Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
I think there is a misconception floating around that processing your data with anomalous turned on will somehow degrade the quality of normal intensity data. I can think of very few circumstances when I would NOT want anomalous data, yet for many data processing pipelines, it is the default not to give you the I+ and I- separately. Anomalous data are very useful for locating metal ions that you might not even have suspected to exist in your structure. Can I make a plea that all data processing packages/pipelines give you anomalous data by default? Can anyone think of a good reason why they shouldn't? James -- Dr. James W. Murray David Phillips Research Fellow Division of Molecular Biosciences Imperial College, LONDON Tel: +44 (0)20 759 48895 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of James Holton [jmhol...@lbl.gov] Sent: Wednesday, June 13, 2012 3:47 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique? I think there is a misconception floating around that processing your data with anomalous turned on will somehow degrade the quality of normal intensity data. I'm not exactly sure where this rumor comes from, but I imagine it has something to do with confusion about all the various anomalous options different scaling programs have. For example, some programs offer the option to treat all I+ and all I- as completely separate data sets, scaled and merged independently. I think this is called scale anomalous in SCALEPACK and intensities anomalous in SCALA. Neither of these is the default because such treatment is only helpful if the anomalous signal is absolutely huge (I have only seen this once). So, I imagine people who have never done experimental phasing (there are lots of them!) might read things like Switching ANOMALOUS ON does affect the statistics and the outlier rejection in the SCALA manual and decide that they had better turn off all those evil anomalous things. Then they tell their students to do the same, etc. -James Holton MAD Scientist On Tue, Jun 12, 2012 at 3:17 AM, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Why would anyone ignore the anomalous data they had collected? It will always help the phasing, and decide the hand for you.. Eleanor On 6 Jun 2012, at 03:55, Stefan Gajewski wrote: Hey! I was just wondering, do you know of any recent (~10y) publication that presented a structure solution solely based on MIR? Without the use of any anomalous signal of some sort? When was the last time you saw a structure that was solved without the use of anomalous signal or homology model? Is there a way to look up the answer (e.g. filter settings in the RCSB) I am not aware of? Thanks, S. (Disclaimer: I am aware that isomorpous data is a valuable source of information)
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
Just to be clear, the CCP4 data processing programs (SCALA and its replacement AIMLESS) always give you I+ and I- in the output. The only difference between anomalous on off is in the outlier rejection, since if you have a large anomalous signal you don't want to reject as outliers reflections with a good strong anomalous difference. AIMLESS now automatically detects whether there is a substantial anomalous signal and switches this option ON if there is (unless you specify the option explicitly). There are also different Rmeas etc values within I+/I- sets and over all data. In the scaling, as James points out, it is nearly always best to ignore the I+/I- distinction, unless you really have a huge anomalous signal (almost impossible for macromolecules), since you want to try to minimise anomalous differences to reduce systematic errors, so that what is left is more likely to be real signal. SCALA allows you the (unrecommended) option to separate I+ and I- in scaling, but I haven't programmed this in AIMLESS since I have never seen a case where it would be a good idea. As far as I know, in CCP4 you only lose I+ and I- if you explicitly remove them. Phil On 13 Jun 2012, at 08:03, Murray, James W wrote: I think there is a misconception floating around that processing your data with anomalous turned on will somehow degrade the quality of normal intensity data. I can think of very few circumstances when I would NOT want anomalous data, yet for many data processing pipelines, it is the default not to give you the I+ and I- separately. Anomalous data are very useful for locating metal ions that you might not even have suspected to exist in your structure. Can I make a plea that all data processing packages/pipelines give you anomalous data by default? Can anyone think of a good reason why they shouldn't? James -- Dr. James W. Murray David Phillips Research Fellow Division of Molecular Biosciences Imperial College, LONDON Tel: +44 (0)20 759 48895 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of James Holton [jmhol...@lbl.gov] Sent: Wednesday, June 13, 2012 3:47 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique? I think there is a misconception floating around that processing your data with anomalous turned on will somehow degrade the quality of normal intensity data. I'm not exactly sure where this rumor comes from, but I imagine it has something to do with confusion about all the various anomalous options different scaling programs have. For example, some programs offer the option to treat all I+ and all I- as completely separate data sets, scaled and merged independently. I think this is called scale anomalous in SCALEPACK and intensities anomalous in SCALA. Neither of these is the default because such treatment is only helpful if the anomalous signal is absolutely huge (I have only seen this once). So, I imagine people who have never done experimental phasing (there are lots of them!) might read things like Switching ANOMALOUS ON does affect the statistics and the outlier rejection in the SCALA manual and decide that they had better turn off all those evil anomalous things. Then they tell their students to do the same, etc. -James Holton MAD Scientist On Tue, Jun 12, 2012 at 3:17 AM, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Why would anyone ignore the anomalous data they had collected? It will always help the phasing, and decide the hand for you.. Eleanor On 6 Jun 2012, at 03:55, Stefan Gajewski wrote: Hey! I was just wondering, do you know of any recent (~10y) publication that presented a structure solution solely based on MIR? Without the use of any anomalous signal of some sort? When was the last time you saw a structure that was solved without the use of anomalous signal or homology model? Is there a way to look up the answer (e.g. filter settings in the RCSB) I am not aware of? Thanks, S. (Disclaimer: I am aware that isomorpous data is a valuable source of information)
