Re: [ccp4bb] MAD data process problem
Thank you very much for your reply. In my own understanding, We collect the peak dataset, because of the large F'', and we can get strong anomalous signal. We collect the edge dataset, because of the large F', and combined with the remote dataset, we can use the method just like SIR to get some information about the phase. so I think for peak dataset, anomalous processing is necessary, and for edge and remote dataset, anomalous processing is not necessary. Is my understanding correct? Thank you very much for your help. Best wish, Qixu Cai 2012/5/29 Tim Gruene t...@shelx.uni-ac.gwdg.de -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Qixu Cai, MAD phasing is based on the comparison of Bijvoet-pairs, i.e. I(hkl) with I(-h-k-l), both within one data set and between data sets. Therefore you might get better results if your integration program does not assume Friedel-pairs to have identical intensities, even though the difference is probably only marginal (integration programs do not merge data). So it is safest click on 'anomalous' for all data sets involved . Tim On 05/29/12 11:11, Qixu Cai wrote: Dear all, Sorry for the question from MAD beginner. When we process the MAD datasets, including the peak-data, edge-data and remote-data, which datasets need to be process with anomalous? I know peak-data obviously need data processing with anomalous, but what about edge-data and remote-data when we want to use MAD method? Thank you very much! Best wishes, Qixu Cai - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPxJfaUxlJ7aRr7hoRAm3EAKCKkyvT8z0wg6MFjflkHkiq8RR5GQCgyvF3 lOIOLypSzCcN3N6OR/3NcC8= =m6ax -END PGP SIGNATURE-
Re: [ccp4bb] MAD data process problem
Hi, you are right, the peak dataset corresponds to the highest f'' value. However, this does not mean that f'' is null for the other wavelengthes... you still have significant anomalous signal at the edge and for the high energy remote wavelength... this will help your phasing, so use it ! As Tim mentionned it : process all wavelength with anomalous switched on ! laurent Le 30/05/2012 07:59, Qixu Cai a écrit : Thank you very much for your reply. In my own understanding, We collect the peak dataset, because of the large F'', and we can get strong anomalous signal. We collect the edge dataset, because of the large F', and combined with the remote dataset, we can use the method just like SIR to get some information about the phase. so I think for peak dataset, anomalous processing is necessary, and for edge and remote dataset, anomalous processing is not necessary. Is my understanding correct? Thank you very much for your help. Best wish, Qixu Cai 2012/5/29 Tim Gruene t...@shelx.uni-ac.gwdg.de mailto:t...@shelx.uni-ac.gwdg.de -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Qixu Cai, MAD phasing is based on the comparison of Bijvoet-pairs, i.e. I(hkl) with I(-h-k-l), both within one data set and between data sets. Therefore you might get better results if your integration program does not assume Friedel-pairs to have identical intensities, even though the difference is probably only marginal (integration programs do not merge data). So it is safest click on 'anomalous' for all data sets involved . Tim On 05/29/12 11:11, Qixu Cai wrote: Dear all, Sorry for the question from MAD beginner. When we process the MAD datasets, including the peak-data, edge-data and remote-data, which datasets need to be process with anomalous? I know peak-data obviously need data processing with anomalous, but what about edge-data and remote-data when we want to use MAD method? Thank you very much! Best wishes, Qixu Cai - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPxJfaUxlJ7aRr7hoRAm3EAKCKkyvT8z0wg6MFjflkHkiq8RR5GQCgyvF3 lOIOLypSzCcN3N6OR/3NcC8= =m6ax -END PGP SIGNATURE- -- -- Laurent Maveyraud laurent.maveyraud AT ipbs DOT fr Université Paul Sabatier / CNRS / I.P.B.S. UMR 5089 PICT -- Plateforme Intégrée de Criblage de Toulouse Département BiologieStructurale et Biophysique BP 64182 - 205 rte de Narbonne - 31077 TOULOUSE FRANCE Tél: +33 (0)561 175 435 Fax : +33 (0)561 175 994 --
Re: [ccp4bb] MAD data process problem
Dear Qixu Cai, The following paper should be informative for your query:- http://dx.doi.org/10.1107/S0909049595013288 Best wishes, John Prof John R Helliwell DSc On 29 May 2012, at 10:11, Qixu Cai caiq...@gmail.com wrote: Dear all, Sorry for the question from MAD beginner. When we process the MAD datasets, including the peak-data, edge-data and remote-data, which datasets need to be process with anomalous? I know peak-data obviously need data processing with anomalous, but what about edge-data and remote-data when we want to use MAD method? Thank you very much! Best wishes, Qixu Cai
[ccp4bb] MAD data process problem
Dear all, Sorry for the question from MAD beginner. When we process the MAD datasets, including the peak-data, edge-data and remote-data, which datasets need to be process with anomalous? I know peak-data obviously need data processing with anomalous, but what about edge-data and remote-data when we want to use MAD method? Thank you very much! Best wishes, Qixu Cai
Re: [ccp4bb] MAD data process problem
Hi, when processing MAD data, all wavelength should be processed without enforcing the Friedel's law... If you look at your fluorescence spectrum, you will see that you have anomalous signal for the peak (obviously) for the high energy remote and even forh the inflexion point. For example, in the case of Se-MAD : peak : f'=-6, f''-8 inflexion : f'=-11, f''= 4 high remote : f'= -4, f''= 4 the low energy remote is the one with the weakest anamalous signal, close to 0 in the case of Se... hope this helps laurent Le 29/05/2012 11:11, Qixu Cai a écrit : Dear all, Sorry for the question from MAD beginner. When we process the MAD datasets, including the peak-data, edge-data and remote-data, which datasets need to be process with anomalous? I know peak-data obviously need data processing with anomalous, but what about edge-data and remote-data when we want to use MAD method? Thank you very much! Best wishes, Qixu Cai -- -- Laurent Maveyraud laurent.maveyraud AT ipbs DOT fr Université Paul Sabatier / CNRS / I.P.B.S. UMR 5089 PICT -- Plateforme Intégrée de Criblage de Toulouse Département BiologieStructurale et Biophysique BP 64182 - 205 rte de Narbonne - 31077 TOULOUSE FRANCE Tél: +33 (0)561 175 435 Fax : +33 (0)561 175 994 --
Re: [ccp4bb] MAD data process problem
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Qixu Cai, MAD phasing is based on the comparison of Bijvoet-pairs, i.e. I(hkl) with I(-h-k-l), both within one data set and between data sets. Therefore you might get better results if your integration program does not assume Friedel-pairs to have identical intensities, even though the difference is probably only marginal (integration programs do not merge data). So it is safest click on 'anomalous' for all data sets involved . Tim On 05/29/12 11:11, Qixu Cai wrote: Dear all, Sorry for the question from MAD beginner. When we process the MAD datasets, including the peak-data, edge-data and remote-data, which datasets need to be process with anomalous? I know peak-data obviously need data processing with anomalous, but what about edge-data and remote-data when we want to use MAD method? Thank you very much! Best wishes, Qixu Cai - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFPxJfaUxlJ7aRr7hoRAm3EAKCKkyvT8z0wg6MFjflkHkiq8RR5GQCgyvF3 lOIOLypSzCcN3N6OR/3NcC8= =m6ax -END PGP SIGNATURE-
Re: [ccp4bb] MAD
Hi Peter
You are right: the location of the prism experiment is most likely the
study at Woolsthorpe, e.g. see
http://www.isaacnewton.org.uk/texts/OfColours7 . Newton was admitted
to Trinity College in 1661 as a 'sizar' (a paid part-time student
employed by the College) but was forced to return to Woolsthorpe (the
family home) in August 1665 (http://www.isaacnewton.org.uk/Chronology)
to continue studying privately, because the University closed
temporarily as a precaution against the Great Plague ('Black Death')
which was spreading outwards from the initial outbreak in this country
in the London Docklands during the summer of that year. He returned
to Trinity in 1667 as a Fellow of the College.
So I should have been more precise and said that Newton performed the
prism experiment during the time that he was associated with Trinity
(it's not clear what the nature of his association with Trinity was
during the 2 years he spent doing experiments at Woolsthorpe).
Cheers
-- Ian
On 28 January 2012 09:35, Peter Moody pcem1bigfi...@gmail.com wrote:
Ian,
If you visit Isaac Newton's old home at Woolsthorpe (near here) you will see
a conflicting claim for location of the classic prism experiment. You will
also find an apple tree in the garden, but that is another story..
Peter
PS this is my special ccp4bb email account, it doesn't always get the
attention it deserves.
On 19 January 2012 17:50, Ian Tickle ianj...@gmail.com wrote:
Perhaps I could chime in with a bit of history as I understand it.
The term 'dispersion' in optics, as everyone who knows their history
is aware of, refers to the classic experiment by Sir Isaac Newton at
Trinity College here in Cambridge where he observed white light being
split up ('dispersed') into its component colours by a prism. This is
of course due to the variation in refractive index of glass with
wavelength, so then we arrive at the usual definition of optical
dispersion as dn/dlambda, i.e. the first derivative of the refractive
index with respect to the wavelength.
Now the refractive index of an average crystal at around 1 Ang
wavelength differs by about 1 part in a million from 1, however it can
be determined by very careful and precise interferometric experiments.
It's safe to say therefore that the dispersion of X-rays (anomalous
or otherwise) has no measurable effect whatsoever as far as the
average X-ray diffraction experiment (SAD, MAD or otherwise) is
concerned. The question then is how did the term 'anomalous
dispersion' get to be applied to X-ray diffraction? The answer is
that it turns out that the equation ('Kramer-Kronig relationship')
governing X-ray scattering is completely analogous to that governing
optical dispersion, so it's legitimate to use the term 'dispersive'
(meaning 'analogous to dispersion') for the real part of the
wavelength-dependent component of the X-ray scattering factor, because
the real part of the refractive index is what describes dispersion
(the imaginary part in both cases describes absorption).
So then from 'dispersive' to 'dispersion' to describe the wavelength
dependence of X-ray scattering is only a short step, even though it
only behaves _like_ dispersion in its dependence on wavelength.
However having two different meanings for the same word can get
confusing and clearly should be avoided if at all possible.
So what does this have to do with the MAD acronym? I think it stemmed
from a visit by Wayne Hendrickson to Birkbeck in London some time
around 1990: he was invited by Tom Blundell to give a lecture on his
MAD experiments. At that time Wayne called it multi-wavelength
anomalous dispersion. Tom pointed out that this was really a misnomer
for the reasons I've elucidated above. Wayne liked the MAD acronym
and wanted to keep it so he needed a replacement term starting with D
and diffraction was the obvious choice, and if you look at the
literature from then on Wayne at least consistently called it
multi-wavelength anomalous diffraction.
Cheers
-- Ian
On 18 January 2012 18:23, Phil Jeffrey pjeff...@princeton.edu wrote:
Can I be dogmatic about this ?
Multiwavelength anomalous diffraction from Hendrickson (1991) Science
Vol.
254 no. 5028 pp. 51-58
Multiwavelength anomalous diffraction (MAD) from the CCP4 proceedings
http://www.ccp4.ac.uk/courses/proceedings/1997/j_smith/main.html
Multi-wavelength anomalous-diffraction (MAD) from Terwilliger Acta
Cryst.
(1994). D50, 11-16
etc.
I don't see where the problem lies:
a SAD experiment is a single wavelength experiment where you are using
the
anomalous/dispersive signals for phasing
a MAD experiment is a multiple wavelength version of SAD. Hopefully one
picks an appropriate range of wavelengths for whatever complex case one
has.
One can have SAD and MAD datasets that exploit anomalous/dispersive
signals
from multiple difference sources. This after all is one of
Re: [ccp4bb] MAD
For the history buffs and crystallographers needing some RR and chill-out,
an interesting historic fiction read about the era of Newton and Leibnitz
and the foundation of the Royal Society is the Baroque cycle by Neil
Stevenson.
http://en.wikipedia.org/wiki/The_Baroque_Cycle
Cryptonomicon, although written before, picks up a descendent of a character
from the Cycle, and can be considered imho the 4th book
http://en.wikipedia.org/wiki/Cryptonomicon
All together ~ 2400 pages. Cheap on Amazon 3rd party. Book a long vacation.
Best, BR
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ian
Tickle
Sent: Sunday, January 29, 2012 5:23 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] MAD
Hi Peter
You are right: the location of the prism experiment is most likely the study
at Woolsthorpe, e.g. see
http://www.isaacnewton.org.uk/texts/OfColours7 . Newton was admitted to
Trinity College in 1661 as a 'sizar' (a paid part-time student employed by
the College) but was forced to return to Woolsthorpe (the family home) in
August 1665 (http://www.isaacnewton.org.uk/Chronology)
to continue studying privately, because the University closed temporarily as
a precaution against the Great Plague ('Black Death') which was spreading
outwards from the initial outbreak in this country in the London Docklands
during the summer of that year. He returned to Trinity in 1667 as a Fellow
of the College.
So I should have been more precise and said that Newton performed the prism
experiment during the time that he was associated with Trinity (it's not
clear what the nature of his association with Trinity was during the 2 years
he spent doing experiments at Woolsthorpe).
Cheers
-- Ian
On 28 January 2012 09:35, Peter Moody pcem1bigfi...@gmail.com wrote:
Ian,
If you visit Isaac Newton's old home at Woolsthorpe (near here) you
will see a conflicting claim for location of the classic prism
experiment. You will also find an apple tree in the garden, but that is
another story..
Peter
PS this is my special ccp4bb email account, it doesn't always get the
attention it deserves.
On 19 January 2012 17:50, Ian Tickle ianj...@gmail.com wrote:
Perhaps I could chime in with a bit of history as I understand it.
The term 'dispersion' in optics, as everyone who knows their history
is aware of, refers to the classic experiment by Sir Isaac Newton at
Trinity College here in Cambridge where he observed white light being
split up ('dispersed') into its component colours by a prism. This
is of course due to the variation in refractive index of glass with
wavelength, so then we arrive at the usual definition of optical
dispersion as dn/dlambda, i.e. the first derivative of the refractive
index with respect to the wavelength.
Now the refractive index of an average crystal at around 1 Ang
wavelength differs by about 1 part in a million from 1, however it
can be determined by very careful and precise interferometric
experiments.
It's safe to say therefore that the dispersion of X-rays (anomalous
or otherwise) has no measurable effect whatsoever as far as the
average X-ray diffraction experiment (SAD, MAD or otherwise) is
concerned. The question then is how did the term 'anomalous
dispersion' get to be applied to X-ray diffraction? The answer is
that it turns out that the equation ('Kramer-Kronig relationship')
governing X-ray scattering is completely analogous to that governing
optical dispersion, so it's legitimate to use the term 'dispersive'
(meaning 'analogous to dispersion') for the real part of the
wavelength-dependent component of the X-ray scattering factor,
because the real part of the refractive index is what describes
dispersion (the imaginary part in both cases describes absorption).
So then from 'dispersive' to 'dispersion' to describe the wavelength
dependence of X-ray scattering is only a short step, even though it
only behaves _like_ dispersion in its dependence on wavelength.
However having two different meanings for the same word can get
confusing and clearly should be avoided if at all possible.
So what does this have to do with the MAD acronym? I think it
stemmed from a visit by Wayne Hendrickson to Birkbeck in London some
time around 1990: he was invited by Tom Blundell to give a lecture on
his MAD experiments. At that time Wayne called it multi-wavelength
anomalous dispersion. Tom pointed out that this was really a
misnomer for the reasons I've elucidated above. Wayne liked the MAD
acronym and wanted to keep it so he needed a replacement term
starting with D and diffraction was the obvious choice, and if you
look at the literature from then on Wayne at least consistently
called it multi-wavelength anomalous diffraction.
Cheers
-- Ian
On 18 January 2012 18:23, Phil Jeffrey pjeff...@princeton.edu wrote:
Can I be dogmatic about this ?
Multiwavelength anomalous diffraction from
Re: [ccp4bb] MAD
Ian,
If you visit Isaac Newton's old home at Woolsthorpe (near here) you will
see a conflicting claim for location of the classic prism experiment. You
will also find an apple tree in the garden, but that is another story..
Peter
PS this is my special ccp4bb email account, it doesn't always get the
attention it deserves.
