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Thanks all you guys for replying. The problem in my case is the f prime value. I changed it to -10 and all the negative density are gone. The thing that still puzzles me is that I got negative density with the default value when I was using remote dataset, which is supposed to be native like. Well, I guess I can still say the default value is also off from the remote dataset. Zhen Quoting "Stein, ND (Norman)" <[EMAIL PROTECTED]>: > *** For details on how to be removed from this list visit the > *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > Hi Ian, > > Based on the original posting, the density showed up in a 2fo-fc > map, > the selenium atoms themselves fit the density well, and the > strong > negative density was found "arround" the selenium. Sounds like > truncation effects to me. > In an Fo-Fc map with proper scaling the effect will indeed > disappear. > Not necessarily because the truncation effects on Fobs and Fcalc > kancel > eachother out (I expect the truncation effect will still exist on > the > Fo-Fc terms unless the model is near perfect) but because > truncation > effects appear around the strongest density features in the map, > and the > selenium peaks will have disappeared in an Fo-Fc map. > > Bart > > Stein, ND (Norman) wrote: > > *** For details on how to be removed from this list visit the > *** > > *** CCP4 home page http://www.ccp4.ac.uk *** > > > > > > Message posted on behalf of Ian Tickle > > > > -----Original Message----- > > From: Ian Tickle > > Sent: Thursday, September 28, 2006 4:22 PM > > To: '[email protected]' > > 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. > > > > > > > > > > > > > > > -- > > ============================================================================== > > 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 > > ============================================================================== > >