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
Why would anyone ignore the anomalous data they had collected? It will always help the phasing, and decide the hand for you.. Eleanor On 6 Jun 2012, at 03:55, Stefan Gajewski wrote: Hey! I was just wondering, do you know of any recent (~10y) publication that presented a structure solution solely based on MIR? Without the use of any anomalous signal of some sort? When was the last time you saw a structure that was solved without the use of anomalous signal or homology model? Is there a way to look up the answer (e.g. filter settings in the RCSB) I am not aware of? Thanks, S. (Disclaimer: I am aware that isomorpous data is a valuable source of information)
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
One could consider RIP (phasing using radiation induced damage) as SIR technique. At short wavelengths ( Hey! I was just wondering, do you know of any recent (~10y) publication that presented a structure solution solely based on MIR? Without the use of any anomalous signal of some sort? When was the last time you saw a structure that was solved without the use of anomalous signal or homology model? Is there a way to look up the answer (e.g. filter settings in the RCSB) I am not aware of? Thanks, S. (Disclaimer: I am aware that isomorpous data is a valuable source of information)
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
I suspect that pure MIR (without anomalous) was always a fiction. I doubt that anyone has ever used it. Heavy atoms always give an anomalous signal Phil I suspect that there was a time when the anomalous signal in data sets was fictional. Before the invent of flash freezing, systematic errors due to decay and the need of scaling together many derivative data sets collected on multiple crystals could render weak anomalous signal useless. Therefore MIR was needed. Also, current hardware/software produces much better reduced data, so weak signals can become useful. Fred [32m*** Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular BiologyFax: 301-496-0201 DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476...@mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred ***[m
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
No they were not useless! I used them (probably better now with cryo data though) Phil On 6 Jun 2012, at 16:02, Dyda wrote: I suspect that pure MIR (without anomalous) was always a fiction. I doubt that anyone has ever used it. Heavy atoms always give an anomalous signal Phil I suspect that there was a time when the anomalous signal in data sets was fictional. Before the invent of flash freezing, systematic errors due to decay and the need of scaling together many derivative data sets collected on multiple crystals could render weak anomalous signal useless. Therefore MIR was needed. Also, current hardware/software produces much better reduced data, so weak signals can become useful. Fred [32m*** Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular BiologyFax: 301-496-0201 DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476...@mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred ***[m
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
I suspect that there was a time when the anomalous signal in data sets was fictional. Before the invent of flash freezing, systematic errors due to decay and the need of scaling together many derivative data sets collected on multiple crystals could render weak anomalous signal useless. Therefore MIR was needed. Also, current hardware/software produces much better reduced data, so weak signals can become useful. I think that weak beam intensities (home sources), large crystals, big HA signals (f = ~12 @ CuKa for some Lanthanides), and high symmetries could all make measuring anomalous signals much easier even without cryo. And...Phil Evans did it! JPK *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
Anomalous signal even with room temperature capillary data was measurable on diffractometers and early area detectors. However there were misspellings in software packages such as sending anomalous phase 90deg into the wrong direction in one of them or others. After in-house editing, anomalous signal contributed significantly. It was also very instrumental in discovering mis-setings in formats of area detectors. We have used a method as appeared in Tom Blundell and Louise Johnson unrivaled book Protein Crystallography ( I own one!) by checking the peaks of the second derivatives with the phases of the first derivative with the contribution of correct or inverted anomalous signal contribution to get correct detector format or space group or else. I still have a logbook that keep records of getting out correct Xentronics format. So no fiction, just errors… Physics works!!! FF Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Jun 6, 2012, at 18:02 , Dyda wrote: I suspect that pure MIR (without anomalous) was always a fiction. I doubt that anyone has ever used it. Heavy atoms always give an anomalous signal Phil I suspect that there was a time when the anomalous signal in data sets was fictional. Before the invent of flash freezing, systematic errors due to decay and the need of scaling together many derivative data sets collected on multiple crystals could render weak anomalous signal useless. Therefore MIR was needed. Also, current hardware/software produces much better reduced data, so weak signals can become useful. Fred [32m*** Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular BiologyFax: 301-496-0201 DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476...@mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred ***[m
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
There were a number of labs using anomalous dispersion for phasing 40 years ago. The theory for using it dates from the 60s. And careful experimental technique allowed the structure solution of several proteins before 1980 using what would be labeled now as SIRAS. Ron On Wed, 6 Jun 2012, Dyda wrote: I suspect that pure MIR (without anomalous) was always a fiction. I doubt that anyone has ever used it. Heavy atoms always give an anomalous signal Phil I suspect that there was a time when the anomalous signal in data sets was fictional. Before the invent of flash freezing, systematic errors due to decay and the need of scaling together many derivative data sets collected on multiple crystals could render weak anomalous signal useless. Therefore MIR was needed. Also, current hardware/software produces much better reduced data, so weak signals can become useful. Fred [32m*** Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular BiologyFax: 301-496-0201 DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476...@mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred ***[m