On 19 January 2012 17:50, Ian Tickle ianj...@gmail.com wrote:
Perhaps I could chime in with a bit of history as I understand it.
The term 'dispersion' in optics, as everyone who knows their history
is aware of, refers to the classic experiment by Sir Isaac Newton at
Trinity College here in Cambridge where he observed white light being
split up ('dispersed') into its component colours by a prism. This is
of course due to the variation in refractive index of glass with
wavelength, so then we arrive at the usual definition of optical
dispersion as dn/dlambda, i.e. the first derivative of the refractive
index with respect to the wavelength.
Now the refractive index of an average crystal at around 1 Ang
wavelength differs by about 1 part in a million from 1, however it can
be determined by very careful and precise interferometric experiments.
It's safe to say therefore that the dispersion of X-rays (anomalous
or otherwise) has no measurable effect whatsoever as far as the
average X-ray diffraction experiment (SAD, MAD or otherwise) is
concerned. The question then is how did the term 'anomalous
dispersion' get to be applied to X-ray diffraction? The answer is
that it turns out that the equation ('Kramer-Kronig relationship')
governing X-ray scattering is completely analogous to that governing
optical dispersion, so it's legitimate to use the term 'dispersive'
(meaning 'analogous to dispersion') for the real part of the
wavelength-dependent component of the X-ray scattering factor, because
the real part of the refractive index is what describes dispersion
(the imaginary part in both cases describes absorption).
So then from 'dispersive' to 'dispersion' to describe the wavelength
dependence of X-ray scattering is only a short step, even though it
only behaves _like_ dispersion in its dependence on wavelength.
However having two different meanings for the same word can get
confusing and clearly should be avoided if at all possible.
So what does this have to do with the MAD acronym? I think it stemmed
from a visit by Wayne Hendrickson to Birkbeck in London some time
around 1990: he was invited by Tom Blundell to give a lecture on his
MAD experiments. At that time Wayne called it multi-wavelength
anomalous dispersion. Tom pointed out that this was really a misnomer
for the reasons I've elucidated above. Wayne liked the MAD acronym
and wanted to keep it so he needed a replacement term starting with D
and diffraction was the obvious choice, and if you look at the
literature from then on Wayne at least consistently called it
multi-wavelength anomalous diffraction.
Cheers
-- Ian
On 18 January 2012 18:23, Phil Jeffrey pjeff...@princeton.edu wrote:
Can I be dogmatic about this ?
Multiwavelength anomalous diffraction from Hendrickson (1991) Science
Vol.
254 no. 5028 pp. 51-58
Multiwavelength anomalous diffraction (MAD) from the CCP4 proceedings
http://www.ccp4.ac.uk/courses/proceedings/1997/j_smith/main.html
Multi-wavelength anomalous-diffraction (MAD) from Terwilliger Acta Cryst.
(1994). D50, 11-16
etc.
I don't see where the problem lies:
a SAD experiment is a single wavelength experiment where you are using
the
anomalous/dispersive signals for phasing
a MAD experiment is a multiple wavelength version of SAD. Hopefully one
picks an appropriate range of wavelengths for whatever complex case one
has.
One can have SAD and MAD datasets that exploit anomalous/dispersive
signals
from multiple difference sources. This after all is one of the things
that
SHARP is particularly good at accommodating.
If you're not using the anomalous/dispersive signals for phasing, you're
collecting native data. After all C,N,O,S etc all have a small anomalous
signal at all wavelengths, and metalloproteins usually have even larger
signals so the mere presence of a theoretical d difference does not
make it
a SAD dataset. ALL datasets contain some anomalous/dispersive signals,
most
of the time way down in the noise.
Phil Jeffrey
Princeton
On 1/18/12 12:48 PM, Francis E Reyes wrote:
Using the terms 'MAD' and 'SAD' have always been confusing to me when
considering more complex phasing cases. What happens if you have
intrinsic
Zn's, collect a 3wvl experiment and then derivatize it with SeMet or a
heavy
atom? Or the MAD+native scenario (SHARP) ?
Instead of using MAD/SAD nomenclature I favor explicitly stating whether
dispersive/anomalous/isomorphous differences (and what heavy atoms for
each
) were used in phasing. Aren't analyzing the differences (independent
Re: [ccp4bb] MAD
Good description from Ian complemented by an amusing aside from Peter.
One small point. Ian says
The answer is that it turns out that the equation ('Kramer-Kronig
relationship')
governing X-ray scattering is completely analogous to that governing
optical dispersion,
Analogous implies the phenomena are separate. In fact one can derive the
refractive indices from the atomic scattering factors. See for example
http://xdb.lbl.gov/Section1/Sec_1-7.pdf
Particularly equation 1.
Colin
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Peter
Moody
Sent: 28 January 2012 09:35
To: ccp4bb
Subject: Re: [ccp4bb] MAD
Ian,
If you visit Isaac Newton's old home at Woolsthorpe (near here) you will see a
conflicting claim for location of the classic prism experiment. You will also
find an apple tree in the garden, but that is another story..
Peter
PS this is my special ccp4bb email account, it doesn't always get the attention
it deserves.
On 19 January 2012 17:50, Ian Tickle
ianj...@gmail.commailto:ianj...@gmail.com wrote:
Perhaps I could chime in with a bit of history as I understand it.
The term 'dispersion' in optics, as everyone who knows their history
is aware of, refers to the classic experiment by Sir Isaac Newton at
Trinity College here in Cambridge where he observed white light being
split up ('dispersed') into its component colours by a prism. This is
of course due to the variation in refractive index of glass with
wavelength, so then we arrive at the usual definition of optical
dispersion as dn/dlambda, i.e. the first derivative of the refractive
index with respect to the wavelength.
Now the refractive index of an average crystal at around 1 Ang
wavelength differs by about 1 part in a million from 1, however it can
be determined by very careful and precise interferometric experiments.
It's safe to say therefore that the dispersion of X-rays (anomalous
or otherwise) has no measurable effect whatsoever as far as the
average X-ray diffraction experiment (SAD, MAD or otherwise) is
concerned. The question then is how did the term 'anomalous
dispersion' get to be applied to X-ray diffraction? The answer is
that it turns out that the equation ('Kramer-Kronig relationship')
governing X-ray scattering is completely analogous to that governing
optical dispersion, so it's legitimate to use the term 'dispersive'
(meaning 'analogous to dispersion') for the real part of the
wavelength-dependent component of the X-ray scattering factor, because
the real part of the refractive index is what describes dispersion
(the imaginary part in both cases describes absorption).
So then from 'dispersive' to 'dispersion' to describe the wavelength
dependence of X-ray scattering is only a short step, even though it
only behaves _like_ dispersion in its dependence on wavelength.
However having two different meanings for the same word can get
confusing and clearly should be avoided if at all possible.
So what does this have to do with the MAD acronym? I think it stemmed
from a visit by Wayne Hendrickson to Birkbeck in London some time
around 1990: he was invited by Tom Blundell to give a lecture on his
MAD experiments. At that time Wayne called it multi-wavelength
anomalous dispersion. Tom pointed out that this was really a misnomer
for the reasons I've elucidated above. Wayne liked the MAD acronym
and wanted to keep it so he needed a replacement term starting with D
and diffraction was the obvious choice, and if you look at the
literature from then on Wayne at least consistently called it
multi-wavelength anomalous diffraction.
Cheers
-- Ian
On 18 January 2012 18:23, Phil Jeffrey
pjeff...@princeton.edumailto:pjeff...@princeton.edu wrote:
Can I be dogmatic about this ?
Multiwavelength anomalous diffraction from Hendrickson (1991) Science Vol.
254 no. 5028 pp. 51-58
Multiwavelength anomalous diffraction (MAD) from the CCP4 proceedings
http://www.ccp4.ac.uk/courses/proceedings/1997/j_smith/main.html
Multi-wavelength anomalous-diffraction (MAD) from Terwilliger Acta Cryst.
(1994). D50, 11-16
etc.
I don't see where the problem lies:
a SAD experiment is a single wavelength experiment where you are using the
anomalous/dispersive signals for phasing
a MAD experiment is a multiple wavelength version of SAD. Hopefully one
picks an appropriate range of wavelengths for whatever complex case one has.
One can have SAD and MAD datasets that exploit anomalous/dispersive signals
from multiple difference sources. This after all is one of the things that
SHARP is particularly good at accommodating.
If you're not using the anomalous/dispersive signals for phasing, you're
collecting native data. After all C,N,O,S etc all have a small anomalous
signal at all wavelengths, and metalloproteins usually have even larger
signals so the mere presence of a theoretical d difference does not make it
a SAD dataset. ALL datasets contain some anomalous/dispersive signals, most
Re: [ccp4bb] MAD
Dear Colleagues,
The real issue is the 'anomalous' word introduced as an X-ray scattering theory
correction, which was not anomalous but the actual physical situation of
resonance scattering. Thus the most recent of the Anomalous Scattering
conferences was correctly called REXS2011. Ie Resonant Elastic X-ray
Scattering.
The 1975 Anomalous Scattering Conference book incidentally has the Hoppe and
Jakubowski Ni and Co K alpha two wavelength study either side of the Fe K edge
for phase determination of the erythrocruorin protein, in turn based on the
Okaya and Pepinsky 1956 formalism. These are MAD but 'simply' not synchrotron.
Francis Crick's autobiography 'What Mad Pursuit' will give you a further link
to MAD, based on weak ie small intensity changes.
Just to also mention I regularly refer to the 'Hendrickson Se-met MAD' method.
The history is interesting. Keith Hodgson is a must mention name, as is
Stanford Synchrotron Radiation Laboratory.
A most recent wrinkle in nomenclature in this area is the use in chemical
crystallography by some of Resonant scattering for off resonance ie in
determining the hand of organics. At present I see no way around correcting
such mentions but with the unfortunate term:-
Off-resonance resonance scattering Flack parameter determination of the hand.
Greetings,
John
Prof John R Helliwell DSc
On 19 Jan 2012, at 17:50, Ian Tickle ianj...@gmail.com wrote:
Perhaps I could chime in with a bit of history as I understand it.
The term 'dispersion' in optics, as everyone who knows their history
is aware of, refers to the classic experiment by Sir Isaac Newton at
Trinity College here in Cambridge where he observed white light being
split up ('dispersed') into its component colours by a prism. This is
of course due to the variation in refractive index of glass with
wavelength, so then we arrive at the usual definition of optical
dispersion as dn/dlambda, i.e. the first derivative of the refractive
index with respect to the wavelength.
Now the refractive index of an average crystal at around 1 Ang
wavelength differs by about 1 part in a million from 1, however it can
be determined by very careful and precise interferometric experiments.
It's safe to say therefore that the dispersion of X-rays (anomalous
or otherwise) has no measurable effect whatsoever as far as the
average X-ray diffraction experiment (SAD, MAD or otherwise) is
concerned. The question then is how did the term 'anomalous
dispersion' get to be applied to X-ray diffraction? The answer is
that it turns out that the equation ('Kramer-Kronig relationship')
governing X-ray scattering is completely analogous to that governing
optical dispersion, so it's legitimate to use the term 'dispersive'
(meaning 'analogous to dispersion') for the real part of the
wavelength-dependent component of the X-ray scattering factor, because
the real part of the refractive index is what describes dispersion
(the imaginary part in both cases describes absorption).
So then from 'dispersive' to 'dispersion' to describe the wavelength
dependence of X-ray scattering is only a short step, even though it
only behaves _like_ dispersion in its dependence on wavelength.
However having two different meanings for the same word can get
confusing and clearly should be avoided if at all possible.
So what does this have to do with the MAD acronym? I think it stemmed
from a visit by Wayne Hendrickson to Birkbeck in London some time
around 1990: he was invited by Tom Blundell to give a lecture on his
MAD experiments. At that time Wayne called it multi-wavelength
anomalous dispersion. Tom pointed out that this was really a misnomer
for the reasons I've elucidated above. Wayne liked the MAD acronym
and wanted to keep it so he needed a replacement term starting with D
and diffraction was the obvious choice, and if you look at the
literature from then on Wayne at least consistently called it
multi-wavelength anomalous diffraction.
Cheers
-- Ian
On 18 January 2012 18:23, Phil Jeffrey pjeff...@princeton.edu wrote:
Can I be dogmatic about this ?
Multiwavelength anomalous diffraction from Hendrickson (1991) Science Vol.
254 no. 5028 pp. 51-58
Multiwavelength anomalous diffraction (MAD) from the CCP4 proceedings
http://www.ccp4.ac.uk/courses/proceedings/1997/j_smith/main.html
Multi-wavelength anomalous-diffraction (MAD) from Terwilliger Acta Cryst.
(1994). D50, 11-16
etc.
I don't see where the problem lies:
a SAD experiment is a single wavelength experiment where you are using the
anomalous/dispersive signals for phasing
a MAD experiment is a multiple wavelength version of SAD. Hopefully one
picks an appropriate range of wavelengths for whatever complex case one has.
