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/