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
I think some have used anomalous signals since the 1930s-40s, e.g., Bijvoet! JPK On Wed, Jun 6, 2012 at 10:23 AM, Ronald E Stenkamp stenk...@u.washington.edu wrote: There were a number of labs using anomalous dispersion for phasing 40 years ago. The theory for using it dates from the 60s. And careful experimental technique allowed the structure solution of several proteins before 1980 using what would be labeled now as SIRAS. Ron On Wed, 6 Jun 2012, Dyda wrote: I suspect that pure MIR (without anomalous) was always a fiction. I doubt that anyone has ever used it. Heavy atoms always give an anomalous signal Phil I suspect that there was a time when the anomalous signal in data sets was fictional. Before the invent of flash freezing, systematic errors due to decay and the need of scaling together many derivative data sets collected on multiple crystals could render weak anomalous signal useless. Therefore MIR was needed. Also, current hardware/software produces much better reduced data, so weak signals can become useful. Fred [32m*** Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular Biology Fax: 301-496-0201 DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476...@mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred *** [m -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
Bijvoet - 1949 ! FF Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Jun 6, 2012, at 18:28 , Jacob Keller wrote: I think some have used anomalous signals since the 1930s-40s, e.g., Bijvoet! JPK On Wed, Jun 6, 2012 at 10:23 AM, Ronald E Stenkamp stenk...@u.washington.edu wrote: There were a number of labs using anomalous dispersion for phasing 40 years ago. The theory for using it dates from the 60s. And careful experimental technique allowed the structure solution of several proteins before 1980 using what would be labeled now as SIRAS. Ron On Wed, 6 Jun 2012, Dyda wrote: I suspect that pure MIR (without anomalous) was always a fiction. I doubt that anyone has ever used it. Heavy atoms always give an anomalous signal Phil I suspect that there was a time when the anomalous signal in data sets was fictional. Before the invent of flash freezing, systematic errors due to decay and the need of scaling together many derivative data sets collected on multiple crystals could render weak anomalous signal useless. Therefore MIR was needed. Also, current hardware/software produces much better reduced data, so weak signals can become useful. Fred [32m*** Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular BiologyFax: 301-496-0201 DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476...@mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred *** [m -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
Even today, we still try to soak existing native protein crystals with heavy atoms at the same time while SeMet substituted protein is prepared. Nearly half of the times, we are able to solve the structure with HA (always SIRAS) before we have the SeMet protein. A recent example: Structure. 2009 Jul 15;17(7):939-51. Structure and function of an ADP-ribose-dependent transcriptional regulator of NAD metabolism. Huang N, De Ingeniis J, Galeazzi L, Mancini C, Korostelev YD, Rakhmaninova AB, Gelfand MS, Rodionov DA, Raffaelli N, Zhang H. Hong -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ronald E Stenkamp Sent: Wednesday, June 06, 2012 10:23 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique? There were a number of labs using anomalous dispersion for phasing 40 years ago. The theory for using it dates from the 60s. And careful experimental technique allowed the structure solution of several proteins before 1980 using what would be labeled now as SIRAS. Ron On Wed, 6 Jun 2012, Dyda wrote: I suspect that pure MIR (without anomalous) was always a fiction. I doubt that anyone has ever used it. Heavy atoms always give an anomalous signal Phil I suspect that there was a time when the anomalous signal in data sets was fictional. Before the invent of flash freezing, systematic errors due to decay and the need of scaling together many derivative data sets collected on multiple crystals could render weak anomalous signal useless. Therefore MIR was needed. Also, current hardware/software produces much better reduced data, so weak signals can become useful. Fred [32m*** Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular BiologyFax: 301-496-0201 DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476...@mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred ***[m
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
Dear Fred, May I join Phil Evans in trying to dissipate the feeling that anomalous differences were fictional before flash-freezing and all the mod cons. I can remember cutting my teeth as a PhD student by helping Alan Wonacott with the experimental phasing of his B.St. GAPDH structure in 1973-74. The data were collected at room temperature on a rotating-anode source, using film on an Arndt-Wonacott rotation camera (the original prototype!). The films were scanned on a precursor of the Optronics scanner, and the intensities were integrated and scaled with the early versions of the Rotavata and Agrovata programs (mention of which should make many ccp4 old-timers swoon with nostalgia). Even with such primitive techniques, I can remember an HgI4 derivative in which you could safely refine the anomalous occupancies (i.e. f values) for the iodine atoms of the beautiful planar HgI3 anion to 5 electrons. This contributed very substantially to the phasing of the structure. In fact it would be a healthy exercise to RTFL (Read The Fascinating Literature) in this area, in particular the beautiful 1966 papers by Brian Matthews in Acta Cryst. vol 20, to see how seriously anomalous scattering was already taken as a source of phase information in macromolecular crystallography in the 1960's. In spite of that, of course, there would always be the unhappy cases where the anomalous differences were too noisy, or the data processing program too unsophisticated to filter them adequately, so that only the isomorphous differences would be useful. It was in order to carry out such filtering that Brian Matthews made another crucial contribution in the form of the Local Scaling method (Acta Cryst. A31, 480-487). With best wishes, Gerard. -- On Wed, Jun 06, 2012 at 11:02:05AM -0400, Dyda wrote: I suspect that pure MIR (without anomalous) was always a fiction. I doubt that anyone has ever used it. Heavy atoms always give an anomalous signal Phil I suspect that there was a time when the anomalous signal in data sets was fictional. Before the invent of flash freezing, systematic errors due to decay and the need of scaling together many derivative data sets collected on multiple crystals could render weak anomalous signal useless. Therefore MIR was needed. Also, current hardware/software produces much better reduced data, so weak signals can become useful. Fred [32m*** Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular BiologyFax: 301-496-0201 DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476...@mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred ***[m -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
