[ccp4bb] Postdoctoral researcher position at The Walter & Eliza Hall Institute

2018-04-05 Thread Richard Birkinshaw
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

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

2018-04-05 Thread James Holton
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

Re: [ccp4bb] B-factor standardization

2018-04-05 Thread Pavel Afonine
> 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

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

2018-04-05 Thread Pavel Afonine
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

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

2018-04-05 Thread Pearce, N.M. (Nick)
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.

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

2018-04-05 Thread James Holton
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] B-factor standardization

2018-04-05 Thread John R Helliwell
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, >

Re: [ccp4bb] B-factor standardization

2018-04-05 Thread Ethan Merritt
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

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

2018-04-05 Thread Kay Diederichs
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] B-factor standardization

2018-04-05 Thread Daniel M. Himmel, Ph. D.
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

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

2018-04-05 Thread Ian Clifton
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

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

2018-04-05 Thread Ian Clifton
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

[ccp4bb] B-factor standardization

2018-04-05 Thread Oliviero Carugo
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”

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

2018-04-05 Thread Frank von Delft
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

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

2018-04-05 Thread Eleanor Dodson
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

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

2018-04-05 Thread Frank von Delft
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