Re: [ccp4bb] (arcane) How to generate complete set of indices at low res

Oh, sorry, I'm with you — thanks for clarifying. I thought you were suggesting some other effect (that I was unaware of) than standard systematic absences. I don’t think this is the problem in our case, but you’re right the spacegroup issue is an interesting one to look out for if any

Re: [ccp4bb] (arcane) How to generate complete set of indices at low res

Hi Frank I think this is a feature of (c)truncate - to avoid actually absent reflections messing up the French & Wilson correction for present-but-weak-or-negative reflections they are chucked out. If you put data in e.g. P212121 into AIMLESS absent reflections will be written out. They only

Re: [ccp4bb] (arcane) How to generate complete set of indices at low res

Thanks James, that's a very useful steer - this is definitely an easy thing to get mixed up with, we can go scratch around there. I now vaguely recall an ancient BB thread, where people were asking why the systematic absences get scrubbed out of the mtz files at all.  I must agree that I do

Re: [ccp4bb] (arcane) How to generate complete set of indices at low res

I say "putative" because I don't know what your space group is. In P212121 the reflection h,k,l = 0,0,1 is absent, but in P222 it is not absent.  So, if your unit cell is a=30 b=40 c=60 the lowest-angle hkl you will get is at 60 A resolution (0,0,1) in P222, but the lowest-angle reflection

Re: [ccp4bb] (arcane) How to generate complete set of indices at low res

Just in case you find it helpful, you can get 100% complete set of reflections (Fcalc) in specified resolution range using phenix.fmodel model.pdb high_res=2.5 low_res=15 or if you leave out low_res it will go all the way up to theoretical limit of low resolution. If you have/use cctbx then I

Re: [ccp4bb] (arcane) How to generate complete set of indices at low res

Could you expand a bit on what you mean by a “putative” systematic absence? (e.g. why only the lowest order hkl?) On 5 Apr 2018, at 19:39, James Holton > wrote: You need to be careful with the exact space group at the particular

Re: [ccp4bb] (arcane) How to generate complete set of indices at low res

You need to be careful with the exact space group at the particular stage in your pipeline here.  Often the lowest-order hkl is a putative systematic absence, so if you uniqueify in P222 you will get it, but if you uniqueify in P212121, then you won't. That sort of thing.  Note that it doesn't

Re: [ccp4bb] (arcane) How to generate complete set of indices at low res

Hi Frank, could you please be more specific, and give examples - the more the better? That would help enormously in debugging. Information required is cell, spacegroup, and which reflection(s) (as h,k,l triples) is/are missing. best, Kay On Thu, 5 Apr 2018 11:52:37 +0100, Frank von Delft

Re: [ccp4bb] (arcane) How to generate complete set of indices at low res

I wrote: > Frank von Delft writes: > >> No, the point is: uniqueify manages to not always do this. > > The “uniqueify” script depends on the “unique” program, which seems to > contain a built‐in low‐resolution limit of 50Å. Could it be

Re: [ccp4bb] (arcane) How to generate complete set of indices at low res

Frank von Delft writes: > No, the point is: uniqueify manages to not always do this. The “uniqueify” script depends on the “unique” program, which seems to contain a built‐in low‐resolution limit of 50Å. Could it be this isn’t always low enough? -- Ian Clifton ⚗

Re: [ccp4bb] (arcane) How to generate complete set of indices at low res

No, the point is:  uniqueify manages to not /alw//ays/ do this. I suppose I'm really asking:  who wants an example file to debug it?  Because we have failed utterly. Frank On 05/04/2018 12:04, Eleanor Dodson wrote: You need to be a bit more specific! - unbiqueify is meant to do this.. I

Re: [ccp4bb] (arcane) How to generate complete set of indices at low res

You need to be a bit more specific! - unbiqueify is meant to do this.. I didnt know CAD would generate indices not in the input file, unless you asked to generate a full set of FreeR terms, when the job I thought ran uniqueify? Eleanor On 5 April 2018 at 11:52, Frank von Delft