Remember that it's all relative to the length of the FP vector. If your FP vector is small, then the f component can substantially change the phase, even with a small f component. So if you have measured a number of relatively weak reflections with minimal error, there is a substantial anomalous signal. If you have a huge FP vector, then you won't see much of a phase change. Bernie On Wed, June 6, 2012 10:02 am, Dyda wrote: I suspect that pure MIR (without anomalous) was always a fiction. I doubt that anyone has ever used it. Heavy atoms always give an anomalous signal Phil
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
...Even with such primitive techniques, I can remember an HgI4 derivative in which you could safely refine the anomalous occupancies (i.e. f values) for the iodine atoms of the beautiful planar HgI3 anion to 5 electrons. I am surprised--f's of I and Hg are supposed to be around 8 for CuKa (or maybe you weren't using CuKa)? JPK -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
Dear Jacob, I thought that getting 5 for each iodine was doing pretty well, given the circumstances - e.g. the noisy measurements, the primitive software running on slow computers with tiny amounts of memory, etc. . In any case my main point, directed at the original poster, was that reading the early Acta Cryst. issues (RTFL) might be an alternative and perhaps more enlightening way of getting a picture of the evolution of phasing methods than finding some clever filter settings in the RCSB ;-) . With best wishes, Gerard. -- On Wed, Jun 06, 2012 at 11:08:37AM -0500, Jacob Keller wrote: ...Even with such primitive techniques, I can remember an HgI4 derivative in which you could safely refine the anomalous occupancies (i.e. f values) for the iodine atoms of the beautiful planar HgI3 anion to 5 electrons. I am surprised--f's of I and Hg are supposed to be around 8 for CuKa (or maybe you weren't using CuKa)? JPK -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
Dear Jacob and all, I realise that my last statement sounds awfully dour and dismissive, in a way I really didn't intend. Especially as Stefan's original posting was a Fun Question. Apologies to all for this over-the-top statement. I enjoyed a lot of the replies. With best wishes, Gerard. -- On Wed, Jun 06, 2012 at 06:09:33PM +0100, Gerard Bricogne wrote: Dear Jacob, I thought that getting 5 for each iodine was doing pretty well, given the circumstances - e.g. the noisy measurements, the primitive software running on slow computers with tiny amounts of memory, etc. . In any case my main point, directed at the original poster, was that reading the early Acta Cryst. issues (RTFL) might be an alternative and perhaps more enlightening way of getting a picture of the evolution of phasing methods than finding some clever filter settings in the RCSB ;-) . With best wishes, Gerard. -- On Wed, Jun 06, 2012 at 11:08:37AM -0500, Jacob Keller wrote: ...Even with such primitive techniques, I can remember an HgI4 derivative in which you could safely refine the anomalous occupancies (i.e. f values) for the iodine atoms of the beautiful planar HgI3 anion to 5 electrons. I am surprised--f's of I and Hg are supposed to be around 8 for CuKa (or maybe you weren't using CuKa)? JPK -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
I wonder if anyone attempted to write a historic book on development of crystallography. That generation of crystallographers is leaving this world and soon nobody will be able to say how the protein and non-protein structures were solved in those days. Alex On Jun 6, 2012, at 8:48 AM, Gerard Bricogne wrote: Dear Fred, May I join Phil Evans in trying to dissipate the feeling that anomalous differences were fictional before flash-freezing and all the mod cons. I can remember cutting my teeth as a PhD student by helping Alan Wonacott with the experimental phasing of his B.St. GAPDH structure in 1973-74. The data were collected at room temperature on a rotating-anode source, using film on an Arndt-Wonacott rotation camera (the original prototype!). The films were scanned on a precursor of the Optronics scanner, and the intensities were integrated and scaled with the early versions of the Rotavata and Agrovata programs (mention of which should make many ccp4 old-timers swoon with nostalgia). Even with such primitive techniques, I can remember an HgI4 derivative in which you could safely refine the anomalous occupancies (i.e. f values) for the iodine atoms of the beautiful planar HgI3 anion to 5 electrons. This contributed very substantially to the phasing of the structure. In fact it would be a healthy exercise to RTFL (Read The Fascinating Literature) in this area, in particular the beautiful 1966 papers by Brian Matthews in Acta Cryst. vol 20, to see how seriously anomalous scattering was already taken as a source of phase information in macromolecular crystallography in the 1960's. In spite of that, of course, there would always be the unhappy cases where the anomalous differences were too noisy, or the data processing program too unsophisticated to filter them adequately, so that only the isomorphous differences would be useful. It was in order to carry out such filtering that Brian Matthews made another crucial contribution in the form of the Local Scaling method (Acta Cryst. A31, 480-487). With best wishes, Gerard. -- On Wed, Jun 06, 2012 at 11:02:05AM -0400, Dyda wrote: I suspect that pure MIR (without anomalous) was always a fiction. I doubt that anyone has ever used it. Heavy atoms always give an anomalous signal Phil I suspect that there was a time when the anomalous signal in data sets was fictional. Before the invent of flash freezing, systematic errors due to decay and the need of scaling together many derivative data sets collected on multiple crystals could render weak anomalous signal useless. Therefore MIR was needed. Also, current hardware/software produces much better reduced data, so weak signals can become useful. Fred [32m*** Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular BiologyFax: 301-496-0201 DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476...@mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred ***[m -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
