Thanks Doeke (and others who have replied directly). I suppose my big concern with just truncating the data after merging would be the bin size/data processing statistics. If the edge/corner is binned 10x and I end up removing 5 of the bins by truncating the resolution post-merging, the Table 1 reported merged statistics will be based on the entire detector face being scaled rather than if I reprocessed the truncated dataset into 10 bins. I thought maybe that phenix.table_one would fix this by just using the 10% high-resolution reflections and recalculating the merging statistics, but this only does so if you supply the unmerged data (which is missing). I guess the transparent thing to do if I do not reprocess the data is to report the number of bins used and manually curate the high-resolution statistics in Table 1 based on the last bin (at the resolution limit used in refinement or applied with CAD) in scale.log file from HKL2000.
Just want to say thanks again to this community, it's great to get insight in these problems so easily and quickly. Matt On Wed, 17 Apr 2024 at 16:35, 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 > <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=DPfbtiuJFZDsaMqRC3wABRuP0iJZMKOIsdAAHocfxcg&m=hJXGz_3_uI3SAKeW8GEqSK_1Qr5wKgBiSnbDjVjBNhSVakQOsdVMVRRe_MBbhJ4L&s=4rZTwcJhEjd1bJl5IPP_Hx0Y_vlFww2ZSsUH0nDMTQE&e=> > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.jiscmail.ac.uk_CCP4BB&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=DPfbtiuJFZDsaMqRC3wABRuP0iJZMKOIsdAAHocfxcg&m=hJXGz_3_uI3SAKeW8GEqSK_1Qr5wKgBiSnbDjVjBNhSVakQOsdVMVRRe_MBbhJ4L&s=Q9SS6-TevYcWhuxShDbUJofSUXOmTisCs4Ri8YccEHw&e=>, > a mailing list hosted by www.jiscmail.ac.uk > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.jiscmail.ac.uk&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=DPfbtiuJFZDsaMqRC3wABRuP0iJZMKOIsdAAHocfxcg&m=hJXGz_3_uI3SAKeW8GEqSK_1Qr5wKgBiSnbDjVjBNhSVakQOsdVMVRRe_MBbhJ4L&s=9Jze4xWSveGay7htjcwemmwFSwvtjCqm1SvXSmmr3g4&e=>, > terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ > <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_policyandsecurity_&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=DPfbtiuJFZDsaMqRC3wABRuP0iJZMKOIsdAAHocfxcg&m=hJXGz_3_uI3SAKeW8GEqSK_1Qr5wKgBiSnbDjVjBNhSVakQOsdVMVRRe_MBbhJ4L&s=SlvCI5t8-1t-4jbVfCyG2ENCo3VDDqOQbYElsa7eHKc&e=> > > > > > -- > > *Matthew Jordan McLeod, PhD* > > *Post-Doctoral Fellow - Cornell University* > > > > -- *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 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/
