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
[ccp4bb] CSHL X-ray Methods in Structural Biology Course Oct 15-30, 2012: Application deadline June 15th
Once again I wanted to draw everyone's attention to the Cold Spring Harbor Laboratory 2012 X-ray Methods in Structural Biology course which will take place October 15 through October 30, 2012. The official course announcement is here: http://meetings.cshl.edu/courses/c-crys12.shtml I think the course is an outstanding place to learn both the theoretical and practical aspects of Macromolecular Crystallography because of the extensive lectures from world-renowned teachers and the hands-on experiments. Just recently, David Piston of Vanderbilt noted (Understanding how it works (2012) Nature 484, pp 440-441) that We need to do a better job of teaching students how techniques work before they start using them.” The CSHL course has tried to do that since it was first held in 1988 25 years ago when Alex McPherson, Hans Deisenhofer, Alwyn Jones, and Jim Remington joined me for 2 weeks of fun and hard work. This year's course will see the return of the long-time instruction team of Alex McPherson, Gary Gilliland, Bill Furey and myself along with many talented experts to help us give the participants an experience in Macromolecular Crystallography learning that cannot be found anywhere else. (The student:teacher ratio ends up to be about 1:1). We expect to have the participants crystallize several proteins and determine their structures all in about two weeks. The course is limited to 16 participants due to the very hands-on nature of the experiments and the intimate seminar room. Please check the above web site for more details. If anyone has any questions, please send me e-mail, I will be happy to answer all queries. Jim
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 * * * ===
[ccp4bb] postdoctoral position in protein crystallography
A postdoctoral position is available at the University of Maryland, Baltimore, in the Department of Pharmaceutical Sciences. Prior experience in crystallography is NOT required, only willingness to learn the method. Strong background in molecular biology techniques and/or biophysical methods will be considered a plus. Please submit your letter of interest, resume and contact information of 3 references to epozh...@rx.umaryland.edu. -- Ed Pozharski epozh...@umaryland.edu University of Maryland - Baltimore
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
[ccp4bb] Fwd: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
Begin forwarded message: Date: June 6, 2012 3:05:16 PM EDT To: aaleshin aales...@burnham.orgmailto:aales...@burnham.org Subject: Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique? There are four such papers in Methods in Enzymology, Vols 368 and 374: David Blow: How Bijvoet Made the Difference: The Growing Power of Anomalous Scattering V. 374, pp. 3-22 Brian Matthews: Transformations in Structural Biology: A Personal View V. 368 pp. 3-10 Michael Rossmann: Origins V. 368, pp. 11-21 Ulrich W. Arndt: Personal X-ray Reflections V. 368, pp. 21-45 These reminiscences are there entirely because my co-Editor Bob Sweet felt exactly the same way Alex does. Charlie On Jun 6, 2012, at 2:12 PM, aaleshin wrote: 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.netmailto:2022476...@mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred ***[m -- === * * * Gerard Bricogne g...@globalphasing.commailto: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?
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 ***
[ccp4bb] Beamtime @ SLS
=== SYNCHROTRON BEAM TIME FOR MACROMOLECULAR CRYSTALLOGRAPHY AT SLS === Proposal application deadline: Friday, June 15, 2012 Periods: September 1, 2012 - December 31, 2012 (Normal / Test proposals) September 1, 2012 - August 31, 2014 (Long-term proposals) Proposal submission: http://www.psi.ch/sls/px-beamlines-call-for-proposals Travel support: http://www.psi.ch/useroffice/sls-elisa-biostruct PSI DUO application for iphone: http://itunes.apple.com/ch/app/psi-duo/id375328818?mt=8 What's New? - PILATUS detectors at three PX beamlines - X06DA Multi-axis goniometer (PRIGO) - X06DA In-situ X-ray diffraction screening for any SBS format plate - X10SA Single crystal spectroscopy (UV-Vis, fluorescence and Raman), but no open call for this period (see details below). X06SA Beamline features (http://www.psi.ch/sls/pxi/pxi) - Undulator beamline with flux of 2x10^12 photons/sec at 12.4 keV (1Å) and fully tunable from 6.0 to 17.5 keV (2.07 - 0.71 Å) - Focused beam size and divergency: HRD - 85x10 microns and 0.35x0.06 mrad; MD2 - 25x5 microns and 0.5x0.4 mrad - PILATUS 6M pixel detector at the High Resolution Diffractometer, allowing continuous, fine phi-sliced data acquisition (25 frames per second) with 20 bit dynamic range (see http://pilatus.web.psi.ch/ or www.dectris.com for further information) - MAR225 CCD at Micro-Diffractometer MD2, allowing data collection