Re: [ccp4bb] How to evaluate Fourier transform ripples
I think it is important to remember here that although 2Fo-Fc maps can have "Fourier ripples" (AKA series termination errors) difference maps are "resistant" to them. This is because "leaving out" data in a map calculation is equivalent to setting the coefficient to zero, and for a difference map this is not such a bad guess, especially for high-angle data. However, difference maps are not "immune" to other kinds of errors, like Fc not quite capturing the "real" electron density. This can be particularly apparent around heavy atoms, since they are "taller" in electrons/A^3 than protein atoms, and so a ~10% percent error on a Zn atom amounts to 3 electrons, or half a carbon atom! One example of where such a "bump" could come from is if the distribution of Zn positions is not a perfect Gaussian. There is no way to exactly capture non-Gaussian shapes with a Gaussian atom model (B factor). So, the refinement programs does the best it can to line up the shapes, but then you see "ripples". However, these ripples have nothing to do with series-termination artifacts. Note that some call non-Gaussian atomic displacement distributions "anharmonic", but that word assumes the displacements are thermal in origin, and I don't think that's appropriate for cryo-cooled protein crystals. "non-Gaussian" is more general. -James Holton MAD Scientist On Wed, Jul 6, 2011 at 10:58 AM, Fischmann, Thierry wrote: > Dear Zbyszek > > Wouldn't ripples be the results of calculating maps with truncated > Fourier summations (unavoidably), and, consequently, be more obvious > around a sharp feature such as an heavy atom metal center? > > The mathematic basis can be found here: > http://en.wikipedia.org/wiki/Gibbs_phenomenon > > With best regards, > > Thierry > > Note: sent a 2nd time as it seems that it did not reach the BB the first > time. Apologies if the message reaches you twice. > > -Original Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Zbyszek Otwinowski > Sent: Wednesday, July 06, 2011 1:19 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] How to evaluate Fourier transform ripples > > The question about Fourier transformation ripples has a straightforward > answer in a fairly typical situation: > A) data are collected to the resolution limit of diffraction, > B) phases are uniform in quality across the resolution range, which is > equivalent to R-free being uniform with respect to resolution within a > factor of 2 or so, > C) maps are not sharpened. > > The ripples originate from not including unobserved structure factors. > The > intensity of diffraction decreases rapidly past the measurability limit, > so, in the above situation, the unobserved diffraction contributes very > little. Consequently, the answer is that typically one should not see > ripples. > Ripples should not be confused with the effect of electron density maps > being smoothed by vibrations and other forms of disorder. > > Zbyszek Otwinowski > >> >> Dear All, Hi. I was asked in a manuscript revision to discuss >> about the possible effects of Fourier transformation ripples on the >> crystallographic results. Specifically, the reviewers question whether >> ripples may affect on the electron density around heavy metal center > which >> has a Mo-S-As connection. From which angle or in which way this > problem >> should be addressed most convincingly ? Thank you for any >> suggestion.Best,Conan > > > Zbyszek Otwinowski > UT Southwestern Medical Center at Dallas > 5323 Harry Hines Blvd. > Dallas, TX 75390-8816 > Tel. 214-645-6385 > Fax. 214-645-6353 > Notice: This e-mail message, together with any attachments, contains > information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, > New Jersey, USA 08889), and/or its affiliates Direct contact information > for affiliates is available at > http://www.merck.com/contact/contacts.html) that may be confidential, > proprietary copyrighted and/or legally privileged. It is intended solely > for the use of the individual or entity named on this message. If you are > not the intended recipient, and have received this message in error, > please notify us immediately by reply e-mail and then delete it from > your system. >
Re: [ccp4bb] How to evaluate Fourier transform ripples
