Re: [ccp4bb] Anomalous signal to noise details

Hi all, Thanks for the useful advice. Clemens, I was indeed reminded of the vs / discussion when I started this thread. The reason I brought it up here is because the ratio-of-means form is the way it is described in "Estimation of anomalous signal in diffraction data

Re: [ccp4bb] Anomalous signal to noise details

Dear David, Although this is not exactly a topic of your question, an alternative approach is to use the resolution screening and compare the results. I have implemented this approach to my program SHELIXIR (because it uses SHELX C/D/E), which can be found here:

Re: [ccp4bb] Anomalous signal to noise details

Conventionally (e.g. in cryo-EM) the SNR is taken as a ratio of averages, either the ratio of the variance of the signal (average of signal squared) to the variance of the noise, i.e. var(signal) / var(noise), or the square root of that, i.e. sd(signal) / sd(noise). See here:

Re: [ccp4bb] Anomalous signal to noise details

Hi, I am not sure about the 1.2-1.3 limit, but 0.8 probably comes from sqrt(2/pi), which is the ratio of the mean of a half-normal and its sigma when the mean parameter is 0. Best wishes, Gergely From: CCP4 bulletin board On Behalf Of David Waterman Sent: 18 December, 2020 12:53 To:

Re: [ccp4bb] Anomalous signal to noise details

> I don't know the justification; maybe just experience? Surely the higher the > better. I've seen George Sheldrick deriving the value of ~0.8 when there is > _no_ anom signal but I forgot the details, sorry ... It is derived from the mean absolute error (cf. p414 in Chapter 8 of BMC, with

Re: [ccp4bb] Anomalous signal to noise details

Hi David, On Fri, 18 Dec 2020 11:53:08 +, David Waterman wrote: >Hi folks > >The paper "Substructure solution with SHELXD >" >(Schneider & Sheldrick, 2002) describes how > >data can be truncated at the resolution at which [ΔF

Re: [ccp4bb] Anomalous signal to noise details

Dear David, On Fri, Dec 18, 2020 at 11:53:08AM +, David Waterman wrote: > The paper "Substructure solution with SHELXD > " > (Schneider & Sheldrick, 2002) describes how > > data can be truncated at the resolution at which [ΔF

Re: [ccp4bb] anomalous signal

Dear Faisal, you could use Phenix to do an f’’ refinement against the data like described here: Liu, Q., Liu, Q. Hendrickson, W. A. (2013). Acta Cryst. D69, 1314-1332. best regards, Tobias On 30 Apr 2014, at 14:01, Faisal Tarique faisaltari...@gmail.com wrote: Dear all I am working

Re: [ccp4bb] anomalous signal

Well - this is pretty common, and really doesnt matter. I just let SHELXC/D give an occupancy to its anom scatterer solutions and assume that the stronger one is Ca. But in fact it wont matter at all for the phasing, and IF the experiment works it is easy to sort out S from Ca in the final map.

Re: [ccp4bb] anomalous signal

I myself have never seen a separate peak that was a single sulfur atom. I've seen, in a moderately-radiation-damaged dataset, little shards of anomalous scattering density in Phaser-generated LLG maps. They were in the interior of the protein, and the closest possible atoms were sulfurs. They

Re: [ccp4bb] anomalous signal

Look at the aimless plot of CCanom . That is the best indicator I think and very sensitive when you have such high redundancy Eleanor On 25 Apr 2014, at 22:13, Jim Pflugrath wrote: d/sig should be above 0.80 There seems to be plenty of signal there with all values above 1.02. We have

Re: [ccp4bb] anomalous signal

Dear Faisal, the lack of the CCanom line in the shelxc output suggests that your data are already merged, and my guess is you processed your data with HKL2000 - all other integration programs I am aware of do not merge the data at such an early stage giving you access to the CCanom Eleanor

Re: [ccp4bb] anomalous signal

Was there a reason that you turned off the scaling in Aimless (onlymerge)? If the data have come from Mosflm, this is definitely wrong - the result is that (among other things) you have negative CCanom values which is unusual to say the least Just run it with the default options, that's

Re: [ccp4bb] anomalous signal

d/sig should be above 0.80 There seems to be plenty of signal there with all values above 1.02. We have solved structures with less multiplicity and lower d/sig. There is a different criteria of signal for when you know the positions of the anomalous substructure atoms and when you need to

Re: [ccp4bb] anomalous signal for Mg and Calcium

On Mon, Apr 21, 2014 at 3:36 PM, Faisal Tarique faisaltari...@gmail.comwrote: Just in the continuation of my previous mail i again want to ask few question on the metalloprotiens..Apart from factors like occupancy, B factor, coordination sphere and metal ion-ligand distances to distinguish Mg