with a focussed beam size of 25 x 5 micrometers, and smaller beam size with triple-aperture assembly ( 5 x 5, 10 x 10, 20 x 20 micrometer). X06DA Beamline features (http://www.psi.ch/sls/pxiii/pxiii) - Super-bending magnet beamline with flux of 5x10¹¹ photons/sec at 12.4 keV (1Å) and fully tunable from 6.0 to 17.5 keV (2.07 - 0.71 Å) - Focused beam size and divergency: 80x45 microns and 2x0.5 mrad (with possibility to reduce horizontal divergency to 0.4 mrad) - Mini-hutch design for fast manual mounting - PILATUS 2M (60 Hz, 450 um Si sensor) - Multi-axis goniometer (PRIGO) for crystal re-orentation - In-situ X-ray diffraction screening (with any SBS format plate) available during users shifts (R. Bingel-Erlenmeyer, et al., Crystal Growth Design 2011, 11, 916) X10SA Beamline features (http://www.psi.ch/sls/pxii/pxii) - Undulator beamline with flux of 2x10^12 photons/sec at 12.4 keV (1Å) and fully tunable from 6.0 to 20 keV (2.07 - 0.62 Å) - Focused beam size and divergency: 50x10 microns and 0.6x0.1 mrad - In-situ on-axis single crystal UV-Vis, fluorescence, Raman and Resonance Raman microspectrophotometer (http://www.psi.ch/sls/pxii/spectrolab) - PILATUS 6M pixel detector Note: beamtime for single crystal spectroscopy is very limited in this call period due to a scheduled diffractometer upgrade. Best regards, The MX group at SLS __ Meitian Wang Swiss Light Source at Paul Scherrer Institut CH-5232 Villigen PSI - http://www.psi.ch/sls/ Phone: +41 56 310 4175 Fax: +41 56 310 5292
Re: [ccp4bb] Fwd: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
And for more Personal Reflections, one may wish to take a gander at the Rigaku Webinar series with presentations by Brian Matthews and Michael G. Rossmann. Jim From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Carter, Charlie [car...@med.unc.edu] Sent: Wednesday, June 06, 2012 2:05 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Fwd: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique? Begin forwarded message: Date: June 6, 2012 3:05:16 PM EDT To: aaleshin aales...@burnham.orgmailto:aales...@burnham.org Subject: Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique? There are four such papers in Methods in Enzymology, Vols 368 and 374: David Blow: How Bijvoet Made the Difference: The Growing Power of Anomalous Scattering V. 374, pp. 3-22 Brian Matthews: Transformations in Structural Biology: A Personal View V. 368 pp. 3-10 Michael Rossmann: Origins V. 368, pp. 11-21 Ulrich W. Arndt: Personal X-ray Reflections V. 368, pp. 21-45 These reminiscences are there entirely because my co-Editor Bob Sweet felt exactly the same way Alex does. Charlie On Jun 6, 2012, at 2:12 PM, aaleshin wrote: 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?
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
[ccp4bb] sigma levels of averaged maps in coot ( or e/A3)
I calculated threefold averaged omit maps in coot. These maps look nice and clean, but I am having trouble making sense of the displayed sigma levels or e/A3 values. When I display the unaveraged and averaged maps at a similar density level for the protein the unaveraged map is at 0.024 e/A3 and 2.7 sigma, while the averaged map is displayed at 0.0016e/A3 and 7.6 sigma. I read the previous discussion about this issue where it was recommended to rely on the e/A3 values for comparison, but even that doesn't seem to work in this case. Any suggestions? Thanks Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220
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] Fwd: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
While neither of these references detail the development of protein crystallography, they are excellent stories of its birth: 1.) A book written by Richard Dickerson, Present at the flood 2.) A recent review in JMB by Strandberg, Dickerson, and Rossmann: 50 years of Protein Structure Analysis We are lucky to have Richard Dickerson as emeritus faculty here at UCLA, because he cares very much for the history of science. Although I do not have a personal relationship with him, I always enjoy the opportunity to hear him talk about the beginnings. A couple years ago, we had a symposium to celebrate the 50th anniversary of the first protein structures with guest speakers including Richard Dickerson, David Davies, Brian Matthews, Michael Rossmann, and Bob Stroud. Surprisingly, I cannot google my way to a recording of the lectures. I'm sure someone got a video or at least an audio recording, so if I can find it I will post a link. Mike T - Original Message - From: Jim Pflugrath jim.pflugr...@rigaku.com To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, June 6, 2012 12:31:56 PM GMT -08:00 US/Canada Pacific Subject: Re: [ccp4bb] Fwd: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique? And for more Personal Reflections, one may wish to take a gander at the Rigaku Webinar series with presentations by Brian Matthews and Michael G. Rossmann. Jim From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Carter, Charlie [car...