Dear All, Thank you so much for the help and suggestions on the issue of Fourier Transform Ripples. They are really helpful. Best,ConanUniversity of California, Riverside
Re: [ccp4bb] How to evaluate Fourier transform ripples
There is a relatively instructive figure to what Colin describes available from the gallery: http://www.ruppweb.org/garland/gallery/Ch9/pages/Biomolecular_Crystallography_Fig_9-05_PART1.htm For B=10, at 2.5 cutoff, ripples expected; for B=100 and 2.5 A, no ripples expected. One can also generate what Colin says using the FT calculator on my web site: Calculate first SFs with a Metal and a C and low B-factors, but cut the resolution at 2.5 or so. http://www.ruppweb.org/cgi-bin/webfac.exe?cell=20&anode=Cu&resolution=2.5&E1=C&x1=0.1&N1=1.0&B1=5.0&E2=FE&x2=0.7&N2=1.0&B2=5.0&A1=No&OUTFILE=webfac.phs&anoweb=GoGoGo ! Then generate the FT on a fine grid (for esthetics, not information conservation - see Shannon) and observe the big ripples. http://www.ruppweb.org/cgi-bin/webmap.exe?grid=100&resolution=2.5&INFILE=webfac.phs&anoweb=GoGoGo ! (you need to select unique file names or the webserver will overwrite simultaneous submissions) An extreme case of ripples is in the Uranium atom figure. They look similar but not as excessive around real heavy atoms or even Se. http://www.ruppweb.org/garland/gallery/Ch10/pages/Biomolecular_Crystallography_Fig_10-10.htm BR On Thu, Jul 7, 2011 at 2:17 AM, Colin Nave wrote: > Dear Thierry (and others) > > Perhaps a bit confusing to say "a sharp feature such as an heavy atom". > Heavy atoms are, well, heavy (lots of electrons) rather than sharp. Any > ripples around them in a Fourier truncated map could swamp the lighter atoms > nearby. > > If Zbyszek's criteria A (and his other criteria apply), there will be no > sharp cut off in the data and no significant ripples. If the data had a > sharp cut off like a box function (an extreme case), each atom would have > ripples around it like a sinc (sin(x)/x) function. > > This is (or at least used to be) a problem in small molecule > crystallography if the data did not gradually fade to zero at the resolution > of the calculation. > > I am sure this is just rewording what you are saying! > Regards > Colin > > PS Following Nicholas's suggestion, it would be interesting to compare > maximum entropy and Fourier maps particularly at different resolution cut > offs. > > > > > -Original Message- > > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > > Fischmann, Thierry > > Sent: 06 July 2011 18:59 > > To: CCP4BB@JISCMAIL.AC.UK > > Subject: Re: [ccp4bb] How to evaluate Fourier transform ripples > > > > Dear Zbyszek > > > > Wouldn't ripples be the results of calculating maps with truncated > > Fourier summations (unavoidably), and, consequently, be more obvious > > around a sharp feature such as an heavy atom metal center? > > > > The mathematic basis can be found here: > > http://en.wikipedia.org/wiki/Gibbs_phenomenon > > > > With best regards, > > > > Thierry > > > > Note: sent a 2nd time as it seems that it did not reach the BB the > > first > > time. Apologies if the message reaches you twice. > > > > -Original Message- > > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > > Zbyszek Otwinowski > > Sent: Wednesday, July 06, 2011 1:19 PM > > To: CCP4BB@JISCMAIL.AC.UK > > Subject: Re: [ccp4bb] How to evaluate Fourier transform ripples > > > > The question about Fourier transformation ripples has a straightforward > > answer in a fairly typical situation: > > A) data are collected to the resolution limit of diffraction, > > B) phases are uniform in quality across the resolution range, which is > > equivalent to R-free being uniform with respect to resolution within a > > factor of 2 or so, > > C) maps are not sharpened. > > > > The ripples originate from not including unobserved structure factors. > > The > > intensity of diffraction decreases rapidly past the measurability > > limit, > > so, in the above situation, the unobserved diffraction contributes very > > little. Consequently, the answer is that typically one should not see > > ripples. > > Ripples should not be confused with the effect of electron density maps > > being smoothed by vibrations and other forms of disorder. > > > > Zbyszek Otwinowski > > > > > > > > Dear All, Hi. I was asked in a manuscript revision to discuss > > > about the possible effects of Fourier transformation ripples on the > > > crystallographic results. Specifically, the reviewers question > > whether > > > ripples may affect on the electron density around heavy metal center > > which > > > has a Mo-S-As c
