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 <[log in to unmask]> 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 <[log in to unmask]>
> Sent: Wednesday, April 17, 2024 4:12 PM
> To: Hekstra, Doeke Romke <[log in to unmask]>
> Cc: [log in to unmask]
> 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 <[log in to unmask]> 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 <[log in to unmask]> On Behalf Of Matt McLeod
> Sent: Wednesday, April 17, 2024 3:04 PM
> To: [log in to unmask]
> 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,
>
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> --
> Matthew Jordan McLeod, PhD
> Post-Doctoral Fellow - Cornell University
>
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