two ha’porth > > Harry > > > On 17 Apr 2024, at 21:35, Hekstra, Doeke Romke < > doeke_heks...@harvard.edu> wrote: > > > > Hi Matt, > > > > I appreciate disagreement and comments from colleagues. My two cents are > that it seems unnecessary to repeat scaling and merging, or any earlier > step. If you want to remove structure factor amplitudes or merged > intensities from the MTZ file you can do so using MTZUTILS or similar > functionality in CCP4 ( > https://www.ccp4.ac.uk/html/mtzutils.html#generalresolution). For > refinement, you can specify the desired resolution range in your favorite > refinement program. > > > > My personal convention is to use CC1/2 = 0.30 as the point to which > retain data and <I/sigI> = 2 as the nominal resolution of the dataset. If > you have the HKL2000 scaling log, you should be able to retrieve this > information. I frankly wish we’d just deposit all data in the PDB rather > than truncate based on some criterion or another. > > > > Best, Doeke > > > > From: Matt Mcleod <mjmcleo...@gmail.com> > > Sent: Wednesday, April 17, 2024 4:12 PM > > To: Hekstra, Doeke Romke <doeke_heks...@harvard.edu> > > Cc: CCP4BB@JISCMAIL.AC.UK > > Subject: Re: [ccp4bb] Rescale merged data? > > > > Sure thing. > > > > A former student left somewhere between 30-50 datasets but they scaled > the data to the detector corners (or maybe edge) in HKL2000. There are > many of the high-resolution bins with no reflections in them. He then went > forward and merged this data, presumably in HKL2000 again and did his model > building/refinement. We now need to re-refine the models against this > data for publication but we need a more suitable resolution cutoff for the > data. > > > > Rather than go back and index/integrate all the data and then rescale > the data to a more appropriate place (then merge), I was wondering if there > was a way to take the merged reflections as either .sca or .mtz (from > scalepacktomtz output) and then rescale to a more appropriate resolution. > It doesn't seem like the student left unmerged data. > > > > So, nothing fancy (aniostropy etc), there is just a lot of data that > needs to be adjusted and I am trying to avoid reprocessing all the frames > again. > > > > Matt > > > > On Wed, 17 Apr 2024 at 15:59, Hekstra, Doeke Romke < > doeke_heks...@harvard.edu> wrote: > > Hi Matt, > > > > It would be helpful if you could describe your case in more detail. Do > you want to change the resolution cutoff after scaling? Do you want to keep > more data? Fewer? Or do you mean something different such as truncation to > generate amplitudes, application of anisotropic resolution cutoffs, or > outlier rejection? Are you referring to data that were scaled in HKL2000? > > > > Best, Doeke > > > > -----Original Message----- > > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Matt > McLeod > > Sent: Wednesday, April 17, 2024 3:04 PM > > To: CCP4BB@JISCMAIL.AC.UK > > Subject: [ccp4bb] Rescale merged data? > > > > Hi all, > > > > I am looking at a old students data and it looks like they didn't > properly cut off the data during scaling. All of the files I have appear > to be the merged .sca (or mtz after converting with scalepacktomtz) - is > there a way to retruncate the data after merging or do I have to reprocess > the data? > > > > Thanks, > > > > ######################################################################## > > > > 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/ > > > > > > -- > > Matthew Jordan McLeod, PhD > > Post-Doctoral Fellow - Cornell University > > > > > > > > > > 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/ > ######################################################################## 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/