Re: [ccp4bb] How to evaluate Fourier transform ripples
Dear Thierry (and others) Perhaps a bit confusing to say "a sharp feature such as an heavy atom". Heavy atoms are, well, heavy (lots of electrons) rather than sharp. Any ripples around them in a Fourier truncated map could swamp the lighter atoms nearby. If Zbyszek's criteria A (and his other criteria apply), there will be no sharp cut off in the data and no significant ripples. If the data had a sharp cut off like a box function (an extreme case), each atom would have ripples around it like a sinc (sin(x)/x) function. This is (or at least used to be) a problem in small molecule crystallography if the data did not gradually fade to zero at the resolution of the calculation. I am sure this is just rewording what you are saying! Regards Colin PS Following Nicholas's suggestion, it would be interesting to compare maximum entropy and Fourier maps particularly at different resolution cut offs. > -Original Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Fischmann, Thierry > Sent: 06 July 2011 18:59 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] How to evaluate Fourier transform ripples > > Dear Zbyszek > > Wouldn't ripples be the results of calculating maps with truncated > Fourier summations (unavoidably), and, consequently, be more obvious > around a sharp feature such as an heavy atom metal center? > > The mathematic basis can be found here: > http://en.wikipedia.org/wiki/Gibbs_phenomenon > > With best regards, > > Thierry > > Note: sent a 2nd time as it seems that it did not reach the BB the > first > time. Apologies if the message reaches you twice. > > -Original Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Zbyszek Otwinowski > Sent: Wednesday, July 06, 2011 1:19 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] How to evaluate Fourier transform ripples > > The question about Fourier transformation ripples has a straightforward > answer in a fairly typical situation: > A) data are collected to the resolution limit of diffraction, > B) phases are uniform in quality across the resolution range, which is > equivalent to R-free being uniform with respect to resolution within a > factor of 2 or so, > C) maps are not sharpened. > > The ripples originate from not including unobserved structure factors. > The > intensity of diffraction decreases rapidly past the measurability > limit, > so, in the above situation, the unobserved diffraction contributes very > little. Consequently, the answer is that typically one should not see > ripples. > Ripples should not be confused with the effect of electron density maps > being smoothed by vibrations and other forms of disorder. > > Zbyszek Otwinowski > > > > > Dear All, Hi. I was asked in a manuscript revision to discuss > > about the possible effects of Fourier transformation ripples on the > > crystallographic results. Specifically, the reviewers question > whether > > ripples may affect on the electron density around heavy metal center > which > > has a Mo-S-As connection. From which angle or in which way this > problem > > should be addressed most convincingly ? Thank you for any > > suggestion.Best,Conan > > > Zbyszek Otwinowski > UT Southwestern Medical Center at Dallas > 5323 Harry Hines Blvd. > Dallas, TX 75390-8816 > Tel. 214-645-6385 > Fax. 214-645-6353 > Notice: This e-mail message, together with any attachments, contains > information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, > New Jersey, USA 08889), and/or its affiliates Direct contact > information > for affiliates is available at > http://www.merck.com/contact/contacts.html) that may be confidential, > proprietary copyrighted and/or legally privileged. It is intended > solely > for the use of the individual or entity named on this message. If you > are > not the intended recipient, and have received this message in error, > please notify us immediately by reply e-mail and then delete it from > your system.
