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 reindexing
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 v
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 no
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 you
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 ca
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
mailto:jmhol...@slac.stanford.edu>> wrote:
You need to be careful with the exact space group at the particular stage in
your pipeline here.
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
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
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 this isn’t
> always low enough?
No, scrub that—the 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 ⚗ ℡: +44 1865 275
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 did
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
wrote:
> Hello - c
Hello - can anybody shed light on this mystery:
We need (for PanDDA analysis) a lot of datasets each to have the
complete set of low resolution indices, whether measured or not. (Refmac
adds the estimates as DFc, which is crucial when comparing maps.)
In ccp4, there are two obvious ways to ge
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