No offense taken (we all have our dour moments!), but grant me a sincere question: the f occupancy value would have been just as close at 11 as 5 if the true value were 8, am I correct? In other words, do you imply by saying doing well that you got as *much* as 5, or that you got as *close* as 5? I am just trying to see whether I understand these things correctly. Jacob On Wed, Jun 6, 2012 at 12:21 PM, Gerard Bricogne g...@globalphasing.com wrote: Dear Jacob and all, I realise that my last statement sounds awfully dour and dismissive, in a way I really didn't intend. Especially as Stefan's original posting was a Fun Question. Apologies to all for this over-the-top statement. I enjoyed a lot of the replies. With best wishes, Gerard. -- On Wed, Jun 06, 2012 at 06:09:33PM +0100, Gerard Bricogne wrote: Dear Jacob, I thought that getting 5 for each iodine was doing pretty well, given the circumstances - e.g. the noisy measurements, the primitive software running on slow computers with tiny amounts of memory, etc. . In any case my main point, directed at the original poster, was that reading the early Acta Cryst. issues (RTFL) might be an alternative and perhaps more enlightening way of getting a picture of the evolution of phasing methods than finding some clever filter settings in the RCSB ;-) . With best wishes, Gerard. -- On Wed, Jun 06, 2012 at 11:08:37AM -0500, Jacob Keller wrote: ...Even with such primitive techniques, I can remember an HgI4 derivative in which you could safely refine the anomalous occupancies (i.e. f values) for the iodine atoms of the beautiful planar HgI3 anion to 5 electrons. I am surprised--f's of I and Hg are supposed to be around 8 for CuKa (or maybe you weren't using CuKa)? JPK -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * === -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
Richard Dickerson's book is relevant and gripping reading http://www.amazon.com/gp/product/0878931686?ie=UTF8tag=brscrystallot-20lin kCode=as2camp=1789creative=9325creativeASIN=0878931686 BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of aaleshin Sent: Wednesday, June 06, 2012 11:12 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique? I wonder if anyone attempted to write a historic book on development of crystallography. That generation of crystallographers is leaving this world and soon nobody will be able to say how the protein and non-protein structures were solved in those days. Alex
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
There is also a relevant point from the physics of the absorption spectra - the XANES white lines (near edge peaks higher than the continuum transition or edge step) depend on the chemical environment of the anomalous atom in terms of available unoccupied states (which n. b. is something entirely different that the local neighbor environment/geometry which can be backtransformed - although with quite some uncertainty - from the EXAFS wiggles). Any argument about absolute f peak values in absence of experimental evidence (scan) might want to consider that. Best, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob Keller Sent: Wednesday, June 06, 2012 11:30 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique? No offense taken (we all have our dour moments!), but grant me a sincere question: the f occupancy value would have been just as close at 11 as 5 if the true value were 8, am I correct? In other words, do you imply by saying doing well that you got as *much* as 5, or that you got as *close* as 5? I am just trying to see whether I understand these things correctly. Jacob On Wed, Jun 6, 2012 at 12:21 PM, Gerard Bricogne g...@globalphasing.com wrote: Dear Jacob and all, I realise that my last statement sounds awfully dour and dismissive, in a way I really didn't intend. Especially as Stefan's original posting was a Fun Question. Apologies to all for this over-the-top statement. I enjoyed a lot of the replies. With best wishes, Gerard. -- On Wed, Jun 06, 2012 at 06:09:33PM +0100, Gerard Bricogne wrote: Dear Jacob, I thought that getting 5 for each iodine was doing pretty well, given the circumstances - e.g. the noisy measurements, the primitive software running on slow computers with tiny amounts of memory, etc. . In any case my main point, directed at the original poster, was that reading the early Acta Cryst. issues (RTFL) might be an alternative and perhaps more enlightening way of getting a picture of the evolution of phasing methods than finding some clever filter settings in the RCSB ;-) . With best wishes, Gerard. -- On Wed, Jun 06, 2012 at 11:08:37AM -0500, Jacob Keller wrote: ...Even with such primitive techniques, I can remember an HgI4 derivative in which you could safely refine the anomalous occupancies (i.e. f values) for the iodine atoms of the beautiful planar HgI3 anion to 5 electrons. I am surprised--f's of I and Hg are supposed to be around 8 for CuKa (or maybe you weren't using CuKa)? JPK -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * === -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
But the edges for I and Hg are pretty far from CuKa (see attached). I am familiar with their being extra signal (white lines) very close to the peak, but not so far away JPK On Wed, Jun 6, 2012 at 2:15 PM, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com wrote: There is also a relevant point from the physics of the absorption spectra - the XANES white lines (near edge peaks higher than the continuum transition or edge step) depend on the chemical environment of the anomalous atom in terms of available unoccupied states (which n. b. is something entirely different that the local neighbor environment/geometry which can be backtransformed - although with quite some uncertainty - from the EXAFS wiggles). Any argument about absolute f peak values in absence of experimental evidence (scan) might want to consider that. Best, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob Keller Sent: Wednesday, June 06, 2012 11:30 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique? No offense taken (we all have our dour moments!), but grant me a sincere question: the f occupancy value would have been just as close at 11 as 5 if the true value were 8, am I correct? In other words, do you imply by saying doing well that you got as *much* as 5, or that you got as *close* as 5? I am just trying to see whether I understand these things correctly. Jacob On Wed, Jun 6, 2012 at 12:21 PM, Gerard Bricogne g...