One can have SAD and MAD datasets that exploit anomalous/dispersive signals
from multiple difference sources. This after all is one of the things that
SHARP is particularly good at
Re: [ccp4bb] MAD
For those of you interested, the reply to Tassos' question can be found here: http://www.iucr.org/resources/commissions/crystallographic-computing/schools/school96/ccp4-program-system (on-line) as well as here, http://www.*ccp4*.ac.uk/manual.ps (a ps file). McLaughlin, Terry and Zelinka. And yes, I'm over 40 ! I have also dealt with LCF files... Fred. Anastassis Perrakis wrote: A, yes, inventor's names. Anyone reading who is less than 40 and knows what MTZ stands for? ;-) My favorite technique remains SADDAM - a side product of Gerard's War On Error, that never did catch-up with the masses - experimentally or as an acronym. A. On 19 Jan 2012, at 21:51, Petr Leiman wrote: It would be so much more convenient to call these techniques (MAD, SAD, etc.) by their inventor's name. This would simplify things immensely simultaneously eliminating CCP4BB MADisagreements. Although in our days of copyrights wars, the journals and perhaps conferences where these methods were presented for the first time would insist on using their names as part of the method's name... Petr On Jan 19, 2012, at 7:42 PM, Ethan Merritt wrote: On Thursday, 19 January 2012, Ian Tickle wrote: So what does this have to do with the MAD acronym? I think it stemmed from a visit by Wayne Hendrickson to Birkbeck in London some time around 1990: he was invited by Tom Blundell to give a lecture on his MAD experiments. At that time Wayne called it multi-wavelength anomalous dispersion. Tom pointed out that this was really a misnomer for the reasons I've elucidated above. Wayne liked the MAD acronym and wanted to keep it so he needed a replacement term starting with D and diffraction was the obvious choice, and if you look at the literature from then on Wayne at least consistently called it multi-wavelength anomalous diffraction. Ian: The change-over from dispersion to diffraction in MAD protein crystallography happened a couple of years earlier, at least with regard to work being done at SSRL. I think the last paper using the term dispersion was the 1988 Lamprey hemoglobin paper. The next two papers, one a collaboration with Wayne's group and the other a collaboration with Hans Freeman's group, used the term diffraction. WA Hendrickson, JL Smith, RP Phizackerley, EA Merritt. Crystallographic structure-analysis of lamprey hemoglobin from anomalous dispersion of synchrotron radiation. PROTEINS-STRUCTURE FUNCTION AND GENETICS, 4(2):77–88, 1988. JM Guss, EA Merritt, RP Phizackerley, B Hedman, M Murata, KO Hodgson, HC Freeman. Phase determination by multiple-wavelength X-ray-diffraction - crystal-structure of a basic blue copper protein from cucumbers. SCIENCE, 241(4867):806–811, AUG 12 1988. WA Hendrickson, A Pahler, JL Smith, Y Satow, EA Merritt, RP Phizackerley. Crystal structure of core streptavidin determined from multiwavelength anomalous diffraction of synchrotron radiation. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 86(7):2190–2194, APR 1989. On the other hand, David and Lilo Templeton continued to use the term anomalous dispersion for at least another decade, describing their diffraction experiments exploring polarization effects and other characteristics of near-edge X-ray scattering by elements all over the periodic table. Ethan Cheers -- Ian On 18 January 2012 18:23, Phil Jeffrey pjeff...@princeton.edu wrote: Can I be dogmatic about this ? Multiwavelength anomalous diffraction from Hendrickson (1991) Science Vol. 254 no. 5028 pp. 51-58 Multiwavelength anomalous diffraction (MAD) from the CCP4 proceedings http://www.ccp4.ac.uk/courses/proceedings/1997/j_smith/main.html Multi-wavelength anomalous-diffraction (MAD) from Terwilliger Acta Cryst. (1994). D50, 11-16 etc. I don't see where the problem lies: a SAD experiment is a single wavelength experiment where you are using the anomalous/dispersive signals for phasing a MAD experiment is a multiple wavelength version of SAD. Hopefully one picks an appropriate range of wavelengths for whatever complex case one has. One can have SAD and MAD datasets that exploit anomalous/dispersive signals from multiple difference sources. This after all is one of the things that SHARP is particularly good at accommodating. If you're not using the anomalous/dispersive signals for phasing, you're collecting native data. After all C,N,O,S etc all have a small anomalous signal at all wavelengths, and metalloproteins usually have even larger signals so the mere presence of a theoretical d difference does not make it a SAD dataset. ALL datasets contain some anomalous/dispersive signals, most of the time way down in the noise. Phil Jeffrey Princeton On 1/18/12 12:48 PM, Francis E Reyes wrote: Using the terms 'MAD' and 'SAD' have always been confusing to me when considering more complex phasing cases. What happens if you have
[ccp4bb] MAD
As a self-declared MAD Scientist I suppose I should chime in. The acronym MAD has indeed appeared by several different names in the literature. Here is the Google vote: multiwavelength anomalous diffraction - 16500 articles in Google Scholar (including Yang et. al. (1990)) multiwavelength anomalous dispersion - 6890 articles multiple anomalous dispersion - 3250 articles multiple anomalous diffraction - 956 articles multiple anomalous difference - 3 articles Clearly, there are thousands of publications that have gotten this wrong, but which thousands is uncertain. I fully understand that Google Scholar is not the final authority on ... anything, and popular vote is not always the best way to settle scientific naming conventions either. For example, I am still calling Pluto a planet. I am also never going to call San Francisco's Candlestick Park by any of its new names (3COM Park, Monster Park, and now back to Candlestick!). And the Artist Formerly Known as Prince was always Prince to me. The reason for my personal inertia about name changes is that I need to hear a scientifically compelling reason for them. Why do I care? Because the scientific literature is supposed to be archival, and as a scholar who often finds himself going through this archive trying to find the original reference for various things, I find “nomenclature drift” endlessly infuriating. Then again, the name given by the originating author is not always the best name either. Nobody calls Patterson maps an F-square synthesis (as Patterson did). Oh, and although many lemmings do drown in big rivers and even the ocean, their legendary periodic mass suicide runs have been greatly exaggerated. A few years back, the Disney film crew who made the White Wilderness documentary admitted that the little guys did need some encouragement for the really good shots they wanted. So, it would appear that even lemmings have some sense in their tiny little heads? Do we? Does anyone have a scientifically compelling reason to call MAD something other than multiwavelength anomalous diffraction? -James Holton MAD Scientist On Wed, Jan 18, 2012 at 12:28 PM, Ethan Merritt merr...@u.washington.edu wrote: On Wednesday, 18 January 2012, Soisson, Stephen M wrote: But if we were to follow that convention we would have been stuck with Multi-wavelength Resonant Diffraction Experimental Results, or, quite simply, MuRDER. You could switch that to Multiple Energy Resonant Diffraction Experiment but I don't think that would help any. As to anomalous - the term comes from the behaviour of the derivative delta_(optical index) / delta_(wavelength) This term is positive nearly everywhere, but is anomalously negative at the absorption edge. Ethan -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob Keller Sent: Wednesday, January 18, 2012 3:13 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Merging data collected at two different wavelength This begs the question* whether you want the lemmings to understand you. One theory of language, gotten more or less from Strunk and White's Elements of Style, is that the most important feature of language is its transparency to the underlying thoughts. Bad language breaks the transparency, reminds you that you are reading and not simply thinking the thoughts of the author, who should also usually be invisible. Bad writing calls attention to itself and to the author, whereas good writing guides the thoughts of the reader unnoticeably. For Strunk and White, it seems that all rules of writing follow this principle, and it seems to be the right way to think about language. So, conventions, even when somewhat inaccurate, are important in that they are often more transparent, and the reader does not get stuck on them. Anyway, a case in point of lemmings is that once Wayne Hendrickson himself suggested that the term anomalous be decommissioned in favor of resonant. I don't hear any non-lemmings jumping on that bandwagon... JPK *Is this the right use of beg the question? On Wed, Jan 18, 2012 at 1:57 PM, Phoebe Rice pr...@uchicago.edu wrote: Can I be dogmatic about this ? I wish you could, but I don't think so, because even though those sources call it that, others don't. I agree with your thinking, but usage is usage. And 10,000 lemmings can't be wrong?
Re: [ccp4bb] MAD
Perhaps I could chime in with a bit of history as I understand it.
The term 'dispersion' in optics, as everyone who knows their history
is aware of, refers to the classic experiment by Sir Isaac Newton at
Trinity College here in Cambridge where he observed white light being
split up ('dispersed') into its component colours by a prism. This is
of course due to the variation in refractive index of glass with
wavelength, so then we arrive at the usual definition of optical
dispersion as dn/dlambda, i.e. the first derivative of the refractive
index with respect to the wavelength.
Now the refractive index of an average crystal at around 1 Ang
wavelength differs by about 1 part in a million from 1, however it can
be determined by very careful and precise interferometric experiments.
It's safe to say therefore that the dispersion of X-rays (anomalous
or otherwise) has no measurable effect whatsoever as far as the
average X-ray diffraction experiment (SAD, MAD or otherwise) is
concerned. The question then is how did the term 'anomalous
dispersion' get to be applied to X-ray diffraction? The answer is
that it turns out that the equation ('Kramer-Kronig relationship')
governing X-ray scattering is completely analogous to that governing
optical dispersion, so it's legitimate to use the term 'dispersive'
(meaning 'analogous to dispersion') for the real part of the
wavelength-dependent component of the X-ray scattering factor, because
the real part of the refractive index is what describes dispersion
(the imaginary part in both cases describes absorption).
So then from 'dispersive' to 'dispersion' to describe the wavelength
dependence of X-ray scattering is only a short step, even though it
only behaves _like_ dispersion in its dependence on wavelength.
However having two different meanings for the same word can get
confusing and clearly should be avoided if at all possible.
So what does this have to do with the MAD acronym? I think it stemmed
from a visit by Wayne Hendrickson to Birkbeck in London some time
around 1990: he was invited by Tom Blundell to give a lecture on his
MAD experiments. At that time Wayne called it multi-wavelength
anomalous dispersion. Tom pointed out that this was really a misnomer
for the reasons I've elucidated above. Wayne liked the MAD acronym
and wanted to keep it so he needed a replacement term starting with D
and diffraction was the obvious choice, and if you look at the
literature from then on Wayne at least consistently called it
multi-wavelength anomalous diffraction.
Cheers
-- Ian
On 18 January 2012 18:23, Phil Jeffrey pjeff...@princeton.edu wrote:
Can I be dogmatic about this ?
Multiwavelength anomalous diffraction from Hendrickson (1991) Science Vol.
254 no. 5028 pp. 51-58
Multiwavelength anomalous diffraction (MAD) from the CCP4 proceedings
http://www.ccp4.ac.uk/courses/proceedings/1997/j_smith/main.html
Multi-wavelength anomalous-diffraction (MAD) from Terwilliger Acta Cryst.
(1994). D50, 11-16
etc.
I don't see where the problem lies:
a SAD experiment is a single wavelength experiment where you are using the
anomalous/dispersive signals for phasing
a MAD experiment is a multiple wavelength version of SAD. Hopefully one
picks an appropriate range of wavelengths for whatever complex case one has.
One can have SAD and MAD datasets that exploit anomalous/dispersive signals
from multiple difference sources. This after all is one of the things that
SHARP is particularly good at accommodating.
If you're not using the anomalous/dispersive signals for phasing, you're
collecting native data. After all C,N,O,S etc all have a small anomalous
signal at all wavelengths, and metalloproteins usually have even larger
signals so the mere presence of a theoretical d difference does not make it
a SAD dataset. ALL datasets contain some anomalous/dispersive signals, most
of the time way down in the noise.
Phil Jeffrey
Princeton
On 1/18/12 12:48 PM, Francis E Reyes wrote:
Using the terms 'MAD' and 'SAD' have always been confusing to me when
considering more complex phasing cases. What happens if you have intrinsic
Zn's, collect a 3wvl experiment and then derivatize it with SeMet or a heavy
atom? Or the MAD+native scenario (SHARP) ?
Instead of using MAD/SAD nomenclature I favor explicitly stating whether
dispersive/anomalous/isomorphous differences (and what heavy atoms for each
) were used in phasing. Aren't analyzing the differences (independent of
source) the important bit anyway?
F
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
Re: [ccp4bb] MAD
So, with the combined votes of Hendrickson, Blundell, Tickle and Google, can we
safely call it Multi-wavelength Anomalous Diffraction from now on and call
all other names wrong?
Mark
On 19 Jan 2012, at 18:50, Ian Tickle wrote:
Perhaps I could chime in with a bit of history as I understand it.
The term 'dispersion' in optics, as everyone who knows their history
is aware of, refers to the classic experiment by Sir Isaac Newton at
Trinity College here in Cambridge where he observed white light being
split up ('dispersed') into its component colours by a prism. This is
of course due to the variation in refractive index of glass with
wavelength, so then we arrive at the usual definition of optical
dispersion as dn/dlambda, i.e. the first derivative of the refractive
index with respect to the wavelength.
Now the refractive index of an average crystal at around 1 Ang
wavelength differs by about 1 part in a million from 1, however it can
be determined by very careful and precise interferometric experiments.
It's safe to say therefore that the dispersion of X-rays (anomalous
or otherwise) has no measurable effect whatsoever as far as the
average X-ray diffraction experiment (SAD, MAD or otherwise) is
concerned. The question then is how did the term 'anomalous
dispersion' get to be applied to X-ray diffraction? The answer is
that it turns out that the equation ('Kramer-Kronig relationship')
governing X-ray scattering is completely analogous to that governing
optical dispersion, so it's legitimate to use the term 'dispersive'
(meaning 'analogous to dispersion') for the real part of the
wavelength-dependent component of the X-ray scattering factor, because
the real part of the refractive index is what describes dispersion
(the imaginary part in both cases describes absorption).
So then from 'dispersive' to 'dispersion' to describe the wavelength
dependence of X-ray scattering is only a short step, even though it
only behaves _like_ dispersion in its dependence on wavelength.
However having two different meanings for the same word can get
confusing and clearly should be avoided if at all possible.
So what does this have to do with the MAD acronym? I think it stemmed
from a visit by Wayne Hendrickson to Birkbeck in London some time
around 1990: he was invited by Tom Blundell to give a lecture on his
MAD experiments. At that time Wayne called it multi-wavelength
anomalous dispersion. Tom pointed out that this was really a misnomer
for the reasons I've elucidated above. Wayne liked the MAD acronym
and wanted to keep it so he needed a replacement term starting with D
and diffraction was the obvious choice, and if you look at the
literature from then on Wayne at least consistently called it
multi-wavelength anomalous diffraction.
Cheers
-- Ian
On 18 January 2012 18:23, Phil Jeffrey pjeff...@princeton.edu wrote:
Can I be dogmatic about this ?
Multiwavelength anomalous diffraction from Hendrickson (1991) Science Vol.
254 no. 5028 pp. 51-58
Multiwavelength anomalous diffraction (MAD) from the CCP4 proceedings
http://www.ccp4.ac.uk/courses/proceedings/1997/j_smith/main.html
Multi-wavelength anomalous-diffraction (MAD) from Terwilliger Acta Cryst.
(1994). D50, 11-16
etc.
I don't see where the problem lies:
a SAD experiment is a single wavelength experiment where you are using the
anomalous/dispersive signals for phasing
a MAD experiment is a multiple wavelength version of SAD. Hopefully one
picks an appropriate range of wavelengths for whatever complex case one has.
One can have SAD and MAD datasets that exploit anomalous/dispersive signals
from multiple difference sources. This after all is one of the things that
SHARP is particularly good at accommodating.
If you're not using the anomalous/dispersive signals for phasing, you're
collecting native data. After all C,N,O,S etc all have a small anomalous
signal at all wavelengths, and metalloproteins usually have even larger
signals so the mere presence of a theoretical d difference does not make it
a SAD dataset. ALL datasets contain some anomalous/dispersive signals, most
of the time way down in the noise.
Phil Jeffrey
Princeton
On 1/18/12 12:48 PM, Francis E Reyes wrote:
Using the terms 'MAD' and 'SAD' have always been confusing to me when
considering more complex phasing cases. What happens if you have intrinsic
Zn's, collect a 3wvl experiment and then derivatize it with SeMet or a heavy
atom? Or the MAD+native scenario (SHARP) ?
Instead of using MAD/SAD nomenclature I favor explicitly stating whether
dispersive/anomalous/isomorphous differences (and what heavy atoms for each
) were used in phasing. Aren't analyzing the differences (independent of
source) the important bit anyway?
F
-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
[ccp4bb] MAD
... or just call it 'MAD', and you're bound to be correct !!
Everything is in the eye of the beholder, after all.
Marcus.
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Mark J
van Raaij
Sent: 19 January 2012 17:59
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] MAD
So, with the combined votes of Hendrickson, Blundell, Tickle and Google, can we
safely call it Multi-wavelength Anomalous Diffraction from now on and call
all other names wrong?
Mark
On 19 Jan 2012, at 18:50, Ian Tickle wrote:
Perhaps I could chime in with a bit of history as I understand it.
The term 'dispersion' in optics, as everyone who knows their history
is aware of, refers to the classic experiment by Sir Isaac Newton at
Trinity College here in Cambridge where he observed white light being
split up ('dispersed') into its component colours by a prism. This is
of course due to the variation in refractive index of glass with
wavelength, so then we arrive at the usual definition of optical
dispersion as dn/dlambda, i.e. the first derivative of the refractive
index with respect to the wavelength.
Now the refractive index of an average crystal at around 1 Ang
wavelength differs by about 1 part in a million from 1, however it can
be determined by very careful and precise interferometric experiments.
It's safe to say therefore that the dispersion of X-rays (anomalous
or otherwise) has no measurable effect whatsoever as far as the
average X-ray diffraction experiment (SAD, MAD or otherwise) is
concerned. The question then is how did the term 'anomalous
dispersion' get to be applied to X-ray diffraction? The answer is
that it turns out that the equation ('Kramer-Kronig relationship')
governing X-ray scattering is completely analogous to that governing
optical dispersion, so it's legitimate to use the term 'dispersive'
(meaning 'analogous to dispersion') for the real part of the
wavelength-dependent component of the X-ray scattering factor, because
the real part of the refractive index is what describes dispersion
(the imaginary part in both cases describes absorption).
So then from 'dispersive' to 'dispersion' to describe the wavelength
dependence of X-ray scattering is only a short step, even though it
only behaves _like_ dispersion in its dependence on wavelength.
However having two different meanings for the same word can get
confusing and clearly should be avoided if at all possible.
So what does this have to do with the MAD acronym? I think it stemmed
from a visit by Wayne Hendrickson to Birkbeck in London some time
around 1990: he was invited by Tom Blundell to give a lecture on his
MAD experiments. At that time Wayne called it multi-wavelength
anomalous dispersion. Tom pointed out that this was really a misnomer
for the reasons I've elucidated above. Wayne liked the MAD acronym
and wanted to keep it so he needed a replacement term starting with D
and diffraction was the obvious choice, and if you look at the
literature from then on Wayne at least consistently called it
multi-wavelength anomalous diffraction.
Cheers
-- Ian
On 18 January 2012 18:23, Phil Jeffrey pjeff...@princeton.edu wrote:
Can I be dogmatic about this ?
Multiwavelength anomalous diffraction from Hendrickson (1991) Science Vol.
