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 > 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?
>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 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?
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 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?
I can only confirm what Alex said. And the structure was neither a globin or zyme or psin! Victor Quoting aaleshin : 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 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?
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?
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?
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] 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" 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?
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?
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 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.)
> 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 >
> > 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?
>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 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.)
> 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 >
> > 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?
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
> 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?
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.)
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
> 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] 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 mailto: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?
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
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] 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 mailto: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.net<mailto: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<mailto: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?
Richard Dickerson's book is relevant and gripping reading http://www.amazon.com/gp/product/0878931686?ie=UTF8&tag=brscrystallot-20&lin kCode=as2&camp=1789&creative=9325&creativeASIN=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?
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 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?
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?
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?
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?
...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?
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?
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?
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?
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 > 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?
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 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?
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?
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?
> 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?
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 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?
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 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?
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) >
[ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?
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)