@globalphasing.com wrote: Dear Jacob and all, I realise that my last statement sounds awfully dour and dismissive, in a way I really didn't intend. Especially as Stefan's original posting was a Fun Question. Apologies to all for this over-the-top statement. I enjoyed a lot of the replies. With best wishes, Gerard. -- On Wed, Jun 06, 2012 at 06:09:33PM +0100, Gerard Bricogne wrote: Dear Jacob, I thought that getting 5 for each iodine was doing pretty well, given the circumstances - e.g. the noisy measurements, the primitive software running on slow computers with tiny amounts of memory, etc. . In any case my main point, directed at the original poster, was that reading the early Acta Cryst. issues (RTFL) might be an alternative and perhaps more enlightening way of getting a picture of the evolution of phasing methods than finding some clever filter settings in the RCSB ;-) . With best wishes, Gerard. -- On Wed, Jun 06, 2012 at 11:08:37AM -0500, Jacob Keller wrote: ...Even with such primitive techniques, I can remember an HgI4 derivative in which you could safely refine the anomalous occupancies (i.e. f values) for the iodine atoms of the beautiful planar HgI3 anion to 5 electrons. I am surprised--f's of I and Hg are supposed to be around 8 for CuKa (or maybe you weren't using CuKa)? JPK -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * === -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** attachment: I_Hg_edges.png
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
Dear Jacob, What I meant was that I thought it was a pleasant surprise to see that there was enough anomalous signal at all in these noisy data (which were collected from several crystals, suffering from radiation damage at room temperature, from sizeable absorption effects etc.) to get a refined value of 5. You are right to say that it was a case of 8 plus or minus 3, but I was impressed. Remember, that wasn't from data collected on a 4-circle diffractometer (that could be fiendishly accurate): it was the maiden flight of the A-W rotation camera with its reliance on film cassettes, microdensitometry and all that - a set of intrinsically much noisier ways of trying to count X-ray photons than point detectors. It is true, however, that this technology would have been unlikely to support phase determination by SAD. By the way, the Fred I was addressing in my first posting was Fred Dyda (who had floated the idea that there might not have been much useful anomalous signal before flash freezing), and not Fred Vellieux ;-) . With best wishes, Gerard. -- On Wed, Jun 06, 2012 at 01:30:26PM -0500, Jacob Keller wrote: No offense taken (we all have our dour moments!), but grant me a sincere question: the f occupancy value would have been just as close at 11 as 5 if the true value were 8, am I correct? In other words, do you imply by saying doing well that you got as *much* as 5, or that you got as *close* as 5? I am just trying to see whether I understand these things correctly. Jacob On Wed, Jun 6, 2012 at 12:21 PM, Gerard Bricogne g...@globalphasing.com wrote: Dear Jacob and all, I realise that my last statement sounds awfully dour and dismissive, in a way I really didn't intend. Especially as Stefan's original posting was a Fun Question. Apologies to all for this over-the-top statement. I enjoyed a lot of the replies. With best wishes, Gerard. -- On Wed, Jun 06, 2012 at 06:09:33PM +0100, Gerard Bricogne wrote: Dear Jacob, I thought that getting 5 for each iodine was doing pretty well, given the circumstances - e.g. the noisy measurements, the primitive software running on slow computers with tiny amounts of memory, etc. . In any case my main point, directed at the original poster, was that reading the early Acta Cryst. issues (RTFL) might be an alternative and perhaps more enlightening way of getting a picture of the evolution of phasing methods than finding some clever filter settings in the RCSB ;-) . With best wishes, Gerard. -- On Wed, Jun 06, 2012 at 11:08:37AM -0500, Jacob Keller wrote: ...Even with such primitive techniques, I can remember an HgI4 derivative in which you could safely refine the anomalous occupancies (i.e. f values) for the iodine atoms of the beautiful planar HgI3 anion to 5 electrons. I am surprised--f's of I and Hg are supposed to be around 8 for CuKa (or maybe you weren't using CuKa)? JPK -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
Just for clarification: I didn't try to claim that there was no anomalous signal, simply that in some cases it was difficult use it, because the data weren't that great. fred [32m*** Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular BiologyFax: 301-496-0201 DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476...@mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred ***[m
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
From personal and recent experience I've solved a structure using only iodine anomalous at Cu K-alpha from a RT crystal (a capillary mounted one at that). The anomalous signal from iodine is surprisingly robust on a home source even at room temp. Katherine As an aside for those who feel that capillary mounting On Wed, Jun 6, 2012 at 2:34 PM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: But the edges for I and Hg are pretty far from CuKa (see attached). I am familiar with their being extra signal (white lines) very close to the peak, but not so far away JPK On Wed, Jun 6, 2012 at 2:15 PM, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com wrote: There is also a relevant point from the physics of the absorption spectra - the XANES white lines (near edge peaks higher than the continuum transition or edge step) depend on the chemical environment of the anomalous atom in terms of available unoccupied states (which n. b. is something entirely different that the local neighbor environment/geometry which can be backtransformed - although with quite some uncertainty - from the EXAFS wiggles). Any argument about absolute f peak values in absence of experimental evidence (scan) might want to consider that. Best, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob Keller Sent: Wednesday, June 06, 2012 11:30 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique? No offense taken (we all have our dour moments!), but grant me a sincere question: the f occupancy value would have been just as close at 11 as 5 if the true value were 8, am I correct? In other words, do you imply by saying doing well that you got as *much* as 5, or that you got as *close* as 5? I am just trying to see whether I understand these things correctly. Jacob On Wed, Jun 6, 2012 at 12:21 PM, Gerard Bricogne g...