254 no. 5028 pp. 51-58
Multiwavelength anomalous diffraction (MAD) from the CCP4 proceedings
http://www.ccp4.ac.uk/courses/proceedings/1997/j_smith/main.html
Multi-wavelength anomalous-diffraction (MAD) from Terwilliger Acta Cryst.
(1994). D50, 11-16
etc.
I don't see where the problem lies:
a SAD experiment is a single wavelength experiment where you are using the
anomalous/dispersive signals for phasing
a MAD experiment is a multiple wavelength version of SAD. Hopefully one
picks an appropriate range of wavelengths for whatever complex case one has.
One can have SAD and MAD datasets that exploit anomalous/dispersive signals
from multiple difference sources. This after all is one of the things that
SHARP is particularly good at accommodating.
If you're not using the anomalous/dispersive signals for phasing, you're
collecting native data. After all C,N,O,S etc all have a small anomalous
signal at all wavelengths, and metalloproteins usually have even larger
signals so the mere presence of a theoretical d difference does not make it
a SAD dataset. ALL datasets contain some anomalous/dispersive signals, most
of the time way down in the noise.
Phil Jeffrey
Princeton
On 1/18/12 12:48 PM, Francis E Reyes wrote:
Using the terms 'MAD' and 'SAD' have always been confusing to me when
considering more complex phasing cases. What happens if you have intrinsic
Zn's, collect a 3wvl experiment and then derivatize it with SeMet or a heavy
atom? Or the MAD+native scenario (SHARP) ?
Instead of using MAD/SAD nomenclature I favor explicitly stating whether
dispersive
Re: [ccp4bb] MAD
On Thursday, 19 January 2012, Ian Tickle wrote: So what does this have to do with the MAD acronym? I think it stemmed from a visit by Wayne Hendrickson to Birkbeck in London some time around 1990: he was invited by Tom Blundell to give a lecture on his MAD experiments. At that time Wayne called it multi-wavelength anomalous dispersion. Tom pointed out that this was really a misnomer for the reasons I've elucidated above. Wayne liked the MAD acronym and wanted to keep it so he needed a replacement term starting with D and diffraction was the obvious choice, and if you look at the literature from then on Wayne at least consistently called it multi-wavelength anomalous diffraction. Ian: The change-over from dispersion to diffraction in MAD protein crystallography happened a couple of years earlier, at least with regard to work being done at SSRL. I think the last paper using the term dispersion was the 1988 Lamprey hemoglobin paper. The next two papers, one a collaboration with Wayne's group and the other a collaboration with Hans Freeman's group, used the term diffraction. WA Hendrickson, JL Smith, RP Phizackerley, EA Merritt. Crystallographic structure-analysis of lamprey hemoglobin from anomalous dispersion of synchrotron radiation. PROTEINS-STRUCTURE FUNCTION AND GENETICS, 4(2):77–88, 1988. JM Guss, EA Merritt, RP Phizackerley, B Hedman, M Murata, KO Hodgson, HC Freeman. Phase determination by multiple-wavelength X-ray-diffraction - crystal-structure of a basic blue copper protein from cucumbers. SCIENCE, 241(4867):806–811, AUG 12 1988. WA Hendrickson, A Pahler, JL Smith, Y Satow, EA Merritt, RP Phizackerley. Crystal structure of core streptavidin determined from multiwavelength anomalous diffraction of synchrotron radiation. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 86(7):2190–2194, APR 1989. On the other hand, David and Lilo Templeton continued to use the term anomalous dispersion for at least another decade, describing their diffraction experiments exploring polarization effects and other characteristics of near-edge X-ray scattering by elements all over the periodic table. Ethan Cheers -- Ian On 18 January 2012 18:23, Phil Jeffrey pjeff...@princeton.edu wrote: Can I be dogmatic about this ? Multiwavelength anomalous diffraction from Hendrickson (1991) Science Vol. 254 no. 5028 pp. 51-58 Multiwavelength anomalous diffraction (MAD) from the CCP4 proceedings http://www.ccp4.ac.uk/courses/proceedings/1997/j_smith/main.html Multi-wavelength anomalous-diffraction (MAD) from Terwilliger Acta Cryst. (1994). D50, 11-16 etc. I don't see where the problem lies: a SAD experiment is a single wavelength experiment where you are using the anomalous/dispersive signals for phasing a MAD experiment is a multiple wavelength version of SAD. Hopefully one picks an appropriate range of wavelengths for whatever complex case one has. One can have SAD and MAD datasets that exploit anomalous/dispersive signals from multiple difference sources. This after all is one of the things that SHARP is particularly good at accommodating. If you're not using the anomalous/dispersive signals for phasing, you're collecting native data. After all C,N,O,S etc all have a small anomalous signal at all wavelengths, and metalloproteins usually have even larger signals so the mere presence of a theoretical d difference does not make it a SAD dataset. ALL datasets contain some anomalous/dispersive signals, most of the time way down in the noise. Phil Jeffrey Princeton On 1/18/12 12:48 PM, Francis E Reyes wrote: Using the terms 'MAD' and 'SAD' have always been confusing to me when considering more complex phasing cases. What happens if you have intrinsic Zn's, collect a 3wvl experiment and then derivatize it with SeMet or a heavy atom? Or the MAD+native scenario (SHARP) ? Instead of using MAD/SAD nomenclature I favor explicitly stating whether dispersive/anomalous/isomorphous differences (and what heavy atoms for each ) were used in phasing. Aren't analyzing the differences (independent of source) the important bit anyway? F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder
Re: [ccp4bb] MAD
It would be so much more convenient to call these techniques (MAD, SAD, etc.) by their inventor's name. This would simplify things immensely simultaneously eliminating CCP4BB MADisagreements. Although in our days of copyrights wars, the journals and perhaps conferences where these methods were presented for the first time would insist on using their names as part of the method's name... Petr On Jan 19, 2012, at 7:42 PM, Ethan Merritt wrote: On Thursday, 19 January 2012, Ian Tickle wrote: So what does this have to do with the MAD acronym? I think it stemmed from a visit by Wayne Hendrickson to Birkbeck in London some time around 1990: he was invited by Tom Blundell to give a lecture on his MAD experiments. At that time Wayne called it multi-wavelength anomalous dispersion. Tom pointed out that this was really a misnomer for the reasons I've elucidated above. Wayne liked the MAD acronym and wanted to keep it so he needed a replacement term starting with D and diffraction was the obvious choice, and if you look at the literature from then on Wayne at least consistently called it multi-wavelength anomalous diffraction. Ian: The change-over from dispersion to diffraction in MAD protein crystallography happened a couple of years earlier, at least with regard to work being done at SSRL. I think the last paper using the term dispersion was the 1988 Lamprey hemoglobin paper. The next two papers, one a collaboration with Wayne's group and the other a collaboration with Hans Freeman's group, used the term diffraction. WA Hendrickson, JL Smith, RP Phizackerley, EA Merritt. Crystallographic structure-analysis of lamprey hemoglobin from anomalous dispersion of synchrotron radiation. PROTEINS-STRUCTURE FUNCTION AND GENETICS, 4(2):77–88, 1988. JM Guss, EA Merritt, RP Phizackerley, B Hedman, M Murata, KO Hodgson, HC Freeman. Phase determination by multiple-wavelength X-ray-diffraction - crystal-structure of a basic blue copper protein from cucumbers. SCIENCE, 241(4867):806–811, AUG 12 1988. WA Hendrickson, A Pahler, JL Smith, Y Satow, EA Merritt, RP Phizackerley. Crystal structure of core streptavidin determined from multiwavelength anomalous diffraction of synchrotron radiation. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 86(7):2190–2194, APR 1989. On the other hand, David and Lilo Templeton continued to use the term anomalous dispersion for at least another decade, describing their diffraction experiments exploring polarization effects and other characteristics of near-edge X-ray scattering by elements all over the periodic table. Ethan Cheers -- Ian On 18 January 2012 18:23, Phil Jeffrey pjeff...@princeton.edu wrote: Can I be dogmatic about this ? Multiwavelength anomalous diffraction from Hendrickson (1991) Science Vol. 254 no. 5028 pp. 51-58 Multiwavelength anomalous diffraction (MAD) from the CCP4 proceedings http://www.ccp4.ac.uk/courses/proceedings/1997/j_smith/main.html Multi-wavelength anomalous-diffraction (MAD) from Terwilliger Acta Cryst. (1994). D50, 11-16 etc. I don't see where the problem lies: a SAD experiment is a single wavelength experiment where you are using the anomalous/dispersive signals for phasing a MAD experiment is a multiple wavelength version of SAD. Hopefully one picks an appropriate range of wavelengths for whatever complex case one has. One can have SAD and MAD datasets that exploit anomalous/dispersive signals from multiple difference sources. This after all is one of the things that SHARP is particularly good at accommodating. If you're not using the anomalous/dispersive signals for phasing, you're collecting native data. After all C,N,O,S etc all have a small anomalous signal at all wavelengths, and metalloproteins usually have even larger signals so the mere presence of a theoretical d difference does not make it a SAD dataset. ALL datasets contain some anomalous/dispersive signals, most of the time way down in the noise. Phil Jeffrey Princeton On 1/18/12 12:48 PM, Francis E Reyes wrote: Using the terms 'MAD' and 'SAD' have always been confusing to me when considering more complex phasing cases. What happens if you have intrinsic Zn's, collect a 3wvl experiment and then derivatize it with SeMet or a heavy atom? Or the MAD+native scenario (SHARP) ? Instead of using MAD/SAD nomenclature I favor explicitly stating whether dispersive/anomalous/isomorphous differences (and what heavy atoms for each ) were used in phasing. Aren't analyzing the differences (independent of source) the important bit anyway? F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder
Re: [ccp4bb] MAD
A, yes, inventor's names. Anyone reading who is less than 40 and knows what MTZ stands for? ;-) My favorite technique remains SADDAM - a side product of Gerard's War On Error, that never did catch-up with the masses - experimentally or as an acronym. A. On 19 Jan 2012, at 21:51, Petr Leiman wrote: It would be so much more convenient to call these techniques (MAD, SAD, etc.) by their inventor's name. This would simplify things immensely simultaneously eliminating CCP4BB MADisagreements. Although in our days of copyrights wars, the journals and perhaps conferences where these methods were presented for the first time would insist on using their names as part of the method's name... Petr On Jan 19, 2012, at 7:42 PM, Ethan Merritt wrote: On Thursday, 19 January 2012, Ian Tickle wrote: So what does this have to do with the MAD acronym? I think it stemmed from a visit by Wayne Hendrickson to Birkbeck in London some time around 1990: he was invited by Tom Blundell to give a lecture on his MAD experiments. At that time Wayne called it multi-wavelength anomalous dispersion. Tom pointed out that this was really a misnomer for the reasons I've elucidated above. Wayne liked the MAD acronym and wanted to keep it so he needed a replacement term starting with D and diffraction was the obvious choice, and if you look at the literature from then on Wayne at least consistently called it multi-wavelength anomalous diffraction. Ian: The change-over from dispersion to diffraction in MAD protein crystallography happened a couple of years earlier, at least with regard to work being done at SSRL. I think the last paper using the term dispersion was the 1988 Lamprey hemoglobin paper. The next two papers, one a collaboration with Wayne's group and the other a collaboration with Hans Freeman's group, used the term diffraction. WA Hendrickson, JL Smith, RP Phizackerley, EA Merritt. Crystallographic structure-analysis of lamprey hemoglobin from anomalous dispersion of synchrotron radiation. PROTEINS-STRUCTURE FUNCTION AND GENETICS, 4(2):77–88, 1988. JM Guss, EA Merritt, RP Phizackerley, B Hedman, M Murata, KO Hodgson, HC Freeman. Phase determination by multiple-wavelength X-ray-diffraction - crystal-structure of a basic blue copper protein from cucumbers. SCIENCE, 241(4867):806–811, AUG 12 1988. WA Hendrickson, A Pahler, JL Smith, Y Satow, EA Merritt, RP Phizackerley. Crystal structure of core streptavidin determined from multiwavelength anomalous diffraction of synchrotron radiation. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 86(7):2190–2194, APR 1989. On the other hand, David and Lilo Templeton continued to use the term anomalous dispersion for at least another decade, describing their diffraction experiments exploring polarization effects and other characteristics of near-edge X-ray scattering by elements all over the periodic table. Ethan Cheers -- Ian On 18 January 2012 18:23, Phil Jeffrey pjeff...@princeton.edu wrote: Can I be dogmatic about this ? Multiwavelength anomalous diffraction from Hendrickson (1991) Science Vol. 254 no. 5028 pp. 51-58 Multiwavelength anomalous diffraction (MAD) from the CCP4 proceedings http://www.ccp4.ac.uk/courses/proceedings/1997/j_smith/main.html Multi-wavelength anomalous-diffraction (MAD) from Terwilliger Acta Cryst. (1994). D50, 11-16 etc. I don't see where the problem lies: a SAD experiment is a single wavelength experiment where you are using the anomalous/dispersive signals for phasing a MAD experiment is a multiple wavelength version of SAD. Hopefully one picks an appropriate range of wavelengths for whatever complex case one has. One can have SAD and MAD datasets that exploit anomalous/dispersive signals from multiple difference sources. This after all is one of the things that SHARP is particularly good at accommodating. If you're not using the anomalous/dispersive signals for phasing, you're collecting native data. After all C,N,O,S etc all have a small anomalous signal at all wavelengths, and metalloproteins usually have even larger signals so the mere presence of a theoretical d difference does not make it a SAD dataset. ALL datasets contain some anomalous/dispersive signals, most of the time way down in the noise. Phil Jeffrey Princeton On 1/18/12 12:48 PM, Francis E Reyes wrote: Using the terms 'MAD' and 'SAD' have always been confusing to me when considering more complex phasing cases. What happens if you have intrinsic Zn's, collect a 3wvl experiment and then derivatize it with SeMet or a heavy atom? Or the MAD+native scenario (SHARP) ? Instead of using MAD/SAD nomenclature I favor explicitly stating whether dispersive/anomalous/isomorphous differences (and what heavy atoms for each ) were used in phasing. Aren't analyzing the
Re: [ccp4bb] MAD
