Re: [ccp4bb] Anomalous signal to noise details

d solvent > content screening, etc. ;-) Feel free to ask for more. > > Best regards, > > Petr > > > > PS: Although tested on a number of cases, the command line is more stable > than the GUI. > > > > *From:* CCP4 bulletin board *On Behalf Of *David > Wat

Re: [ccp4bb] Anomalous signal to noise details

command line is more stable than the GUI. From: CCP4 bulletin board On Behalf Of David Waterman Sent: Friday, December 18, 2020 12:53 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Anomalous signal to noise details Hi folks The paper "Substructure solution with SHELXD<https://journals.iu

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: https://en.wikipedia.

Re: [ccp4bb] Anomalous signal to noise details

@JISCMAIL.AC.UK Subject: [ccp4bb] Anomalous signal to noise details Hi folks The paper "Substructure solution with SHELXD<https://journals.iucr.org/d/issues/2002/10/02/gr2280/index.html>" (Schneider & Sheldrick, 2002) describes how data can be truncated at the resolution

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 hel

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 t

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 to

[ccp4bb] Anomalous signal to noise details

Hi folks The paper "Substructure solution with SHELXD " (Schneider & Sheldrick, 2002) describes how data can be truncated at the resolution at which [ΔF to its estimated > standard deviation as a function of the resolution] drops to

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 w

Re: [ccp4bb] anomalous signal

; > From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Faisal Tarique > [faisaltari...@gmail.com] > Sent: Wednesday, April 30, 2014 7:01 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] anomalous signal > > Dear all > > I am working on a metalloprotein whi

Re: [ccp4bb] anomalous signal

AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] anomalous signal Dear all I am working on a metalloprotein which probably contains Ca at its active site..The sulfur containing amino acid constitutes almost 5.4% of the total amino acid residues of this protein..I have collected the data at home

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

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 wrote: > Dear all > > I am working on a metalloprotein w

[ccp4bb] anomalous signal

Dear all I am working on a metalloprotein which probably contains Ca at its active site..The sulfur containing amino acid constitutes almost 5.4% of the total amino acid residues of this protein..I have collected the data at home source (CuKalpha=1.54A)..Since f'' of Sulfur is 0.56 and that of Ca

Re: [ccp4bb] anomalous signal

the > >> positions of the anomalous substructure atoms. > >> > >> As for "no signal", I think I am on record that there is always an > >> anomalous signal. :) But can you detect it? > >> > >> Jim > >> > >> From

Re: [ccp4bb] anomalous signal

think I am on record that there is always an anomalous >> signal. :) But can you detect it? >> >> Jim >> >> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Faisal >> Tarique [faisaltari...@gmail.com] >> Sent: Friday, April 25, 2014 4:06 PM >&

Re: [ccp4bb] anomalous signal

"no signal", I think I am on record that there is always an anomalous > signal. :) But can you detect it? > > Jim > > From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Faisal Tarique > [faisaltari...@gmail.com] > Sent: Friday, April 25, 2014 4

Re: [ccp4bb] anomalous signal

Tarique [faisaltari...@gmail.com] Sent: Friday, April 25, 2014 4:06 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] anomalous signal Dear all sorry about my previous mail where i forgot to mention that the data was collected on home source at Cuk alpha and at 1.54A. written below is the log file

[ccp4bb] anomalous signal

Dear all sorry about my previous mail where i forgot to mention that the data was collected on home source at Cuk alpha and at 1.54A. written below is the log file of an anomalous data processed through SHELXC..my question is ..what is the strength of anomalous signal ?? as it is said "For zero s

[ccp4bb] anomalous signal

Dear all written below is the log file of an anomalous data processed through SHELXC..my question is ..what is the strength of anomalous signal ?? as it is said "For zero signal and should be about 0.80". Then in the present case is there really a signal or can be assumed no signal..we are expec

Re: [ccp4bb] anomalous signal for Mg and Calcium

@JISCMAIL.AC.UK] on behalf of Faisal Tarique [faisaltari...@gmail.com] Sent: Monday, April 21, 2014 5:36 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] anomalous signal for Mg and Calcium Dear all Just in the continuation ...

Re: [ccp4bb] anomalous signal for Mg and Calcium

On Mon, Apr 21, 2014 at 3:36 PM, Faisal Tarique wrote: > 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 or calcium, can ano

[ccp4bb] anomalous signal for Mg and Calcium

Dear all 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 or calcium, can anomalous signal tell the identity and the type of metal

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 R

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

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 imp

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: H

Re: [ccp4bb] Anomalous signal for chlorides

Hi Yuri, On Fri, Nov 25, 2011 at 9:05 PM, Yuri Pompeu wrote: > > Is there a utility for calculating anomalous maps, or is it simply an > option in the refinement program? > phenix.refine, for example, always outputs Fourier map coefficients for anomalous difference map if input input data contai

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 for chlorides

cp4bb] Anomalous signal for chlorides Hello everyone, I have a good data set to 1.17A that I solved by MR. I come accross some sites that appear to be chlorides. I was wondering if they could have some anomalous signal. I also have a well ordered phosphate and a couple of S from Met´s. How do I go

[ccp4bb] Anomalous signal for chlorides

Hello everyone, I have a good data set to 1.17A that I solved by MR. I come accross some sites that appear to be chlorides. I was wondering if they could have some anomalous signal. I also have a well ordered phosphate and a couple of S from Met´s. How do I go about probing the signal from these?

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

olin > > > > -Original Message- > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of > Anastassis Perrakis > Sent: 29 February 2008 10:06 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] anomalous signal of Mn and Ca ions > > On Feb 29, 2008, at

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

bject: 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 wa

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 C

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 follow

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 to

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

[ccp4bb] anomalous signal of Mn and Ca ions

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 following was what I did: I processed the data with HKL2000 and select anomalous signal in scaling. In CCP4i, I

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 P

[ccp4bb] anomalous signal

ps perhaps "anomalous" is better than "resonant," as it produces "MAD" and "SAD" and not "MRD" and "SRD"... MRD would indeed be a poor name. For French scientists it might be difficult to get funding for an MRD experiment Regards Yves --