@med.unc.edu] Sent: Wednesday, June 06, 2012 2:05 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Fwd: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique? Begin forwarded message: Date: June 6, 2012 3:05:16 PM EDT To: aaleshin aales...@burnham.org Subject: Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique? There are four such papers in Methods in Enzymology, Vols 368 and 374: David Blow: How Bijvoet Made the Difference: The Growing Power of Anomalous Scattering V. 374, pp. 3-22 Brian Matthews: Transformations in Structural Biology: A Personal View V. 368 pp. 3-10 Michael Rossmann: Origins V. 368, pp. 11-21 Ulrich W. Arndt: Personal X-ray Reflections V. 368, pp. 21-45 These reminiscences are there entirely because my co-Editor Bob Sweet felt exactly the same way Alex does. Charlie On Jun 6, 2012, at 2:12 PM, aaleshin wrote: 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 ... -- Michael C. Thompson Graduate Student Biochemistry Molecular Biology Division Department of Chemistry Biochemistry University of California, Los Angeles mi...@chem.ucla.edu
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] sigma levels of averaged maps in coot ( or e/A3)
Ursula, please don't forget that you are looking at Fourier image of electron density distribution, which may be as different from the true electron density distribution as different from zero the F000 reflection and as different your Fobs data set from being 100% complete for all possible reflections. So all in all my suggestion is to not make too much sense of absolute values of the Fourier map you are looking at. Best, Pavel Afonine On Wed, Jun 6, 2012 at 12:47 PM, Ursula Schulze-Gahmen uschulze-gah...@lbl.gov wrote: I calculated threefold averaged omit maps in coot. These maps look nice and clean, but I am having trouble making sense of the displayed sigma levels or e/A3 values. When I display the unaveraged and averaged maps at a similar density level for the protein the unaveraged map is at 0.024 e/A3 and 2.7 sigma, while the averaged map is displayed at 0.0016e/A3 and 7.6 sigma. I read the previous discussion about this issue where it was recommended to rely on the e/A3 values for comparison, but even that doesn't seem to work in this case. Any suggestions? Thanks Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220
Re: [ccp4bb] sigma levels of averaged maps in coot ( or e/A3)
On 06/06/12 21:47, Ursula Schulze-Gahmen wrote: I calculated threefold averaged omit maps in coot. These maps look nice and clean, but I am having trouble making sense of the displayed sigma levels or e/A3 values. When I display the unaveraged and averaged maps at a similar density level for the protein the unaveraged map is at 0.024 e/A3 and 2.7 sigma, while the averaged map is displayed at 0.0016e/A3 and 7.6 sigma. I read the previous discussion about this issue where it was recommended to rely on the e/A3 values for comparison, but even that doesn't seem to work in this case. Don't forget that in one case you are looking at a whole map and in the other (an average of) maps generated from a box encapsulating each chain. I wouldn't stress if I were you... Paul.
[ccp4bb] 3D projector--LG CF3D
Hi CCP4, I am curious if anyone has setup 3D-projector for large conference room. We have a LG CF3D projector and it is coupled to a Linux machine with Nvidia Quadro FX 3800. We haven't been able to get 3D working. If someone has experience with this projector, could you share the setting on the projector and graphic card? Thanks a lot. Xiaoshan Xiaoshan Min Amgen San Francisco 1120 Veterans Blvd. South San Francisco, CA 94080
Re: [ccp4bb] 3D projector--LG CF3D
ohh this is a passive stereo projector. what's the distance from the projector to the screen? On Wed, Jun 6, 2012 at 6:37 PM, Min, Xiaoshan x...@amgen.com wrote: Hi CCP4, I am curious if anyone has setup 3D-projector for large conference room. We have a LG CF3D projector and it is coupled to a Linux machine with Nvidia Quadro FX 3800. We haven't been able to get 3D working. If someone has experience with this projector, could you share the setting on the projector and graphic card? Thanks a lot. Xiaoshan Xiaoshan Min Amgen San Francisco 1120 Veterans Blvd. South San Francisco, CA 94080
Re: [ccp4bb] ligand geometry evaluation