How many names do you propose to use to describe SIRAS? If someone wrote in their paper the Rossmann method was used to solve this structure what method would come to mind? Dale Tronrud On 1/19/2012 12:51 PM, Petr Leiman wrote: It would be so much more convenient to call these techniques (MAD, SAD, etc.) by their inventor's name. This would simplify things immensely simultaneously eliminating CCP4BB MADisagreements. Although in our days of copyrights wars, the journals and perhaps conferences where these methods were presented for the first time would insist on using their names as part of the method's name... Petr On Jan 19, 2012, at 7:42 PM, Ethan Merritt wrote: On Thursday, 19 January 2012, Ian Tickle wrote: So what does this have to do with the MAD acronym? I think it stemmed from a visit by Wayne Hendrickson to Birkbeck in London some time around 1990: he was invited by Tom Blundell to give a lecture on his MAD experiments. At that time Wayne called it multi-wavelength anomalous dispersion. Tom pointed out that this was really a misnomer for the reasons I've elucidated above. Wayne liked the MAD acronym and wanted to keep it so he needed a replacement term starting with D and diffraction was the obvious choice, and if you look at the literature from then on Wayne at least consistently called it multi-wavelength anomalous diffraction. Ian: The change-over from dispersion to diffraction in MAD protein crystallography happened a couple of years earlier, at least with regard to work being done at SSRL. I think the last paper using the term dispersion was the 1988 Lamprey hemoglobin paper. The next two papers, one a collaboration with Wayne's group and the other a collaboration with Hans Freeman's group, used the term diffraction. WA Hendrickson, JL Smith, RP Phizackerley, EA Merritt. Crystallographic structure-analysis of lamprey hemoglobin from anomalous dispersion of synchrotron radiation. PROTEINS-STRUCTURE FUNCTION AND GENETICS, 4(2):77–88, 1988. JM Guss, EA Merritt, RP Phizackerley, B Hedman, M Murata, KO Hodgson, HC Freeman. Phase determination by multiple-wavelength X-ray-diffraction - crystal-structure of a basic blue copper protein from cucumbers. SCIENCE, 241(4867):806–811, AUG 12 1988. WA Hendrickson, A Pahler, JL Smith, Y Satow, EA Merritt, RP Phizackerley. Crystal structure of core streptavidin determined from multiwavelength anomalous diffraction of synchrotron radiation. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 86(7):2190–2194, APR 1989. On the other hand, David and Lilo Templeton continued to use the term anomalous dispersion for at least another decade, describing their diffraction experiments exploring polarization effects and other characteristics of near-edge X-ray scattering by elements all over the periodic table. Ethan Cheers -- Ian On 18 January 2012 18:23, Phil Jeffreypjeff...@princeton.edu wrote: Can I be dogmatic about this ? Multiwavelength anomalous diffraction from Hendrickson (1991) Science Vol. 254 no. 5028 pp. 51-58 Multiwavelength anomalous diffraction (MAD) from the CCP4 proceedings http://www.ccp4.ac.uk/courses/proceedings/1997/j_smith/main.html Multi-wavelength anomalous-diffraction (MAD) from Terwilliger Acta Cryst. (1994). D50, 11-16 etc. I don't see where the problem lies: a SAD experiment is a single wavelength experiment where you are using the anomalous/dispersive signals for phasing a MAD experiment is a multiple wavelength version of SAD. Hopefully one picks an appropriate range of wavelengths for whatever complex case one has. One can have SAD and MAD datasets that exploit anomalous/dispersive signals from multiple difference sources. This after all is one of the things that SHARP is particularly good at accommodating. If you're not using the anomalous/dispersive signals for phasing, you're collecting native data. After all C,N,O,S etc all have a small anomalous signal at all wavelengths, and metalloproteins usually have even larger signals so the mere presence of a theoretical d difference does not make it a SAD dataset. ALL datasets contain some anomalous/dispersive signals, most of the time way down in the noise. Phil Jeffrey Princeton On 1/18/12 12:48 PM, Francis E Reyes wrote: Using the terms 'MAD' and 'SAD' have always been confusing to me when considering more complex phasing cases. What happens if you have intrinsic Zn's, collect a 3wvl experiment and then derivatize it with SeMet or a heavy atom? Or the MAD+native scenario (SHARP) ? Instead of using MAD/SAD nomenclature I favor explicitly stating whether dispersive/anomalous/isomorphous differences (and what heavy atoms for each ) were used in phasing. Aren't analyzing the differences (independent of source) the important bit anyway? F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder
Re: [ccp4bb] MAD
On Jan 19, 2012, at 10:05 PM, Dale Tronrud wrote: ... If someone wrote in their paper the Rossmann method was used to solve this structure what method would come to mind? The American method of course! Place the crystal in the beam, allow the autoindexing routine to find the crystal orientation (here the American method stops however), then continue to process the data. Then take a sphere, do MR, and phase extend using NCS and solvent flattening. My previous message, as well as this one, was intended to be a joke (kind of). Sincerely, Petr P.S. Dale, I am sorry you are likely to receive this message twice... Dale Tronrud On 1/19/2012 12:51 PM, Petr Leiman wrote: It would be so much more convenient to call these techniques (MAD, SAD, etc.) by their inventor's name. This would simplify things immensely simultaneously eliminating CCP4BB MADisagreements. Although in our days of copyrights wars, the journals and perhaps conferences where these methods were presented for the first time would insist on using their names as part of the method's name... Petr On Jan 19, 2012, at 7:42 PM, Ethan Merritt wrote: On Thursday, 19 January 2012, Ian Tickle wrote: So what does this have to do with the MAD acronym? I think it stemmed from a visit by Wayne Hendrickson to Birkbeck in London some time around 1990: he was invited by Tom Blundell to give a lecture on his MAD experiments. At that time Wayne called it multi-wavelength anomalous dispersion. Tom pointed out that this was really a misnomer for the reasons I've elucidated above. Wayne liked the MAD acronym and wanted to keep it so he needed a replacement term starting with D and diffraction was the obvious choice, and if you look at the literature from then on Wayne at least consistently called it multi-wavelength anomalous diffraction. Ian: The change-over from dispersion to diffraction in MAD protein crystallography happened a couple of years earlier, at least with regard to work being done at SSRL. I think the last paper using the term dispersion was the 1988 Lamprey hemoglobin paper. The next two papers, one a collaboration with Wayne's group and the other a collaboration with Hans Freeman's group, used the term diffraction. WA Hendrickson, JL Smith, RP Phizackerley, EA Merritt. Crystallographic structure-analysis of lamprey hemoglobin from anomalous dispersion of synchrotron radiation. PROTEINS-STRUCTURE FUNCTION AND GENETICS, 4(2):77–88, 1988. JM Guss, EA Merritt, RP Phizackerley, B Hedman, M Murata, KO Hodgson, HC Freeman. Phase determination by multiple-wavelength X-ray-diffraction - crystal-structure of a basic blue copper protein from cucumbers. SCIENCE, 241(4867):806–811, AUG 12 1988. WA Hendrickson, A Pahler, JL Smith, Y Satow, EA Merritt, RP Phizackerley. Crystal structure of core streptavidin determined from multiwavelength anomalous diffraction of synchrotron radiation. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 86(7):2190–2194, APR 1989. On the other hand, David and Lilo Templeton continued to use the term anomalous dispersion for at least another decade, describing their diffraction experiments exploring polarization effects and other characteristics of near-edge X-ray scattering by elements all over the periodic table. Ethan Cheers -- Ian On 18 January 2012 18:23, Phil Jeffreypjeff...@princeton.edu wrote: Can I be dogmatic about this ? Multiwavelength anomalous diffraction from Hendrickson (1991) Science Vol. 254 no. 5028 pp. 51-58 Multiwavelength anomalous diffraction (MAD) from the CCP4 proceedings http://www.ccp4.ac.uk/courses/proceedings/1997/j_smith/main.html Multi-wavelength anomalous-diffraction (MAD) from Terwilliger Acta Cryst. (1994). D50, 11-16 etc. I don't see where the problem lies: a SAD experiment is a single wavelength experiment where you are using the anomalous/dispersive signals for phasing a MAD experiment is a multiple wavelength version of SAD. Hopefully one picks an appropriate range of wavelengths for whatever complex case one has. One can have SAD and MAD datasets that exploit anomalous/dispersive signals from multiple difference sources. This after all is one of the things that SHARP is particularly good at accommodating. If you're not using the anomalous/dispersive signals for phasing, you're collecting native data. After all C,N,O,S etc all have a small anomalous signal at all wavelengths, and metalloproteins usually have even larger signals so the mere presence of a theoretical d difference does not make it a SAD dataset. ALL datasets contain some anomalous/dispersive signals, most of the time way down in the noise. Phil Jeffrey Princeton On 1/18/12 12:48 PM, Francis E Reyes wrote: Using the terms 'MAD' and 'SAD' have always been confusing to me when considering more complex phasing cases.
Re: [ccp4bb] MAD
I never weigh in, so I don't know if I'll get in trouble here... How would we distinguish MAD (to now be called The Hendrickson Method) from SAD (The Hendrickson Method - remeber crambin? Nature, 1981)? On Thu, Jan 19, 2012 at 3:59 PM, Anastassis Perrakis a.perra...@nki.nl wrote: A, yes, inventor's names. Anyone reading who is less than 40 and knows what MTZ stands for? ;-) My favorite technique remains SADDAM - a side product of Gerard's War On Error, that never did catch-up with the masses - experimentally or as an acronym. A. On 19 Jan 2012, at 21:51, Petr Leiman wrote: It would be so much more convenient to call these techniques (MAD, SAD, etc.) by their inventor's name. This would simplify things immensely simultaneously eliminating CCP4BB MADisagreements. Although in our days of copyrights wars, the journals and perhaps conferences where these methods were presented for the first time would insist on using their names as part of the method's name... Petr On Jan 19, 2012, at 7:42 PM, Ethan Merritt wrote: On Thursday, 19 January 2012, Ian Tickle wrote: So what does this have to do with the MAD acronym? I think it stemmed from a visit by Wayne Hendrickson to Birkbeck in London some time around 1990: he was invited by Tom Blundell to give a lecture on his MAD experiments. At that time Wayne called it multi-wavelength anomalous dispersion. Tom pointed out that this was really a misnomer for the reasons I've elucidated above. Wayne liked the MAD acronym and wanted to keep it so he needed a replacement term starting with D and diffraction was the obvious choice, and if you look at the literature from then on Wayne at least consistently called it multi-wavelength anomalous diffraction. Ian: The change-over from dispersion to diffraction in MAD protein crystallography happened a couple of years earlier, at least with regard to work being done at SSRL. I think the last paper using the term dispersion was the 1988 Lamprey hemoglobin paper. The next two papers, one a collaboration with Wayne's group and the other a collaboration with Hans Freeman's group, used the term diffraction. WA Hendrickson, JL Smith, RP Phizackerley, EA Merritt. Crystallographic structure-analysis of lamprey hemoglobin from anomalous dispersion of synchrotron radiation. PROTEINS-STRUCTURE FUNCTION AND GENETICS, 4(2):77–88, 1988. JM Guss, EA Merritt, RP Phizackerley, B Hedman, M Murata, KO Hodgson, HC Freeman. Phase determination by multiple-wavelength X-ray-diffraction - crystal-structure of a basic blue copper protein from cucumbers. SCIENCE, 241(4867):806–811, AUG 12 1988. WA Hendrickson, A Pahler, JL Smith, Y Satow, EA Merritt, RP Phizackerley. Crystal structure of core streptavidin determined from multiwavelength anomalous diffraction of synchrotron radiation. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 86(7):2190–2194, APR 1989. On the other hand, David and Lilo Templeton continued to use the term anomalous dispersion for at least another decade, describing their diffraction experiments exploring polarization effects and other characteristics of near-edge X-ray scattering by elements all over the periodic table. Ethan Cheers -- Ian On 18 January 2012 18:23, Phil Jeffrey pjeff...@princeton.edu wrote: Can I be dogmatic about this ? Multiwavelength anomalous diffraction from Hendrickson (1991) Science Vol. 254 no. 5028 pp. 51-58 Multiwavelength anomalous diffraction (MAD) from the CCP4 proceedings http://www.ccp4.ac.uk/courses/proceedings/1997/j_smith/main.html Multi-wavelength anomalous-diffraction (MAD) from Terwilliger Acta Cryst. (1994). D50, 11-16 etc. I don't see where the problem lies: a SAD experiment is a single wavelength experiment where you are using the anomalous/dispersive signals for phasing a MAD experiment is a multiple wavelength version of SAD. Hopefully one picks an appropriate range of wavelengths for whatever complex case one has. One can have SAD and MAD datasets that exploit anomalous/dispersive signals from multiple difference sources. This after all is one of the things that SHARP is particularly good at accommodating. If you're not using the anomalous/dispersive signals for phasing, you're collecting native data. After all C,N,O,S etc all have a small anomalous signal at all wavelengths, and metalloproteins usually have even larger signals so the mere presence of a theoretical d difference does not make it a SAD dataset. ALL datasets contain some anomalous/dispersive signals, most of the time way down in the noise. Phil Jeffrey Princeton On 1/18/12 12:48 PM, Francis E Reyes wrote: Using the terms 'MAD' and 'SAD' have always been confusing to me when considering more complex phasing cases. What happens if you have intrinsic Zn's, collect a 3wvl experiment and then derivatize it with SeMet or a heavy atom?
Re: [ccp4bb] MAD
Dear Petr and other contributors to this thread, I think it is never easy to call a method by that of its inventor, as there are usually many more than one inventor of the total know-how that gets incorporated into the finished product that people end up using. Names such as those of James Phillips, Roger Fourme and Richard Kahn, spring to mind when it comes to the early histories of the MAD and SAD methods. In my opinion, thought and effort would be much better spent revisiting these methods from the point of view of applying them better (e.g by providing better protocols on beamlines to optimise the signal-to-noise ratio of anomalous and dispersive differences) rather than deconstructing acronyms and launching popularity contests for putative single inventors. The latter is a profound misunderstanding of how methods appear and are developed, and this kind of personality cult is best left to cheap TV entertainment :-) - a baseline above which this BB surely wishes to remain. With best wishes, Gerard. -- On Thu, Jan 19, 2012 at 09:31:33PM +, Petr Leiman wrote: On Jan 19, 2012, at 10:05 PM, Dale Tronrud wrote: ... If someone wrote in their paper the Rossmann method was used to solve this structure what method would come to mind? The American method of course! Place the crystal in the beam, allow the autoindexing routine to find the crystal orientation (here the American method stops however), then continue to process the data. Then take a sphere, do MR, and phase extend using NCS and solvent flattening. My previous message, as well as this one, was intended to be a joke (kind of). Sincerely, Petr P.S. Dale, I am sorry you are likely to receive this message twice... Dale Tronrud On 1/19/2012 12:51 PM, Petr Leiman wrote: It would be so much more convenient to call these techniques (MAD, SAD, etc.) by their inventor's name. This would simplify things immensely simultaneously eliminating CCP4BB MADisagreements. Although in our days of copyrights wars, the journals and perhaps conferences where these methods were presented for the first time would insist on using their names as part of the method's name... Petr On Jan 19, 2012, at 7:42 PM, Ethan Merritt wrote: On Thursday, 19 January 2012, Ian Tickle wrote: So what does this have to do with the MAD acronym? I think it stemmed from a visit by Wayne Hendrickson to Birkbeck in London some time around 1990: he was invited by Tom Blundell to give a lecture on his MAD experiments. At that time Wayne called it multi-wavelength anomalous dispersion. Tom pointed out that this was really a misnomer for the reasons I've elucidated above. Wayne liked the MAD acronym and wanted to keep it so he needed a replacement term starting with D and diffraction was the obvious choice, and if you look at the literature from then on Wayne at least consistently called it multi-wavelength anomalous diffraction. Ian: The change-over from dispersion to diffraction in MAD protein crystallography happened a couple of years earlier, at least with regard to work being done at SSRL. I think the last paper using the term dispersion was the 1988 Lamprey hemoglobin paper. The next two papers, one a collaboration with Wayne's group and the other a collaboration with Hans Freeman's group, used the term diffraction. WA Hendrickson, JL Smith, RP Phizackerley, EA Merritt. Crystallographic structure-analysis of lamprey hemoglobin from anomalous dispersion of synchrotron radiation. PROTEINS-STRUCTURE FUNCTION AND GENETICS, 4(2):77–88, 1988. JM Guss, EA Merritt, RP Phizackerley, B Hedman, M Murata, KO Hodgson, HC Freeman. Phase determination by multiple-wavelength X-ray-diffraction - crystal-structure of a basic blue copper protein from cucumbers. SCIENCE, 241(4867):806–811, AUG 12 1988. WA Hendrickson, A Pahler, JL Smith, Y Satow, EA Merritt, RP Phizackerley. Crystal structure of core streptavidin determined from multiwavelength anomalous diffraction of synchrotron radiation. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 86(7):2190–2194, APR 1989. On the other hand, David and Lilo Templeton continued to use the term anomalous dispersion for at least another decade, describing their diffraction experiments exploring polarization effects and other characteristics of near-edge X-ray scattering by elements all over the periodic table. Ethan Cheers -- Ian On 18 January 2012 18:23, Phil Jeffreypjeff...@princeton.edu wrote: Can I be dogmatic about this ? Multiwavelength anomalous diffraction from Hendrickson (1991) Science Vol. 254 no. 5028 pp. 51-58 Multiwavelength anomalous diffraction (MAD) from the CCP4 proceedings http://www.ccp4.ac.uk/courses/proceedings/1997/j_smith/main.html Multi-wavelength
