You can also calculate expected anomalous scattering signal <|Delta F|> / <F> at low resolution range for your structure for different wavelenghts using a webpage:
http://alfa.p.lodz.pl/assc/ The webpage is not in its final form and still under development, but should work OK. (abreviation "SOF" used on this webpage stands for "site occupancy factor"). You can then compare the calculated value of <|Delta F|> / <F> with the experimental one (which should be greater because of the experimental errors) to get some notion about how large the signal is in comparison to the experimental errors. Regards, Andrzej Olczak > Dear all > If you simply want to see if Ca and Mn are in your sample, you could > also use x-ray fluorescence excited by the x-rays on the beamline used > to collect the diffraction data. It doesn't need the energy set to be at > each absorption edge, it just has to be above the edges. One then sets > the fluorescence detector (used for wavelength setting in MAD > experiments) to MCA mode, giving a spectrum showing the characteristic > lines for each element present. > > I believe the PIXIE technique has certain advantages. However it is not > available on the beamlines used to collect the data. > > Of course, I think the question related to whether specific peaks in a > map were Mn or Ca. Then, as stated before, diffraction data collection > on either side of the Mn edge should reveal all, with good data of > sufficient resolution. > > The x-ray fluorescence technique was used at the SSRL to reveal details > of the Archimedes Palimsest. This showed there were in fact two geniuses > coming from Greece - not just Tassos. > > Cheers > Colin > > > > -----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 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 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 selected "Run FFT-Creat Map" in the "Map& Mask > >> Utilities". > > > > What labels did you assign, and did you select 'anomalous map'? > > This is crucial, as the protein (model) phase needs to be shifted by > > 90 degrees, and this is done 'automatically' by FFT when you ask for > > an anomalous map. Certainly with data of sufficient quality collected > > on a home source with Cu radiation anomalous maps may well show up > > such ions. > > Exactly! Thats the most important bit to get right. > > Another comment is that if you want to be sure about the nature of the > ions, you might want to try PIXE. > > http://www.ee.surrey.ac.uk/IBC/index.php?target=13:68 > > I think all other suggestions are of course valid, but, without being > sure, the X-ray suggestions I see, need high resolution data ? PIXE is a > more direct method if it works well for your sample. > > A. > > > I select "O format to cover asymmetric unit" and "Plot > > > >> section on Z axis from 0 to 1 in steps on 10". All others were by > >> default values. I display in ono10. > >> I collected the data at the wavelength of 1 A. Do I need to > >> adjust the wavelength to maximize the anomalous signal from Mn or Ca? > >> Any ideas and suggestions are greatly appreciated! > >> Sun Tang > >> --------------------------------------------------------------------- > >> > >> --- > >> Never miss a thing. Make Yahoo your homepage. <http:// > >> us.rd.yahoo.com/evt=51438/*http://www.yahoo.com/r/hs> > > > > -- > > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > Dr. Johan P. Turkenburg X-ray facilities manager > > York Structural Biology Laboratory > > University of York Phone (+) 44 1904 328251 > > York YO10 5DD UK Fax (+) 44 1904 328266 > > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > <DIV><FONT size="1" color="gray">This e-mail and any attachments may > contain confidential, copyright and or privileged material, and are for the > use of the intended addressee only. If you are not the intended addressee > or an authorised recipient of the addressee please notify us of receipt by > returning the e-mail and do not use, copy, retain, distribute or disclose > the information in or attached to the e-mail. Any opinions expressed within > this e-mail are those of the individual and not necessarily of Diamond > Light Source Ltd. 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