Re: [ccp4bb] anomalous signal for Mg and Calcium

Further to what Nat wrote which I completely agree with, you should tell us the following: 1. Expecting signal of a Calcium atom and expected signal of a Magnesium atom. 2. Are there any intrinsic anomalous scatterers in the structure that you trust such as sulfurs from methionines and

Re: [ccp4bb] Anomalous signal for chlorides

There are many ways of course to do this.. But if you are using the CCP4 GUI, refmac refinement it is a 2 step process. CAD to add the DANO SIGDANO columns from the input data back into the refmac output fft Select anomalous map Use DANO SIGDANO PHIC FOM asinput Switch on the peak search

Re: [ccp4bb] Anomalous signal for chlorides

Dear Yuri, The new program ANODE (J.Appl.Cryst. (2011) 44, 1285-7, Open Access) is designed for this and is very simple to use. It may be downloaded from the SHELX beta-test server (please email me if you require downloading intructions). George On 11/26/2011 06:05 AM, Yuri Pompeu wrote:

Re: [ccp4bb] Anomalous signal for chlorides

Dear Yuri, In addition to the other good options that have been presented, you can use the log-likelihood gradient maps in Phaser to find anomalous scatterers. We find this to be very sensitive, and it has the advantage of being iterative (i.e. when you find some anomalous scatterers, this

Re: [ccp4bb] Anomalous signal for chlorides

Not that Phaser needs my approval, but I recently did exactly what Randy recommended and it really found basically all of the S and Cl sites, with data at resolution 2.2 Ang and wavelength 0.979 Ang, too. I also played a bit with the sigma cutoff for adding new sites so that the stronger sites (Se

Re: [ccp4bb] Anomalous signal for chlorides

Hi, You could calculate an anomalous difference map using your current phases and see whether you see any peaks around the atoms you suspect are Cl, S or P (although the latter should have a clear tetrahedral geometry, certainly at your resolution). It all depends of course on the wavelength

Re: [ccp4bb] Anomalous signal for chlorides

Hi Boaz, Yes indeed, the phosphate group of the molecule looks quite beautiful at 1.17A and it has a really big peak 18sigma! Is there a utility for calculating anomalous maps, or is it simply an option in the refinement program?

Re: [ccp4bb] anomalous signal of Mn and Ca ions

: Re: [ccp4bb] anomalous signal of Mn and Ca ions On Feb 29, 2008, at 10:29, Johan Turkenburg wrote: Hi, You need to firstly check that you did the map calculation correctly, see comments below: Sun Tang wrote: Dear All, In my structures, I want to assign Mn or Ca ions for some densities

Re: [ccp4bb] anomalous signal of Mn and Ca ions

February 2008 10:06 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] anomalous signal of Mn and Ca ions On Feb 29, 2008, at 10:29, Johan Turkenburg wrote: Hi, You need to firstly check that you did the map calculation correctly, see comments below: Sun Tang wrote: Dear All, In my

Re: [ccp4bb] anomalous signal of Mn and Ca ions

As Ethan mentions, your best bet for an 100% positive ID would be to collect a dataset above and below the Mn edge and see the anomalous signal from the Mn atom disappear. If that is not an option, there is a great paper by George Sheldrick and friends regards using the Calcium Bond Valence Sum

Re: [ccp4bb] anomalous signal of Mn and Ca ions

Hi, You need to firstly check that you did the map calculation correctly, see comments below: Sun Tang wrote: Dear All, In my structures, I want to assign Mn or Ca ions for some densities. But when I did not have anomalous density in CCP4i. I am not sure whether I was correct. The

Re: [ccp4bb] anomalous signal of Mn and Ca ions

On Feb 29, 2008, at 10:29, Johan Turkenburg wrote: Hi, You need to firstly check that you did the map calculation correctly, see comments below: Sun Tang wrote: Dear All, In my structures, I want to assign Mn or Ca ions for some densities. But when I did not have anomalous density in

Re: [ccp4bb] anomalous signal of Mn and Ca ions

On Thursday 28 February 2008 19:54, Sun Tang wrote: Dear All, In my structures, I want to assign Mn or Ca ions for some densities. But when I did not have anomalous density in CCP4i. [snip] I collected the data at the wavelength of 1 A. Mn has only about 1e of anomalous

Re: [ccp4bb] anomalous signal

Hi In the same way the Toyota MRD-2 doesn't sell in France? MRD would indeed be a poor name. For French scientists it might be difficult to get funding for an MRD experiment Regards Yves -- Prof. Yves Muller