Re: [ccp4bb] MAD
With the starting remark that Wayne is larger than life in my mind, we could call SAD the Teeter Method? I think it has a very nice ring to it and perhaps Wayne would approve. I learned something new today. Until now I thought that of course it is called dispersion. That is because in the late 1980s I started studying MAD and used it as topic for my PhD qualifier (which was not allowed to be the same topic as one's dissertation). So I read every paper I could get my hands on (this was before internet and electronic access to journals, yes it once was that way, hard to believe these days). I worried a lot at the time about how it works exactly, not what it is (was) called. It is probably the case that crystallography itself isn't intuitive for someone who has never done it and to add MAD (or SAD) to it... I shall try to practice diffraction from now on. It seems scientifically preferable. Mark -Original Message- From: Lawrence Shapiro l...@columbia.edu To: CCP4BB CCP4BB@JISCMAIL.AC.UK Sent: Thu, Jan 19, 2012 2:48 pm Subject: Re: [ccp4bb] MAD I never weigh in, so I don't know if I'll get in trouble here... How would we distinguish MAD (to now be called The Hendrickson Method) from SAD (The Hendrickson Method - remeber crambin? Nature, 1981)? On Thu, Jan 19, 2012 at 3:59 PM, Anastassis Perrakis a.perra...@nki.nl wrote: A, yes, inventor's names. Anyone reading who is less than 40 and knows what MTZ stands for? ;-) My favorite technique remains SADDAM - a side product of Gerard's War On Error, that never did catch-up with the masses - experimentally or as an acronym. A. On 19 Jan 2012, at 21:51, Petr Leiman wrote: It would be so much more convenient to call these techniques (MAD, SAD, etc.) by their inventor's name. This would simplify things immensely simultaneously eliminating CCP4BB MADisagreements. Although in our days of copyrights wars, the journals and perhaps conferences where these methods were presented for the first time would insist on using their names as part of the method's name... Petr On Jan 19, 2012, at 7:42 PM, Ethan Merritt wrote: On Thursday, 19 January 2012, Ian Tickle wrote: So what does this have to do with the MAD acronym? I think it stemmed from a visit by Wayne Hendrickson to Birkbeck in London some time around 1990: he was invited by Tom Blundell to give a lecture on his MAD experiments. At that time Wayne called it multi-wavelength anomalous dispersion. Tom pointed out that this was really a misnomer for the reasons I've elucidated above. Wayne liked the MAD acronym and wanted to keep it so he needed a replacement term starting with D and diffraction was the obvious choice, and if you look at the literature from then on Wayne at least consistently called it multi-wavelength anomalous diffraction. Ian: The change-over from dispersion to diffraction in MAD protein crystallography happened a couple of years earlier, at least with regard to work being done at SSRL. I think the last paper using the term dispersion was the 1988 Lamprey hemoglobin paper. The next two papers, one a collaboration with Wayne's group and the other a collaboration with Hans Freeman's group, used the term diffraction. WA Hendrickson, JL Smith, RP Phizackerley, EA Merritt. Crystallographic structure-analysis of lamprey hemoglobin from anomalous dispersion of synchrotron radiation. PROTEINS-STRUCTURE FUNCTION AND GENETICS, 4(2):77–88, 1988. JM Guss, EA Merritt, RP Phizackerley, B Hedman, M Murata, KO Hodgson, HC Freeman. Phase determination by multiple-wavelength X-ray-diffraction - crystal-structure of a basic blue copper protein from cucumbers. SCIENCE, 241(4867):806–811, AUG 12 1988. WA Hendrickson, A Pahler, JL Smith, Y Satow, EA Merritt, RP Phizackerley. Crystal structure of core streptavidin determined from multiwavelength anomalous diffraction of synchrotron radiation. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 86(7):2190–2194, APR 1989. On the other hand, David and Lilo Templeton continued to use the term anomalous dispersion for at least another decade, describing their diffraction experiments exploring polarization effects and other characteristics of near-edge X-ray scattering by elements all over the periodic table. Ethan Cheers -- Ian On 18 January 2012 18:23, Phil Jeffrey pjeff...@princeton.edu wrote: Can I be dogmatic about this ? Multiwavelength anomalous diffraction from Hendrickson (1991) Science Vol. 254 no. 5028 pp. 51-58 Multiwavelength anomalous diffraction (MAD) from the CCP4 proceedings http://www.ccp4.ac.uk/courses/proceedings/1997/j_smith/main.html Multi-wavelength anomalous-diffraction (MAD) from Terwilliger Acta Cryst. (1994). D50, 11-16 etc. I don't see where the problem lies: a SAD experiment is a single wavelength experiment where you are using the anomalous/dispersive signals for phasing
Re: [ccp4bb] MAD wavelength
Use the scan. And yes, don't fry your crystal doing it. The best way to do this is put the fluorescence detector as close to the sample as you can and then optimize the count rate by attenuating the beam. However, some beamlines are set up to hit your crystal with full beam and then back off the fluorescence detector to the other side of the room where it can bask in the warm sunny glow of your precious crystal. On beamlines like this, you must use a sacrificial crystal to do your absorption scan. Obviously, I am not a fan of the latter method, but it really does depend on what beamline you are going to use. Ask your beamline scientist about this! Note: technically, a MAD scan is not a fluorescence scan, it is an absorption scan. You are measuring absorption and using fluorescence as a tally. A fluorescence scan would have the fluorescent photon energy on the x-axis. Unfortunately, methods of doing absorption scans are not the only thing that differs from beamline to beamline and wavelength calibration is notoriously difficult to do with an accuracy of five decimal places (1 eV in 12 keV). Personally, I calibrate on copper metal, since it is very stable and well understood, and the absolute Bragg angle I see from silicon powder gives me a consistent wavelength. Some beamlines calibrate on SeMet, but the problem with SeMet is that the actual energy of the edge is NOT the canonical Se edge found in the literature (it is about 1 eV higher). SeMet is also relatively toxic, expensive and tends to oxidize, shifting the peak. Probably the best example of the shifting edge of Se I know of is figure 1 in Sarret et. al. (2005) Applied and Environmental Microbiology, 71(5), 2331–2337. This paper contains spectra for nine Se-containing reference compound, a substantial fraction of the total that are known. Because of all this, I have been pushing the use of dandruff shampoo as an internationally recognized, inexpensive and particularly rad-hard selenium reference. Selsun Blue(R) (and the extra strength variety of Head Shoulders(R)) is 1% selenium sulfide, and gives a nice clear spectrum with a sharp white line. What remains is to calibrate this stuff against some NIST-traceable Standard Reference Material. So, my advice is to ask your beamline scientist, and don't forget to pack shampoo. -James Holton MAD Scientist Jerry McCully wrote: Dear All: Next week we are going to try some seleno-Met labeled crystals. We checked the literature to try to find out the peak wavelength that has been used for SAD or MAD data collection. But they are slightly different ( may be 50 ev) in different papers. I guess this is due to the discrepancy between the fluorescence scanning and the theoretical vaules of f' and f''. When we collect the data, which wavelength should we use? Should we trust the scanning results? Thanks a lot for your comments. All the best, Jerry McCully Insert movie times and more without leaving Hotmail®. See how. http://windowslive.com/Tutorial/Hotmail/QuickAdd?ocid=TXT_TAGLM_WL_HM_Tutorial_QuickAdd_062009
[ccp4bb] MAD wavelength
Dear All: Next week we are going to try some seleno-Met labeled crystals. We checked the literature to try to find out the peak wavelength that has been used for SAD or MAD data collection. But they are slightly different ( may be 50 ev) in different papers. I guess this is due to the discrepancy between the fluorescence scanning and the theoretical vaules of f' and f''. When we collect the data, which wavelength should we use? Should we trust the scanning results? Thanks a lot for your comments. All the best, Jerry McCully _ Insert movie times and more without leaving Hotmail®. http://windowslive.com/Tutorial/Hotmail/QuickAdd?ocid=TXT_TAGLM_WL_HM_Tutorial_QuickAdd_062009
Re: [ccp4bb] MAD wavelength
I think scans are better than theory, and there can also be white lines which are often dramatically higher than predicted. Just make sure that you do not roast your best crystal when you do your scan! Jacob *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** - Original Message - From: Jerry McCully To: CCP4BB@JISCMAIL.AC.UK Sent: Thursday, July 16, 2009 12:15 PM Subject: [ccp4bb] MAD wavelength Dear All: Next week we are going to try some seleno-Met labeled crystals. We checked the literature to try to find out the peak wavelength that has been used for SAD or MAD data collection. But they are slightly different ( may be 50 ev) in different papers. I guess this is due to the discrepancy between the fluorescence scanning and the theoretical vaules of f' and f''. When we collect the data, which wavelength should we use? Should we trust the scanning results? Thanks a lot for your comments. All the best, Jerry McCully -- Insert movie times and more without leaving Hotmail®. See how.
Re: [ccp4bb] MAD wavelength
Always take the scan results ahead of the typical values unless they are obviously wrong. Only use the predicted values if the scan is broken or too weak (e.g. very small crystals) and in that case I'd be tempted to add 10-20 eV to the typical peak wavelength to make sure you weren't actually collecting the inflection point since they are typically very close in SeMet. In my NSLS X29-dominated data collections, I find I end up using something like this for non-oxidized SeMet: Peak: 12664 eV, 0.9790 Angstrom (usually in range 12662-12664) Infl: 12662 eV, 0.9792 Angstrom (usually in range 12660-12662) I also typically use high energy remote: 12860 eV, 0.964 Angstrom give or take a few eV. This tends to translate well between the relatively small number of beamlines that I personally end up using. But I always prefer to take the results from the Chooch analysis of the scan from the actual crystal. Cheers (and good luck) Phil Jeffrey Princeton Jerry McCully wrote: Dear All: Next week we are going to try some seleno-Met labeled crystals. We checked the literature to try to find out the peak wavelength that has been used for SAD or MAD data collection. But they are slightly different ( may be 50 ev) in different papers. I guess this is due to the discrepancy between the fluorescence scanning and the theoretical vaules of f' and f''. When we collect the data, which wavelength should we use? Should we trust the scanning results?
Re: [ccp4bb] MAD wavelength
Just checking my oxidized Se-Met experiments, I have 12658 to 12661 eV for my peak energies, and 3 eV lower for the inflection. As others have said, do the fluorescence scan. Use your experimentally determined values. Engin On 7/16/09 11:54 AM, Phil Jeffrey wrote: Always take the scan results ahead of the typical values unless they are obviously wrong. Only use the predicted values if the scan is broken or too weak (e.g. very small crystals) and in that case I'd be tempted to add 10-20 eV to the typical peak wavelength to make sure you weren't actually collecting the inflection point since they are typically very close in SeMet. In my NSLS X29-dominated data collections, I find I end up using something like this for non-oxidized SeMet: Peak: 12664 eV, 0.9790 Angstrom (usually in range 12662-12664) Infl: 12662 eV, 0.9792 Angstrom (usually in range 12660-12662) I also typically use high energy remote: 12860 eV, 0.964 Angstrom give or take a few eV. This tends to translate well between the relatively small number of beamlines that I personally end up using. But I always prefer to take the results from the Chooch analysis of the scan from the actual crystal. Cheers (and good luck) Phil Jeffrey Princeton Jerry McCully wrote: Dear All: Next week we are going to try some seleno-Met labeled crystals. We checked the literature to try to find out the peak wavelength that has been used for SAD or MAD data collection. But they are slightly different ( may be 50 ev) in different papers. I guess this is due to the discrepancy between the fluorescence scanning and the theoretical vaules of f' and f''. When we collect the data, which wavelength should we use? Should we trust the scanning results? -- Engin Özkan Post-doctoral Scholar Laboratory of K. Christopher Garcia Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111
Re: [ccp4bb] MAD wavelength
I second Phil's opinion - it is better to scan and be sure - as long as the scan results are not hideously abnormal. If you cannot scan for whatever reason but are sure that the X-ray optical system is properly calibrated - then use Phil's numbers below :) Artem Always take the scan results ahead of the typical values unless they are obviously wrong. Only use the predicted values if the scan is broken or too weak (e.g. very small crystals) and in that case I'd be tempted to add 10-20 eV to the typical peak wavelength to make sure you weren't actually collecting the inflection point since they are typically very close in SeMet. In my NSLS X29-dominated data collections, I find I end up using something like this for non-oxidized SeMet: Peak: 12664 eV, 0.9790 Angstrom (usually in range 12662-12664) Infl: 12662 eV, 0.9792 Angstrom (usually in range 12660-12662) I also typically use high energy remote: 12860 eV, 0.964 Angstrom give or take a few eV. This tends to translate well between the relatively small number of beamlines that I personally end up using. But I always prefer to take the results from the Chooch analysis of the scan from the actual crystal. Cheers (and good luck) Phil Jeffrey Princeton Jerry McCully wrote: Dear All: Next week we are going to try some seleno-Met labeled crystals. We checked the literature to try to find out the peak wavelength that has been used for SAD or MAD data collection. But they are slightly different ( may be 50 ev) in different papers. I guess this is due to the discrepancy between the fluorescence scanning and the theoretical vaules of f' and f''. When we collect the data, which wavelength should we use? Should we trust the scanning results?