Re: [ccp4bb] How to evaluate Fourier transform ripples
Hi Conan, > Specifically, the reviewers question whether ripples may affect on the > electron density around heavy metal center which has a Mo-S-As > connection. From which angle or in which way this problem should be > addressed most convincingly ? The maximum entropy estimate of the map should be insensitive to series termination errors, and would thus answer the referee's concerns. You could give it a try with the program 'graphent' which can read mtz files and produce ccp4 map files. Whether the referee considers maximum entropy methods 'convincing' remains to be seen ... ;-) My twocents, Nicholas -- Dr Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620, Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/
Re: [ccp4bb] How to evaluate Fourier transform ripples
Dear Zbyszek Wouldn't ripples be the results of calculating maps with truncated Fourier summations (unavoidably), and, consequently, be more obvious around a sharp feature such as an heavy atom metal center? The mathematic basis can be found here: http://en.wikipedia.org/wiki/Gibbs_phenomenon With best regards, Thierry Note: sent a 2nd time as it seems that it did not reach the BB the first time. Apologies if the message reaches you twice. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Zbyszek Otwinowski Sent: Wednesday, July 06, 2011 1:19 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] How to evaluate Fourier transform ripples The question about Fourier transformation ripples has a straightforward answer in a fairly typical situation: A) data are collected to the resolution limit of diffraction, B) phases are uniform in quality across the resolution range, which is equivalent to R-free being uniform with respect to resolution within a factor of 2 or so, C) maps are not sharpened. The ripples originate from not including unobserved structure factors. The intensity of diffraction decreases rapidly past the measurability limit, so, in the above situation, the unobserved diffraction contributes very little. Consequently, the answer is that typically one should not see ripples. Ripples should not be confused with the effect of electron density maps being smoothed by vibrations and other forms of disorder. Zbyszek Otwinowski > > Dear All, Hi. I was asked in a manuscript revision to discuss > about the possible effects of Fourier transformation ripples on the > crystallographic results. Specifically, the reviewers question whether > ripples may affect on the electron density around heavy metal center which > has a Mo-S-As connection. From which angle or in which way this problem > should be addressed most convincingly ? Thank you for any > suggestion.Best,Conan Zbyszek Otwinowski UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas, TX 75390-8816 Tel. 214-645-6385 Fax. 214-645-6353 Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
Re: [ccp4bb] How to evaluate Fourier transform ripples
The question about Fourier transformation ripples has a straightforward answer in a fairly typical situation: A) data are collected to the resolution limit of diffraction, B) phases are uniform in quality across the resolution range, which is equivalent to R-free being uniform with respect to resolution within a factor of 2 or so, C) maps are not sharpened. The ripples originate from not including unobserved structure factors. The intensity of diffraction decreases rapidly past the measurability limit, so, in the above situation, the unobserved diffraction contributes very little. Consequently, the answer is that typically one should not see ripples. Ripples should not be confused with the effect of electron density maps being smoothed by vibrations and other forms of disorder. Zbyszek Otwinowski > > Dear All, Hi. I was asked in a manuscript revision to discuss > about the possible effects of Fourier transformation ripples on the > crystallographic results. Specifically, the reviewers question whether > ripples may affect on the electron density around heavy metal center which > has a Mo-S-As connection. From which angle or in which way this problem > should be addressed most convincingly ? Thank you for any > suggestion.Best,Conan Zbyszek Otwinowski UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas, TX 75390-8816 Tel. 214-645-6385 Fax. 214-645-6353
Re: [ccp4bb] How to evaluate Fourier transform ripples
I would be very careful about any bond to As. I would imagine such bonds would be very susceptible to radiolysis with typical radiation used in the diffraction data collection. Have you performed some diffraction experiments of various time lengths (or flux) and seen what happens around this region of the electron density map? Jim On Wed, 6 Jul 2011, conan wrote: Dear All, Hi. I was asked in a manuscript revision to discuss about the possible effects of Fourier transformation ripples on the crystallographic results. Specifically, the reviewers question whether ripples may affect on the electron density around heavy metal center which has a Mo-S-As connection. From which angle or in which way this problem should be addressed most convincingly ? Thank you for any suggestion. Best, Conan
Re: [ccp4bb] How to evaluate Fourier transform ripples
I note that all three of those atoms should have anomalous scattering and should show up as peaks in anomalous Fourier maps if you collected data carefully enough at multiple wavelengths. The As K edge is 1.04 A, which is easily within reach of most MAD synchrotron beamlines. The Mo peaks are out of range, but you should still see a peak, and could differentiate it from other metals by other methods, such as AAS. On 07/06/11 05:15, conan仙人指路 wrote: > Dear All, > > Hi. I was asked in a manuscript revision to discuss about the possible > effects of Fourier transformation ripples on the crystallographic > results. Specifically, the reviewers question whether ripples may > affect on the electron density around heavy metal center which has a > Mo-S-As connection. From which angle or in which way this problem > should be addressed most convincingly ? > > Thank you for any suggestion. > > Best, > Conan -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
[ccp4bb] How to evaluate Fourier transform ripples
Dear All, Hi. I was asked in a manuscript revision to discuss about the possible effects of Fourier transformation ripples on the crystallographic results. Specifically, the reviewers question whether ripples may affect on the electron density around heavy metal center which has a Mo-S-As connection. From which angle or in which way this problem should be addressed most convincingly ? Thank you for any suggestion.Best,Conan
