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Message posted on behalf of Ian Tickle -----Original Message----- From: Ian Tickle Sent: Thursday, September 28, 2006 4:22 PM To: 'ccp4bb@dl.ac.uk' Subject: [ccp4bb]: Negative density arround Selenium There are several possible explanations of negative difference density at 'heavy' atom positions (e.g. partial incorporation/occupancy, radiation damage, over-tight B-factor restraints, lack of f' correction, errors in FFT approximation of density etc.), however I don't think series termination error is one of them. The reason is that the summations of both Fobs & Fcalc will suffer from the same series termination error and will effectively cancl in the wFo-DFc map. Looked at another way, series termination _does_ explain why the Se peak height in a Fobs map is always less than you would expect from a calculation of the theoretical electron density of a Se atom (e.g. using an infinite Fourier integral of the scattering factor curve), but it doesn't explain why it should be less than the calculated electron density from a series truncated at the same resolution. Of course theory has been proved wrong before and someone may well come up with some results showing that when atomic resolution data is used the effect disappears, assuming all else is unchanged, i.e. you haven't also corrected for occupancy, B-factor, f' etc. Has anyone actually done this? -- Ian > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On > Behalf Of Bart Hazes > Sent: Tuesday, September 26, 2006 7:23 PM > To: [EMAIL PROTECTED] > Cc: [EMAIL PROTECTED] > Subject: Re: [ccp4bb]: Negative density arround Selenium > > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > Hi Zhen, > > Does your crystal diffract to better than 1.7A, in other > words is I/SigI > still considerably larger than 2 in your highest resolution > shell. If so > then you are most likely looking at Fourier truncation effects. > Basically, many Fourier terms try to come together to build a peak at > your selenium positions, but since the Fourier terms are > cosine waves, > when many cosine maxima come together many cosine minima will > be nearby > causing an artificial dip in the electron density, especially near > strong scatterers like your selenium. It's not a real problem and to > solve it the best thing is to collect a proper native data set that > includes all the weak high resolution data. > > Bart > > [EMAIL PROTECTED] wrote: > > *** For details on how to be removed from this list visit the *** > > *** CCP4 home page http://www.ccp4.ac.uk *** > > > > > > Deal all, > > > > I recently solved a structure at 1.7A by MAD. However, there is > > always strong negative density arround all 8 selenium in the > > protein during CNS refinement. The Selenium-methionines fit 2fo-fc > > density well. I tried to use peak, edge or remote dataset with or > > without scale anomalous flag on and all did not matter. Does > > anybody have a solution for this matter? > > > > Thanks. > > > > Zhen > > > > > > > -- > > ============================================================== > ================ > > Bart Hazes (Assistant Professor) > Dept. of Medical Microbiology & Immunology > University of Alberta > 1-15 Medical Sciences Building > Edmonton, Alberta > Canada, T6G 2H7 > phone: 1-780-492-0042 > fax: 1-780-492-7521 > > ============================================================== > ================ > > Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof.