Re: [ccp4bb] MAD wavelength
On Thursday 16 July 2009 10:15:51 Jerry McCully wrote: Dear All: Next week we are going to try some seleno-Met labeled crystals. We checked the literature to try to find out the peak wavelength that has been used for SAD or MAD data collection. But they are slightly different ( may be 50 ev) in different papers. I guess this is due to the discrepancy between the fluorescence scanning and the theoretical vaules of f' and f''. When we collect the data, which wavelength should we use? Should we trust the scanning results? Yes. You should definitely trust the scanning results over any literature value. Let's leave aside for the moment that people may deliberately choose to collect data at 50-100 eV above the peak, and consider only the question of how accurately we can determine what beamline setting corresponds to where the peak is. A fluorescence scan tells you that the fluorescence peak was observed when the monochromator motor readout was N steps (where each step is typically less than 0.001 degree). This is reproducible over the short term, as you should be able to confirm by running the scan again. The nominal energy readout comes from converting the steps to degrees, and then converting the Bragg angle in degrees to an acceptance energy in eV. But these conversion assume a known setting at 0 motor steps, and if this zero point is off by even 0.001 degree that shifts the nominal energy readout near the Se edge by roughly 5 eV as I recall (depends on the monochromator crystal being used). The calibration of the beamline optics is always going to be imperfect, and is subject to minor drift over the course of time. You can ask your friendly neighborhood beamline support people to explain what factors are the most likely to affect calibration of their particular beamline. The usual culprits include heat load on the monochromator or upstream mirrors, and tunable steering of the stored particles in the ring. Not that you can do much about any of this, other than to scan again before collecting your next data set :-) -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742
Re: [ccp4bb] MAD wavelength
On a different note,it seems as if SeMet is not a regular experiment in your lab. So I would recommend not to burn your crystals and rather sacrifice the resolution versus loosing your SeMet anomalous signal after couple of degrees into the data collection. It would also be wise to run Mosflm STRATEGY ANOMALOUS to figure out where you should start collecting your data. Good luck, Jürgen On Jul 16, 2009, at 1:15 PM, Jerry McCully wrote: Dear All: Next week we are going to try some seleno-Met labeled crystals. We checked the literature to try to find out the peak wavelength that has been used for SAD or MAD data collection. But they are slightly different ( may be 50 ev) in different papers. I guess this is due to the discrepancy between the fluorescence scanning and the theoretical vaules of f' and f''. When we collect the data, which wavelength should we use? Should we trust the scanning results? Thanks a lot for your comments. All the best, Jerry McCully Insert movie times and more without leaving Hotmail®. See how. - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.me.com/bosch_lab/
Re: [ccp4bb] MAD wavelength
My 2 cents: Cent #1 But they are slightly different ( may be 50 ev) in different papers. This statement itself contains the answer - always scan, but it was already suggested by many. I'd like to get to slightly different issue here. No oxidation or any other interaction in protein crystals moves the Se edge 50 ev from its theoretical value. It is obvious that in that particular experiment the monochromator was not calibrated properly. Ethan already touched on this but I wanted to emphasize again: when a scan identifies the edge to be way out of reasonable, the beamline support staff should be asked to check the monochromator calibration before publishing such exotic results. On our beamlines at GM/CA-CAT at APS, we do calibration at the start of each user group. It's easy, fast, and Se edges from sample to sample, project to project, user to user, are remarkably stable. Cent #2 Often orientation of your sample crystal has far greater effect on the way your scan as well as f' and f curves look than oxidation or other issues in the protein molecule. Check out Bricogne's publications few years back. Cheers, Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishv...@anl.gov From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Jerry McCully Sent: Thursday, July 16, 2009 12:16 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] MAD wavelength Dear All: Next week we are going to try some seleno-Met labeled crystals. We checked the literature to try to find out the peak wavelength that has been used for SAD or MAD data collection. But they are slightly different ( may be 50 ev) in different papers. I guess this is due to the discrepancy between the fluorescence scanning and the theoretical vaules of f' and f''. When we collect the data, which wavelength should we use? Should we trust the scanning results? Thanks a lot for your comments. All the best, Jerry McCully Insert movie times and more without leaving Hotmail(r). See how. http://windowslive.com/Tutorial/Hotmail/QuickAdd?ocid=TXT_TAGLM_WL_HM_T utorial_QuickAdd_062009
Re: [ccp4bb] Re :Re: [ccp4bb] MAD phasing
You need to try both P61 22 and P6522 with the Se sites changed fron x,y,z to -x,-y,-z. The anom differences can be explained by either solution. But maybe these programs automatically check both hands? Eleanor Dodson Ethayathulla Abdulsamath wrote: hi BertThank you for your reply. Your are right about the values for your Pattersons and NatFourier, but the systematic absences and pointless suggested me to be P6122 and according to mathews coeff i get nbsp; 1 molecule with Vm=nbsp; 2.06 solvent=nbsp; 40.42. My protein has two SeMet sites so i searched for two sites. I have just pasted few reflections which showed me P61. then based on pointless i tried P6122nbsp;nbsp; 0nbsp;nbsp; 0nbsp;nbsp; 3nbsp;nbsp;nbsp;nbsp; 1.9nbsp;nbsp;nbsp;nbsp; 1.8nbsp;nbsp;nbsp;nbsp; 0.5nbsp;nbsp;nbsp;nbsp; 1.8nbsp;nbsp; 0nbsp;nbsp; 0nbsp;nbsp; 4nbsp;nbsp;nbsp;nbsp; 0.0nbsp;nbsp;nbsp;nbsp; 2.7nbsp;nbsp;nbsp;nbsp; 1.1nbsp;nbsp;nbsp;nbsp; 2.5nbsp;nbsp; 0nbsp;nbsp; 0nbsp;nbsp; 5nbsp;nbsp;nbsp;nbsp; 0.4nbsp;nbsp;nbsp;nbsp; 3.5nbsp;nbsp;nbsp; -0.5nbsp;nbsp;nbsp;nbsp; 3.3nbsp;nbsp; 0nbsp;nbsp; 0nbsp;nbsp; 6nbsp;nbsp; 427.5nbsp;nbsp;nbsp; 33.6nbsp;nbsp; 399.9nbsp;nbsp;nbsp; 30.3nbsp;nbsp; 0nbsp;nbsp; 0nbsp;nbsp; 7nbsp;nbsp;nbsp; 14.3nbsp;nbsp;nbsp;nbsp; 5.9nbsp;nbsp;nbsp;nbsp; 4.0nbsp;nbsp;nbsp;nbsp; 4.8nbsp;nbsp; 0nbsp;nbsp; 0nbsp;nbsp; 8nbsp;nbsp;nbsp;nbsp; 1.5nbsp;nbsp;nbsp;nbsp; 5.8nbsp;nbsp;nbsp; -4.4nbsp;nbsp;nbsp;nbsp; 6.3nbsp;nbsp; 0nbsp;nbsp; 0nbsp;nbsp; 9nbsp;nbsp;nbsp; 10.8nbsp;nbsp;nbsp;nbsp; 6.7nbsp;nbsp;nbsp; -2.1nbsp;nbsp;nbsp;nbsp; 7.5nbsp;nbsp; 0nbsp;nbsp; 0nbsp; 10nbsp;nbsp;nbsp;nbsp; 7.0nbsp;nbsp;nbsp;nbsp; 7.3nbsp;nbsp;nbsp;nbsp; 1.5nbsp;nbsp;nbsp;nbsp; 7.2nbsp;nbsp; 0nbsp;nbsp; 0nbsp; 11nbsp;nbsp;nbsp; -3.8nbsp;nbsp;nbsp;nbsp; 9.3nbsp;nbsp;nbsp; -2.7nbsp;nbsp;nbsp;nbsp; 8.4nbsp;nbsp; 0nbsp;nbsp; 0nbsp; 12nbsp;nbsp; 201.7nbsp;nbsp;nbsp; 19.1nbsp;nbsp; 198.6nbsp;nbsp;nbsp; 19.8nbsp;nbsp; 0nbsp;nbsp; 0nbsp; 13nbsp;nbsp;nbsp; 22.5nbsp;nbsp;nbsp;nbsp; 9.6nbsp;nbsp;nbsp; 12.5nbsp;nbsp;nbsp;nbsp; 9.9nbsp;nbsp; 0nbsp;nbsp; 0nbsp; 14nbsp;nbsp;nbsp;nbsp; 2.9nbsp;nbsp;nbsp; 10.7nbsp;nbsp;nbsp;nbsp; 0.0nbsp;nbsp;nbsp;nbsp; 8.5nbsp;nbsp; 0nbsp;nbsp; 0nbsp; 15nbsp;nbsp; -21.0nbsp;nbsp;nbsp; 12.6nbsp;nbsp;nbsp;nbsp; 1.4nbsp;nbsp;nbsp; 12.1nbsp;nbsp; 0nbsp;nbsp; 0nbsp; 16nbsp;nbsp;nbsp; -1.6nbsp;nbsp;nbsp; 12.6nbsp;nbsp;nbsp; 10.8nbsp;nbsp;nbsp; 12.3nbsp;nbsp; 0nbsp;nbsp; 0nbsp; 18nbsp; 6649.0nbsp;nbsp; 474.7nbsp; 6423.4nbsp;nbsp; 460.5nbsp;nbsp; 0nbsp;nbsp; 0nbsp; 19nbsp;nbsp;nbsp; -4.6nbsp;nbsp;nbsp; 16.5nbsp;nbsp;nbsp; -8.5nbsp;nbsp;nbsp; 15.1nbsp;nbsp; 0nbsp;nbsp; 0nbsp; 20nbsp;nbsp; -44.1nbsp;nbsp;nbsp; 17.0nbsp;nbsp; -16.3nbsp;nbsp;nbsp; 16.7nbsp;nbsp; 0nbsp;nbsp; 0nbsp; 21nbsp;nbsp;nbsp; 34.6nbsp;nbsp;nbsp; 20.7nbsp;nbsp;nbsp; 61.8nbsp;nbsp;nbsp; 18.5nbsp;nbsp; 0nbsp;nbsp; 0nbsp; 22nbsp;nbsp; -16.7nbsp;nbsp;nbsp; 12.5nbsp;nbsp; -15.4nbsp;nbsp;nbsp; 15.9nbsp;nbsp; 0nbsp;nbsp; 0nbsp; 23nbsp;nbsp; -46.2nbsp;nbsp;nbsp; 18.7nbsp;nbsp; -35.9nbsp;nbsp;nbsp; 18.2nbsp;pointless resultsBest Solutionnbsp;nbsp;nbsp;nbsp; space group P 61 2 2nbsp;nbsp; Reindex operator:nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; [h,k,l]nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; nbsp;nbsp; Laue group probability:nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 1.000nbsp;nbsp; Systematic absence probability:nbsp;nbsp;nbsp;nbsp; 0.963nbsp;nbsp; Total probability:nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 0.963nbsp;nbsp; Space group confidence:nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 0.949nbsp;nbsp; Laue group confidencenbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 1.000thank youEthayathullaOn Thu, 21 May 2009 19:44:27 -0400 Bert Van Den Berg wrote Re: [ccp4bb] MAD phasing Hi,My guess is that you don’t have the right space group. The values for your Pattersons and NatFourier are way too low, especially the NatFourier you would like to be at least 2-3 or so. In your assigned space group, do you have a reasonable value for nbsp;the matthews coefficient? Is there NCS? Are you finding the expected number of Se sites? Again, I would try to investigate alternative SGs.Also it would be a good idea to take the sites and refine them with SHARP.Good luck, Bert On 5/21/09 6:38 PM, Ethayathulla Abdulsamath wrote:helloI am have a MAD dataset collected upto 2.3A but anomalous signal is upto 3.5A. The dataset is in P6 and based on pointless and absences it is P6122. Overall Rlin/rsym is (0.07/ 0.06). the overall redundancy is 10. I have two Se peaks, i used solve/resolve to find those peaks. I used datasets from 3.5 to 20A to find peaks i got two good peaks of occ (1.4 amp; 0.92). I did analyze_solve and refined those peaks. Then i tried resolve to autobuild and phasing but it didnt work. The r-factor FC vs FP is 0.40 and FOM 0.6, although
Re: [ccp4bb] MAD phasing
You need to try alternative space groups, such as P6522, which has the same extinctions and merging statistics as P6122. What do the maps look like coming out of SOLVE/RESOLVE? Ho UC Berkeley
[ccp4bb] MAD phasing
helloI am have a MAD dataset collected upto 2.3A but anomalous signal is upto 3.5A. The dataset is in P6 and based on pointless and absences it is P6122. Overall Rlin/rsym is (0.07/ 0.06). the overall redundancy is 10. I have two Se peaks, i used solve/resolve to find those peaks. I used datasets from 3.5 to 20A to find peaks i got two good peaks of occ (1.4 amp; 0.92). I did analyze_solve and refined those peaks. Then i tried resolve to autobuild and phasing but it didnt work. The r-factor FC vs FP is 0.40 and FOM 0.6, although the results looks promising i couldnt find proper phasing using phenix, resolve.autobuild.nbsp; i tried phenix.autosol also but it didnt work. how can i check the peaks are real.nbsp; can anybody suggest me how do I proceed further and what r the mistakes i am doing..Thank you EthayathullaFROM SOLVEnbsp; Sitenbsp;nbsp;nbsp; xnbsp;nbsp;nbsp;nbsp;nbsp;nbsp; ynbsp;nbsp;nbsp;nbsp;nbsp;nbsp; znbsp;nbsp;nbsp;nbsp;nbsp;nbsp; occnbs! p;nbsp;nbsp;nbsp;nbsp;nbsp; Bnbsp;nbsp;nbsp;nbsp; -- PEAKnbsp; HEIGHT --nbsp;nbsp;nbsp; 1nbsp;nbsp; 0.386nbsp;nbsp; 0.986nbsp;nbsp; 0.050nbsp;nbsp; 1.449nbsp; 60.000nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 23.82nbsp;nbsp;nbsp; 2nbsp;nbsp; 0.623nbsp;nbsp; 0.997nbsp;nbsp; 0.046nbsp;nbsp; 0.921nbsp; 60.000nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 22.11nbsp;Summary of scoring for this solution:nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; -- over many solutions--nbsp;nbsp;nbsp; -- this solution --nbsp;Criterianbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; MEANnbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; SDnbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; VALUEnbsp;nbsp;nbs! p;nbsp;nbsp;nbsp;nbsp; Z-SCOREnbsp;Pattersons:nbsp;nbsp;nbsp; nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 0.129nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 0.500nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 0.279nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 0.299nbsp;Cross-validation Fourier:nbsp;nbsp;nbsp;nbsp; 4.83nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 2.62nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 41.8nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 14.1nbsp;NatFourier CCx100:nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 3.28nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 1.24nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 3.93nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 0.521nbsp;Mean figure of meritx100:nbsp;nbsp;nbsp;nbsp; 0.00nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 7.16nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 53.5nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 7.48nbsp;Correction for Z-scores:nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nb! sp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; -10.5nbsp;Overall Z-score value:nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 11.9RESOLVE resultsnbsp;CORRECTED OVERALL FIGURE OF MERIT OF PHASING:nbsp;nbsp; 0.61nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; *nbsp;*nbsp;nbsp;nbsp;nbsp; ESTIMATED FRACTION OF PHASE INFORMATION FROM PRIOR:nbsp; 0.39nbsp;nbsp;nbsp;nbsp;nbsp; *nbsp;*nbsp;nbsp;nbsp;nbsp; ESTIMATED FRACTION OF PHASE INFORMATION FROM MAP:nbsp;nbsp;nbsp; 0.61nbsp;nbsp;nbsp;nbsp;nbsp; *nbsp;*nbsp;nbsp;nbsp;nbsp; NOTE: The fract! ion from prior will be roughly proportional tonbsp; *nbsp;nbsp;nbs p; Overall average CC:nbsp;nbsp; 0.5423778nbsp;Results of wilson scaling of model Fc to Fo :nbsp;Scale on I to apply to Fc =nbsp;nbsp;nbsp;nbsp;nbsp; 1.934nbsp;B-value to apply to Fc=nbsp;nbsp;nbsp;nbsp;nbsp; 1.971nbsp;Overall R-factor for FC vs FP: 0.404 fornbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 3288 reflectionsnbsp;Leaving outnbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 1nbsp; reflections with FC=0 and correcting R-factor tonbsp; 0.4036375nbsp; fromnbsp;nbsp; 0.4035717nbsp;nbsp;nbsp;nbsp;nbsp; as onlynbsp;nbsp; 99.96960nbsp;nbsp;nbsp;nbsp; % of the reflections are oknbsp;Writing overall R-factornbsp;nbsp; 0.4036375nbsp;nbsp;nbsp;nbsp;nbsp; to resolve.rfactor ### A.S.Ethayathulla,Ph.D. Department of Biophysics All India Institute of Medical Sciences Ansari Nagar New Delhi-110029 India. ###
[ccp4bb] Re :Re: [ccp4bb] MAD phasing