@globalphasing.com wrote: Dear Jacob and all, I realise that my last statement sounds awfully dour and dismissive, in a way I really didn't intend. Especially as Stefan's original posting was a Fun Question. Apologies to all for this over-the-top statement. I enjoyed a lot of the replies. With best wishes, Gerard. -- On Wed, Jun 06, 2012 at 06:09:33PM +0100, Gerard Bricogne wrote: Dear Jacob, I thought that getting 5 for each iodine was doing pretty well, given the circumstances - e.g. the noisy measurements, the primitive software running on slow computers with tiny amounts of memory, etc. . In any case my main point, directed at the original poster, was that reading the early Acta Cryst. issues (RTFL) might be an alternative and perhaps more enlightening way of getting a picture of the evolution of phasing methods than finding some clever filter settings in the RCSB ;-) . With best wishes, Gerard. -- On Wed, Jun 06, 2012 at 11:08:37AM -0500, Jacob Keller wrote: ...Even with such primitive techniques, I can remember an HgI4 derivative in which you could safely refine the anomalous occupancies (i.e. f values) for the iodine atoms of the beautiful planar HgI3 anion to 5 electrons. I am surprised--f's of I and Hg are supposed to be around 8 for CuKa (or maybe you weren't using CuKa)? JPK -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * === -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
It would be helpful if I finished my own sentences. As an aside for those who feel that capillary mounting is a lost art among the newer generation I assure you it isn't. All you need is a busted cryo system and a crystal backlog to get past the intimidation factor. Katherine On Wed, Jun 6, 2012 at 2:34 PM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: But the edges for I and Hg are pretty far from CuKa (see attached). I am familiar with their being extra signal (white lines) very close to the peak, but not so far away JPK On Wed, Jun 6, 2012 at 2:15 PM, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com wrote: There is also a relevant point from the physics of the absorption spectra - the XANES white lines (near edge peaks higher than the continuum transition or edge step) depend on the chemical environment of the anomalous atom in terms of available unoccupied states (which n. b. is something entirely different that the local neighbor environment/geometry which can be backtransformed - although with quite some uncertainty - from the EXAFS wiggles). Any argument about absolute f peak values in absence of experimental evidence (scan) might want to consider that. Best, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob Keller Sent: Wednesday, June 06, 2012 11:30 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique? No offense taken (we all have our dour moments!), but grant me a sincere question: the f occupancy value would have been just as close at 11 as 5 if the true value were 8, am I correct? In other words, do you imply by saying doing well that you got as *much* as 5, or that you got as *close* as 5? I am just trying to see whether I understand these things correctly. Jacob On Wed, Jun 6, 2012 at 12:21 PM, Gerard Bricogne g...@globalphasing.com wrote: Dear Jacob and all, I realise that my last statement sounds awfully dour and dismissive, in a way I really didn't intend. Especially as Stefan's original posting was a Fun Question. Apologies to all for this over-the-top statement. I enjoyed a lot of the replies. With best wishes, Gerard. -- On Wed, Jun 06, 2012 at 06:09:33PM +0100, Gerard Bricogne wrote: Dear Jacob, I thought that getting 5 for each iodine was doing pretty well, given the circumstances - e.g. the noisy measurements, the primitive software running on slow computers with tiny amounts of memory, etc. . In any case my main point, directed at the original poster, was that reading the early Acta Cryst. issues (RTFL) might be an alternative and perhaps more enlightening way of getting a picture of the evolution of phasing methods than finding some clever filter settings in the RCSB ;-) . With best wishes, Gerard. -- On Wed, Jun 06, 2012 at 11:08:37AM -0500, Jacob Keller wrote: ...Even with such primitive techniques, I can remember an HgI4 derivative in which you could safely refine the anomalous occupancies (i.e. f values) for the iodine atoms of the beautiful planar HgI3 anion to 5 electrons. I am surprised--f's of I and Hg are supposed to be around 8 for CuKa (or maybe you weren't using CuKa)? JPK -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * === -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
Given Cu, yes, the five M edges between 2.3keV and 3.6keV contribute a continuum transition signal of the 8e- you initially referred to. -Original Message- From: Jacob Keller [mailto:j-kell...@fsm.northwestern.edu] Sent: Wednesday, June 06, 2012 12:35 PM To: b...@hofkristallamt.org Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique? But the edges for I and Hg are pretty far from CuKa (see attached). I am familiar with their being extra signal (white lines) very close to the peak, but not so far away JPK
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
So if get the gist of the thread right, am I correct in assuming that the last protein structures to be solved strictly by MIR are haemoglobin/myoglobin, lysozyme and chymotrypsin and perhaps one or two more in the late sixties? In which case the answer to the original question about MIR being obsolete, is yes it is since a long time? Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Phil Evans [p...@mrc-lmb.cam.ac.uk] Sent: Wednesday, June 06, 2012 6:04 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique? No they were not useless! I used them (probably better now with cryo data though) Phil On 6 Jun 2012, at 16:02, Dyda wrote: I suspect that pure MIR (without anomalous) was always a fiction. I doubt that anyone has ever used it. Heavy atoms always give an anomalous signal Phil I suspect that there was a time when the anomalous signal in data sets was fictional. Before the invent of flash freezing, systematic errors due to decay and the need of scaling together many derivative data sets collected on multiple crystals could render weak anomalous signal useless. Therefore MIR was needed. Also, current hardware/software produces much better reduced data, so weak signals can become useful. Fred ?[32m*** Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular BiologyFax: 301-496-0201 DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476...@mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred ***?[m