Hi Ivan, I'm not sure which version of phenix you are using, but in 1.7.3-928 GUI restraints are generated for metals using the ReadySet. ReadySet creates a file called your_pdb_file_name.metal.edits. The file I generated gave standard deviations to bond lengths of 0.05-0.25. Prior to generating this file including it in refinements I found phenix treated the Mg ions in the structure I was refining like waters thus it kept blowing-up the coordinated ligands and waters around the Mg. I'm not sure if you've been struggling with a similar problem. There is probably a non-GUI way of running ReadySet (phenix.ready_set - maybe?). I was unable to find out from my log files where the ideal values in the .metal.edits file come from but they look consistent with those reported in Harding, Small revisions to predicted distances around metal sites in proteins, Acta Cryst. (2006). D62, 678–682. Genevieve Dr Genevieve Evans Laboratory of Structural Biology Maurice Wilkins Centre School of Biological Sciences University of Auckland From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Ivan Shabalin [shabali...@inbox.ru] Sent: Friday, 25 May 2012 5:58 a.m. To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] ligand geometry evaluation Dear all, I found that thread in my search of what ideal values for metal Phenix is using. I tried to use that command phenix.pdb_interpretation model.pdb write_geo_files=true for my pdb file, and I get all the values for most atoms, like: bond pdb= CB LEU B 332 segid=B pdb= CG LEU B 332 segid=B ideal model deltasigma weight residual 1.530 1.511 0.019 2.00e-02 2.50e+03 9.40e-01 but for Mg ions i did not find the ideal value: nonbonded pdb= O HOH C 405 pdb=MGMG M 1 model vdw 1.906 3.250 Can I specify some keywords to get it also for Mg? I looked through phenix folders and I found energy_lib.cif file. There are the following records for Mg: MG NPA metal 500.0002.090 . MG NPB metal 500.0002.090 . MG OHA metal 500.0002.150 . # ? MG OHB metal 500.0002.150 . # ? MG OHC metal 500.0002.150 . # ? MG Ometal 500.0002.180 . # ? Do I understand correctly, that these are actually the default values? If I use Phenix with default parameters, then distances will tend to become ideal? Especially at low resolution when X-ray weight is low? And what does mean, that for Mg there is no standard deviation of the bonds (. # ? is placed instead)? How phenix will handle it? will it assign some default esd? I appreciate any comments! Thanks a lot!! With best regards, Ivan Shabalin, Ph.D. Research Associate at Minor Lab, University of Virginia 4-224 Jordan Hall, 1340 Jefferson Park Ave. Charlottesville, VA 22908
Re: [ccp4bb] sigma levels of averaged maps in coot ( or e/A3)
I'm afraid I seriously mistrust the sigma and e/A^3 numbers reported by Coot for ncs averaged maps. I work with a crystal with near perfect 6-fold ncs and the e/A^3 numbers make no sense. For a 2Fo-Fc style map the e/A^3 values should be nearly the same after as before. They are not. The sigma of an averaged map has a definitional problem - what is the volume to normalized over. With a map with crystal symmetry the answer is pretty clear, use the asymmetric unit. The asymmetric unit of an averaged map will be the least-common-multiple of the rotated unit cells and could easily measure in hundreds if not thousands of unit cells. Not very practical and not very useful. Paul says that he normalizes over a box, which is the easy way out, but I don't believe it has any statistical meaning. The box will contain some parts of the ncs asymmetric unit multiple times, and include some cs related regions. My opinion is that the e/A^3 calculation for ncs averaged density in Coot is broken. (I have not used the daily-build version, just the stable releases, but none have worked in my hands for years.) I usually contour an unaveraged map at my desired level, and then adjust the averaged map so that it mostly matches those contours. If your ncs is less perfect this will not work as well for you. Dale Tronrud On 6/6/2012 2:20 PM, Paul Emsley wrote: On 06/06/12 21:47, Ursula Schulze-Gahmen wrote: I calculated threefold averaged omit maps in coot. These maps look nice and clean, but I am having trouble making sense of the displayed sigma levels or e/A3 values. When I display the unaveraged and averaged maps at a similar density level for the protein the unaveraged map is at 0.024 e/A3 and 2.7 sigma, while the averaged map is displayed at 0.0016e/A3 and 7.6 sigma. I read the previous discussion about this issue where it was recommended to rely on the e/A3 values for comparison, but even that doesn't seem to work in this case. Don't forget that in one case you are looking at a whole map and in the other (an average of) maps generated from a box encapsulating each chain. I wouldn't stress if I were you... Paul.
[ccp4bb] a question on presenting 3-D crystal structure in the paper
Dear All, I want to use dash line to present the salt bridge in a crystal structure in the paper publication, for example the salt bridge formed between Glu (OE1 and OE2) and Lys (terminal N). Do you suggest I only draw a single dashed line between the terminal N of the Lys and the closer atom to N among the Glu OE1 and Glu OE2 in the final publication, or in the final publication I will have 2 dashed lines, one is between terminal N of Lys and OE1 of the Glu, the other is between terminal N of Lys and OE2 of the Glu, supposing the distance of both the 2 dash lines are within the acceptable range for salt bridge? I am looking forward to getting a reply from you. Cheers, Acoot