hi BertThank you for your reply. Your are right about the values for your Pattersons and NatFourier, but the systematic absences and pointless suggested me to be P6122 and according to mathews coeff i get nbsp; 1 molecule with Vm=nbsp; 2.06 solvent=nbsp; 40.42. My protein has two SeMet sites so i searched for two sites. I have just pasted few reflections which showed me P61. then based on pointless i tried P6122nbsp;nbsp; 0nbsp;nbsp; 0nbsp;nbsp; 3nbsp;nbsp;nbsp;nbsp; 1.9nbsp;nbsp;nbsp;nbsp; 1.8nbsp;nbsp;nbsp;nbsp; 0.5nbsp;nbsp;nbsp;nbsp; 1.8nbsp;nbsp; 0nbsp;nbsp; 0nbsp;nbsp; 4nbsp;nbsp;nbsp;nbsp; 0.0nbsp;nbsp;nbsp;nbsp; 2.7nbsp;nbsp;nbsp;nbsp; 1.1nbsp;nbsp;nbsp;nbsp; 2.5nbsp;nbsp; 0nbsp;nbsp; 0nbsp;nbsp; 5nbsp;nbsp;nbsp;nbsp; 0.4nbsp;nbsp;nbsp;nbsp; 3.5nbsp;nbsp;nbsp; -0.5nbsp;nbsp;nbsp;nbsp; 3.3nbsp;nbsp; 0nbsp;nbsp; 0nbsp;nbsp; 6nbsp;nbsp; 427.5nbsp;nbsp;nbsp; 33.6nbsp;nbsp; 399.9nbsp;nbsp;nbsp; 30.3nbsp;nbsp; 0nbsp;nbsp; 0nbsp;nbsp; 7nbsp;nbsp;nbsp; 14.3nbsp;nbsp;nbsp;nbsp; 5.9nbsp;nbsp;nbsp;nbsp; 4.0nbsp;nbsp;nbsp;nbsp; 4.8nbsp;nbsp; 0nbsp;nbsp; 0nbsp;nbsp; 8nbsp;nbsp;nbsp;nbsp; 1.5nbsp;nbsp;nbsp;nbsp; 5.8nbsp;nbsp;nbsp; -4.4nbsp;nbsp;nbsp;nbsp; 6.3nbsp;nbsp; 0nbsp;nbsp; 0nbsp;nbsp; 9nbsp;nbsp;nbsp; 10.8nbsp;nbsp;nbsp;nbsp; 6.7nbsp;nbsp;nbsp; -2.1nbsp;nbsp;nbsp;nbsp; 7.5nbsp;nbsp; 0nbsp;nbsp; 0nbsp; 10nbsp;nbsp;nbsp;nbsp; 7.0nbsp;nbsp;nbsp;nbsp; 7.3nbsp;nbsp;nbsp;nbsp; 1.5nbsp;nbsp;nbsp;nbsp; 7.2nbsp;nbsp; 0nbsp;nbsp; 0nbsp; 11nbsp;nbsp;nbsp; -3.8nbsp;nbsp;nbsp;nbsp; 9.3nbsp;nbsp;nbsp; -2.7nbsp;nbsp;nbsp;nbsp; 8.4nbsp;nbsp; 0nbsp;nbsp; 0nbsp; 12nbsp;nbsp; 201.7nbsp;nbsp;nbsp; 19.1nbsp;nbsp; 198.6nbsp;nbsp;nbsp; 19.8nbsp;nbsp; 0nbsp;nbsp; 0nbsp; 13nbsp;nbsp;nbsp; 22.5nbsp;nbsp;nbsp;nbsp; 9.6nbsp;nbsp;nbsp; 12.5nbsp;nbsp;nbsp;nbsp; 9.9nbsp;nbsp; 0nbsp;nbsp; 0nbsp; 14nbsp;nbsp;nbsp;nbsp; 2.9nbsp;nbsp;nbsp; 10.7nbsp;nbsp;nbsp;nbsp; 0.0nbsp;nbsp;nbsp;nbsp; 8.5nbsp;nbsp; 0nbsp;nbsp; 0nbsp; 15nbsp;nbsp; -21.0nbsp;nbsp;nbsp; 12.6nbsp;nbsp;nbsp;nbsp; 1.4nbsp;nbsp;nbsp; 12.1nbsp;nbsp; 0nbsp;nbsp; 0nbsp; 16nbsp;nbsp;nbsp; -1.6nbsp;nbsp;nbsp; 12.6nbsp;nbsp;nbsp; 10.8nbsp;nbsp;nbsp; 12.3nbsp;nbsp; 0nbsp;nbsp; 0nbsp; 18nbsp; 6649.0nbsp;nbsp; 474.7nbsp; 6423.4nbsp;nbsp; 460.5nbsp;nbsp; 0nbsp;nbsp; 0nbsp; 19nbsp;nbsp;nbsp; -4.6nbsp;nbsp;nbsp; 16.5nbsp;nbsp;nbsp; -8.5nbsp;nbsp;nbsp; 15.1nbsp;nbsp; 0nbsp;nbsp; 0nbsp; 20nbsp;nbsp; -44.1nbsp;nbsp;nbsp; 17.0nbsp;nbsp; -16.3nbsp;nbsp;nbsp; 16.7nbsp;nbsp; 0nbsp;nbsp; 0nbsp; 21nbsp;nbsp;nbsp; 34.6nbsp;nbsp;nbsp; 20.7nbsp;nbsp;nbsp; 61.8nbsp;nbsp;nbsp; 18.5nbsp;nbsp; 0nbsp;nbsp; 0nbsp; 22nbsp;nbsp; -16.7nbsp;nbsp;nbsp; 12.5nbsp;nbsp; -15.4nbsp;nbsp;nbsp; 15.9nbsp;nbsp; 0nbsp;nbsp; 0nbsp; 23nbsp;nbsp; -46.2nbsp;nbsp;nbsp; 18.7nbsp;nbsp; -35.9nbsp;nbsp;nbsp; 18.2nbsp;pointless resultsBest Solutionnbsp;nbsp;nbsp;nbsp; space group P 61 2 2nbsp;nbsp; Reindex operator:nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; [h,k,l]nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; nbsp;nbsp; Laue group probability:nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 1.000nbsp;nbsp; Systematic absence probability:nbsp;nbsp;nbsp;nbsp; 0.963nbsp;nbsp; Total probability:nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 0.963nbsp;nbsp; Space group confidence:nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 0.949nbsp;nbsp; Laue group confidencenbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 1.000thank youEthayathullaOn Thu, 21 May 2009 19:44:27 -0400 Bert Van Den Berg wrote Re: [ccp4bb] MAD phasing Hi,My guess is that you dont have the right space group. The values for your Pattersons and NatFourier are way too low, especially the NatFourier you would like to be at least 2-3 or so. In your assigned space group, do you have a reasonable value for nbsp;the matthews coefficient? Is there NCS? Are you finding the expected number of Se sites? Again, I would try to investigate alternative SGs.Also it would be a good idea to take the sites and refine them with SHARP.Good luck, Bert On 5/21/09 6:38 PM, Ethayathulla Abdulsamath wrote:helloI am have a MAD dataset collected upto 2.3A but anomalous signal is upto 3.5A. The dataset is in P6 and based on pointless and absences it is P6122. Overall Rlin/rsym is (0.07/ 0.06). the overall redundancy is 10. I have two Se peaks, i used solve/resolve to find those peaks. I used datasets from 3.5 to 20A to find peaks i got two good peaks of occ (1.4 amp; 0.92). I did analyze_solve and refined those peaks. Then i tried resolve to autobuild and phasing but it didnt work. The r-factor FC vs FP is 0.40 and FOM 0.6, although the results looks promising i couldnt find proper phasing using phenix, resolve.autobuild. nbsp;i tried phenix.autosol also but it didnt work. how can i check the peaks are real. nbsp;can
[ccp4bb] Re :Re: [ccp4bb] MAD phasing
hello peteri tried phenix.autosol. It gave me following results.nbsp; but the data analyses says that my data pseudo translational symmetry, I have pasted it. Do phenix handle pseudotranslation. Need suggestion on thisSolution # 1nbsp; BAYES-CC: 15.3 +/- 27.3 Dataset #1nbsp;nbsp; SG: P 61 2 2nbsp;nbsp; FOM: 0.4Score type:nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; SKEWnbsp;nbsp;nbsp; CORR_RMSRaw scores:nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 0.04nbsp;nbsp;nbsp;nbsp;nbsp; 0.67100x EST OF CC:nbsp;nbsp; 18.93nbsp;nbsp;nbsp;nbsp; 15.24nbsp; Refined heavy atom sites (fractional): xyznbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 0.865nbsp;nbsp;nbsp;nbsp;nbsp; 0.471nbsp;nbsp;nbsp;nbsp;nbsp; 0.070 xyznbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 0.099nbsp;nbsp;nbsp;nbsp;nbsp; 0.513nbsp;nbsp;nbsp;nbsp;nbsp; 0.070 Twinning and intensity statistics summary (acentric data):Statistics independent of twin lawsnbsp; - lt;I^2gt;/lt;Igt;^2 : 2.545nbsp; - lt;Fgt;^2/lt;F^2gt; : 0.718nbsp; - lt;|E^2-1|gt;nbsp;nbsp; : 0.852nbsp; - lt;|L|gt! ;, lt;L^2gt;: 0.530, 0.370nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; Multivariate Z score L-test: 4.008nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; The multivariate Z score is a quality measure of the givennbsp;nbsp;nbsp;nbsp;nbsp;nbsp; spread in intensities. Good to reasonable data are expectednbsp;nbsp;nbsp;nbsp;nbsp;nbsp; to have a Z score lower than 3.5.nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; Large values can indicate twinning, but small values do notnbsp;nbsp;nbsp;nbsp;nbsp;nbsp; necessarily exclude it.Statistics depending on twin laws--| Operatornbsp; | type | R obs. | Britton alpha | H alpha | ML alpha |--| h,-h-k,-l |nbsp;nbsp; Mnbsp; | 0.032nbsp; | 0.455nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; | 0.470nbsp;nbsp; | 0.478nbsp;nbsp;nbsp; |--Patterson analyses! nbsp; - Largest peak heightnbsp;nbsp; : 61.921nbsp;nbsp; (correspo nding p value : 1.218e-05)The analyses of the Patterson function reveals a significant off-origin peak that is 61.92 % of the origin peak, indicating pseudo translational symmetry. The chance of finding a peak of this or larger height by random in a structure without pseudo translational symmetry is equal to the 1.2181e-05. The detected tranlational NCS is most likely also responsible for the elevated intensity ratio. See the relevant section of the logfile for more details. The results of the L-test indicate that the intensity statistics Show more centric character than is expected for acentric data. This behavoir might be explained by the presence of the detected pseudo translation.+Thank youEthayathullaOn Thu, 21 May 2009 16:34:28 -0700 Peter Zwart wrote Did you check for twinning?Why don't you try to use phenix.autosol alone?P 2009/5/21 Ethayathulla Abdulsamath : gt; hello gt; gt; ! I am have a MAD dataset collected upto 2.3A but anomalous signal is upto gt; 3.5A. The dataset is in P6 and based on pointless and absences it is P6122. gt; Overall Rlin/rsym is (0.07/ 0.06). the overall redundancy is 10. I have two gt; Se peaks, i used solve/resolve to find those peaks. I used datasets from 3.5 gt; to 20A to find peaks i got two good peaks of occ (1.4 amp; 0.92). I did gt; analyze_solve and refined those peaks. Then i tried resolve to autobuild and gt; phasing but it didnt work. The r-factor FC vs FP is 0.40 and FOM 0.6, gt; although the results looks promising i couldnt find proper phasing using gt; phenix, resolve.autobuild.nbsp; i tried phenix.autosol also but it didnt work. gt; how can i check the peaks are real.nbsp; can anybody suggest me how do I proceed gt; further and what r the mistakes i am doing.. gt; gt; Thank you gt; Ethayathulla gt; FROM SOLVE gt; nbsp; Sitenbsp;nbsp;nbsp; xnbsp;nbsp;nbsp;nbsp;nbsp;! nbsp; ynbsp;nbsp;nbsp;nbsp;nbsp;nbsp; znbsp;nbsp;nbsp;nbsp; nbsp;nbsp; occnbsp;nbsp;nbsp;nbsp;nbsp;nbsp; Bnbsp;nbsp;nbsp;nbsp; -- PEAKnbsp; HEIGHT -- gt; nbsp;nbsp;nbsp; 1nbsp;nbsp; 0.386nbsp;nbsp; 0.986nbsp;nbsp; 0.050nbsp;nbsp; 1.449nbsp; 60.000nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 23.82 gt; nbsp;nbsp;nbsp; 2nbsp;nbsp; 0.623nbsp;nbsp; 0.997nbsp;nbsp; 0.046nbsp;nbsp; 0.921nbsp; 60.000nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; 22.11 gt; nbsp;Summary of scoring for this solution: gt; nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; -- over many solutions--nbsp;nbsp;nbsp; -- this solution -- gt; nbsp;Criterianbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; MEANnbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp;nbsp; SDnbsp;nbsp;nbsp! ;nbsp;nbsp;nbsp;nbsp;nbsp; VALUE gt; Z-SCORE gt;
Re: [ccp4bb] MAD screen pattern
The probably more elegant way is to perform ESI-MS of the protein. Best wishes Kornelius On Fri, 20 Jul 2007 12:22:27 +0800 劉家欣(OZ) [EMAIL PROTECTED] wrote: Dear all: A dataset of Sel-Met crystal was collected in synchotron. However, I am not sure whether the sel-Met is incoperated in the protein. The screen pattern is decribed as below. Anybady had the experiences about this? Best wish jaishin -- Kornelius Zeth Max Planck Institute for Developmental Biology Dept. Protein Evolution Spemannstr. 35 72076 Tuebingen, Germany [EMAIL PROTECTED] Tel -49 7071 601 323 Fax -49 7071 601 349
Re: [ccp4bb] MAD and twinning
XPREP may well be the only program that can read a .sca file, detwin it as you suggest, and write another .sca file directly. Since it is a MAD experiment and the true space group is probably P31 or P32, you must be careful to check that the different wavelengths have been indexed consistently. Even if you get the same twin fraction for each wavelength independently and the merging R-index is not too bad, they could still be indexed inconsistently! George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-2582 On Tue, 24 Apr 2007, Jordi Benach wrote: Hi, I just got a MAD dataset (~2.5A) of a crystal that so far seems to belong to P31 or P32 space group and that also scales pretty well in P3121 or P3221. According to the UCLA twinning server, the P31/P32 crystal is merohedrally twinned with a twinning fraction of 0.33 and following a twinning operation h,-h-k,-l. CNS gives a twinning fraction of 0.42. Although we have solved twinned crystals in the lab with similar twinning fractions/resolution in the past using SOLVE or BnP/SHELX, only realizing that the crystal was twinned during refinement when the R values wouldn't go down. In this P31/P32 case, however, I can't solve the twinned data with any program, or at least I can't get interpretable electron density maps. Any ideas, clues? Is there a way to get a program that will detwin raw intensity data (like *.sca files directly from scalepack)? Thanks, Jordi
Re: [ccp4bb] MAD and twinning
So one obvious questions: was your crystal fully bathed in the beam ? If not: would be interesting to try having a look at the unmerged data...Well, easier to suggest than to do... I recall being frowned upon by my former supervisor (a small molecule crystallographer) for having crystals larger than the beam and for looking at fishnets In any case, xtriage will detwin data with anomalous signal properly. download the latest version from www.phenix-online.org (either cci_apps or the latest phenix development release) Note that according to Dauter (sorry, i forgot the reference), finding a substructure in twinned data is usually not a problem (given reasonable data). Improvement on the density modification according to Dauter can be obtained by performing density modification on detwinned data. HTH Peter
[ccp4bb] MAD/SAD data collection strategy
Hi all, I'm looking for some advices on some general hints on how to carry out a MAD/SAD data collection. We had SeMet crystals that diffracted to ca. 3.5 Angs, with anomalous signal only at ca. 5-5.5 Angs, with diffraction decaying on brilliant beamlines (ID29 or ID23 at the ESRF) in a matter of ca. 300 degrees... Needless to say, that was not sufficient to solve the structure... We do have improved the crystals that look now nicer and bigger, and have some beamtime next weeks both at BM16 and ID29 at the ESRF. Assumed that we do see diffraction higher that 3 Angs, what would people suggest? Collecting first at the high energy remote for a SAD experiment and then going for peak and inflection point, or rather going for the peak first, then remote and ip? I personally would avoid the continuous switch of wavelengths, but I know there are some fans of this technique, either... Let the gurus talk! Any advice is obviously highly appreciated! Thanks in advance, Sebastiano and Claudio -- Sebastiano Pasqualato, PhD IFOM Istituto FIRC di Oncologia Molecolare via Adamello, 16 20139 Milano Italy tel +39 02 574 303 325 fax +39 02 574 303 310
Re: [ccp4bb] MAD/SAD data collection strategy
Hi Sebastiano, think of it this way: it's not your crystals that decay within 300 degrees, it's you who let them decay that quickly, by not attenuating the beam sufficiently. But now that you know approximately how long they survive (which won't change just because the crystal is bigger, I think), you should figure out how much to attenuate the beam so you can get all the degrees you need. RESIST THE URGE TO BURN FOR RESOLUTION. If your crystal dies, your resolution is useless. If you have enough Se atoms, SAD may be enough to phase, but my rule of thumb is, the fewer Se atoms or the worse the resolution, the more you need to consider getting at least a second wavelength. (Don't stress about the 3rd, not with your crystal dying.) I'd do them sequentially, because if it dies halfway through the second dataset, at least you still have one complete first dataset to do something with maybe. And you want the first to be the one most likely to work as SAD, so I'd do the peak, and then remote (which gets biggest delta-f' from peak). Hope that helps. Above all: DO NOT KILL YOUR CRYSTAL. phx. _ From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Sebastiano Pasqualato Sent: 15 February 2007 14:01 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] MAD/SAD data collection strategy Hi all, I'm looking for some advices on some general hints on how to carry out a MAD/SAD data collection. We had SeMet crystals that diffracted to ca. 3.5 Angs, with anomalous signal only at ca. 5-5.5 Angs, with diffraction decaying on brilliant beamlines (ID29 or ID23 at the ESRF) in a matter of ca. 300 degrees... Needless to say, that was not sufficient to solve the structure... We do have improved the crystals that look now nicer and bigger, and have some beamtime next weeks both at BM16 and ID29 at the ESRF. Assumed that we do see diffraction higher that 3 Angs, what would people suggest? Collecting first at the high energy remote for a SAD experiment and then going for peak and inflection point, or rather going for the peak first, then remote and ip? I personally would avoid the continuous switch of wavelengths, but I know there are some fans of this technique, either... Let the gurus talk! Any advice is obviously highly appreciated! Thanks in advance, Sebastiano and Claudio -- Sebastiano Pasqualato, PhD IFOM Istituto FIRC di Oncologia Molecolare via Adamello, 16 20139 Milano Italy tel +39 02 574 303 325 fax +39 02 574 303 310