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
No, I listed a few recent ones V. Gaur, et al., Plant Physiol., 152(4), 1842-1850 (2010) O. Antipova, J Biol Chem. 2010 Mar 5;285(10):7087-96. Epub 2010 Jan 6. Y. Nakajima, J Bacteriol. 2008 Dec;190(23):7819-29. Epub 2008 Sep 26. S. Stayrook, Nature. 2008 Apr 24;452(7190):1022-5. Many MIRAS, so the MIR part helped to get forms, and then collected with AS. On Wed, June 6, 2012 3:42 pm, Boaz Shaanan wrote: So if get the gist of the thread right, am I correct in assuming that the last protein structures to be solved strictly by MIR are haemoglobin/myoglobin, lysozyme and chymotrypsin and perhaps one or two more in the late sixties? In which case the answer to the original question about MIR being obsolete, is yes it is since a long time? Boaz
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
MIRAS doesn't count, only MIR (If I understand the original question correctly). Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Santarsiero, Bernard D. [b...@uic.edu] Sent: Wednesday, June 06, 2012 11:46 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique? No, I listed a few recent ones V. Gaur, et al., Plant Physiol., 152(4), 1842-1850 (2010) O. Antipova, J Biol Chem. 2010 Mar 5;285(10):7087-96. Epub 2010 Jan 6. Y. Nakajima, J Bacteriol. 2008 Dec;190(23):7819-29. Epub 2008 Sep 26. S. Stayrook, Nature. 2008 Apr 24;452(7190):1022-5. Many MIRAS, so the MIR part helped to get forms, and then collected with AS. On Wed, June 6, 2012 3:42 pm, Boaz Shaanan wrote: So if get the gist of the thread right, am I correct in assuming that the last protein structures to be solved strictly by MIR are haemoglobin/myoglobin, lysozyme and chymotrypsin and perhaps one or two more in the late sixties? In which case the answer to the original question about MIR being obsolete, is yes it is since a long time? Boaz
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
I and Victor Lamzin solved our first protein structure (3A resolution) in 80-s using pure MIR and a home made (Russian) diffractometer... Alex On Jun 6, 2012, at 1:42 PM, Boaz Shaanan wrote: So if get the gist of the thread right, am I correct in assuming that the last protein structures to be solved strictly by MIR are haemoglobin/myoglobin, lysozyme and chymotrypsin and perhaps one or two more in the late sixties? In which case the answer to the original question about MIR being obsolete, is yes it is since a long time? Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Phil Evans [p...@mrc-lmb.cam.ac.uk] Sent: Wednesday, June 06, 2012 6:04 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique? No they were not useless! I used them (probably better now with cryo data though) Phil On 6 Jun 2012, at 16:02, Dyda wrote: I suspect that pure MIR (without anomalous) was always a fiction. I doubt that anyone has ever used it. Heavy atoms always give an anomalous signal Phil I suspect that there was a time when the anomalous signal in data sets was fictional. Before the invent of flash freezing, systematic errors due to decay and the need of scaling together many derivative data sets collected on multiple crystals could render weak anomalous signal useless. Therefore MIR was needed. Also, current hardware/software produces much better reduced data, so weak signals can become useful. Fred ?[32m*** Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular BiologyFax: 301-496-0201 DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476...@mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred ***?[m
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
I can only confirm what Alex said. And the structure was neither a globin or zyme or psin! Victor Quoting aaleshin aales...@burnham.org: I and Victor Lamzin solved our first protein structure (3A resolution) in 80-s using pure MIR and a home made (Russian) diffractometer... Alex On Jun 6, 2012, at 1:42 PM, Boaz Shaanan wrote: So if get the gist of the thread right, am I correct in assuming that the last protein structures to be solved strictly by MIR are haemoglobin/myoglobin, lysozyme and chymotrypsin and perhaps one or two more in the late sixties? In which case the answer to the original question about MIR being obsolete, is yes it is since a long time? Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Phil Evans [p...@mrc-lmb.cam.ac.uk] Sent: Wednesday, June 06, 2012 6:04 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique? No they were not useless! I used them (probably better now with cryo data though) Phil On 6 Jun 2012, at 16:02, Dyda wrote: I suspect that pure MIR (without anomalous) was always a fiction. I doubt that anyone has ever used it. Heavy atoms always give an anomalous signal Phil I suspect that there was a time when the anomalous signal in data sets was fictional. Before the invent of flash freezing, systematic errors due to decay and the need of scaling together many derivative data sets collected on multiple crystals could render weak anomalous signal useless. Therefore MIR was needed. Also, current hardware/software produces much better reduced data, so weak signals can become useful. Fred ?[32m*** Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular BiologyFax: 301-496-0201 DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476...@mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred ***?[m
Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
On Tuesday, 05 June 2012, Stefan Gajewski wrote: Hey! I was just wondering, do you know of any recent (~10y) publication that presented a structure solution solely based on MIR? Without the use of any anomalous signal of some sort? A text search for MIR returns 1377 PDB structures overall. Of these 706 were deposited in the last 10 years, and 34 were deposited in the last 12 months. The most recent was released today (6 Jun 2012) HEADERHYDROLASE 17-APR-12 4EPC TITLE CRYSTAL STRUCTURE OF AUTOLYSIN REPEAT DOMAINS FROM STAPHYLOCOCCUS REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL Caveats: I have no idea how many of those structures say MIR because it's part of the protein name or some such, I have no idea how accurate the REMARK 200 fields are in any case, and I don't really trust the www.pdb.org search interface in general. When was the last time you saw a structure that was solved without the use of anomalous signal or homology model? Is there a way to look up the answer (e.g. filter settings in the RCSB) I am not aware of? Thanks, S. (Disclaimer: I am aware that isomorpous data is a valuable source of information)
