Posted on behalf of Alan F. Cowman:
We are hiring a protein chemist/structural biologist. Please see below or click
on link below for other details.
https://www.wehi.edu.au/research-officer-cowman-laboratory
About the position
The postdoctoral scientist who fills this position will be an expe
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
> If I am not wrong, I remember that someone proposed to standardize
> B-factors of protein atoms as “BS = B - Bave”, where Bave is the average
> B-factor of the protein.
This will make some of BS negative (if B
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
Dear Oliviero,
On one aspect of your query, this analysis dissected the different sources
of disorder contributions to B factors:-
Diamond, R Acta Cryst (1990). *A46*, 425-435
All best wishes,
John
On Thu, Apr 5, 2018 at 2:49 PM, Oliviero Carugo <
oliviero.car...@univie.ac.at> wrote:
> Dears,
>
On Thursday, 05 April 2018 15:49:44 Oliviero Carugo wrote:
> Dears,
>
> everybody knows that B-factors may change amongst different crystal
> structures and that they need to be standardized when different protein
> crystal structures are compared.
>
> If I am not wrong, I remember that someone
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
Oliviero,
We published a paper in 2003 in which we normalized B-factors
to do a comparison of relative mobility or flexibility. The reference
is: Gourinath et al. Structure 11:1621-1627 (2003). The jargon
we used for Bave of the protein is . In our case, to be
conservative in our interpretatio
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
Dears,
everybody knows that B-factors may change amongst different crystal
structures and that they need to be standardized when different protein
crystal structures are compared.
If I am not wrong, I remember that someone proposed to standardize
B-factors of protein atoms as “BS = B - Bave”
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
16 matches
Mail list logo
