Re: [ccp4bb] AW: [ccp4bb] Dependency of theta on n/d in Bragg's law

[Petr Leiman]

Dear Dom,

No attachment here in either of your messages...

Maybe you can put it up on Dropbox or Google drive and send us the URL?

Thanks,

Petr

On 08/23/2013 04:33 AM, Dom Bellini wrote:
> Hi
>
> Some people emailed me saying that the attachment did not get through.
>
> I hope this will work.
>
> Sorry.
>
> D
>
> 
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Edward A. 
> Berry [ber...@upstate.edu]
> Sent: 23 August 2013 00:01
> To: ccp4bb
> Subject: Re: [ccp4bb] AW: [ccp4bb] Dependency of theta on n/d in Bragg's law
>
> OK, I see my mistake. n has nothing to do with higher-order
> reflections or planes at closer spacing than unit cell dimensions.
> n >1 implies larger d, like the double layer mentioned by the original
> poster, and those turn out to give the same structure factor as the
> n=1 reflection so we only consider n=1 (for monochromatic).
> The higher order reflection from closer spaced miller planes
> of course do not satisfy bragg lawat the same lambda and theta.
> So I hope people will disregard my confused post (but I think the
> one before was somewhat in the right direction)
>
> The higher order diffractions come from finding planes through
> the latticethat intersect a large number of points? no- planes
> corresponding to 0,0,5 in an orthorhombic crystal do not  all
> intersect lattice points, and anyway protein crystals aren't
> made of lattice points, they havecontinuous density.
>
> Applying Braggs law to these closer-spaced miller planes
> will tell you that points in one plane will diffract in phase.
> But since the protein in the five layers between the planes
> will be different, in fact the layers will not diffract in
> phase  and diffraction condition will not be met.
>
> You could say OK, each of the 5 layesr will diffract
> with different amplitude and out of phase, but their
> vector-sum resultant will be the same as that of
> every other five layers, so diffraction from points
> through the whole crystal  will interfere constructively.
>
> Or you could say that this theta and lambda satisfy the
> bragg equation with d= c axis and n=5, so that points
> separated by cell dimensions, which are equal due to
> the periodicity of the crystal, will diffract in phase.
> That would be a use for n>1 with monochromatic light.
> The points separated by the small d-spacing scatter in
> phase, but that is irrelevant since they are not
> crystallographically equivalent. But they also scatter in phase
> (actually out of phase by 5 wavelengths) with points separated
> by one unit cell, because they satisfy braggs law with
> d=c and n=5 (for 0,0,5 reflection still).
> So then the higher-order reflections do involve n,
> but it is the small d-spacing that corresponds to n=1
> and the unit cell spacing which corresponds to the higher n.
> The latter results in the diffraction condition being met.
> (or am I still confused?)
> (and I hope I've got my line-wrapping under control now so this won't be so 
> hard to read)
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> Ethan Merritt wrote:
>> On Thursday, August 22, 2013 02:19:11 pm Edward A. Berry wrote:
>>> One thing I find confusing is the different ways in which d is used.
>>> In deriving Braggs law, d is often presented as a unit cell dimension,
>>> and "n" accounts for the higher order miller planes within the cell.
>> It's already been pointed out above, and you sort of paraphrase it later,
>> but let me give my spin on a non-confusing order of presentation.
>>
>> I think it is best to tightly associate n and lambda in your mind
>> (and in the mind of a student). If you solve the Bragg's law equation for
>> the wavelength, you don't get a unique answer because you are actually
>> solving for n*lambda rather than lambda.
>>
>> There is no ambiguity about the d-spacing, only about the wavelength
>> that d and theta jointly select for.
>>
>> That's why, as James Holton mentioned, when dealing with a white radiation
>> source you need to do something to get rid of the harmonics of the wavelength
>> you are interested in.
>>
>>> But then when you ask a student to use Braggs law to calculate the 
>>> resolution
>>> of a spot at 150 mm from the beam center at given camera length and 
>>> wavelength,
>>> without mentioning any unit cell, they ask, "do you mean the first order 
>>> reflection?"
>> I would answer that with "Assume a true monochromatic beam, so n is 
>> necessarily
>> equal to 1".
>>
>>> Yes, it would be the first order reflection from planes whose spacing is the
>>> answer i am looking for, but going back to Braggs law derived with the unit 
>>> cell
>>> it would be a high order reflection for any reasonable sized protein 
>>> crystal.
>> For what it's worth, when I present Bragg's law I do it in three stages.
>> 1) Explain the periodicity of the lattice (use a 2D lattice for clarity).
>> 2) Show that a pair of indices hk defines some set of planes (lines)
>>  through the 

[ccp4bb] Post-doc position for SAXS at the MAX IV Laboratory

[Marjolein Thunnissen]

The MAX IV laboratory in Lund has opened a position for a Postdoctoral fellow 
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about the MAX IV laboratory can be obtained at the homepage 
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best regards

Marjolein Thunnissen


 Marjolein Thunnissen Phone +46-(0)76-632 0417
 Associate Professor  Fax   +46-(0)46-22 24692
 Dept of Biochemistry and Structural Biology, Lund University
http://www.mps.lu.se
 PO-Box 124 S-221 00 Lund, Sweden

Scientific coordinator MX (The MAX IV Laboratory): I911 and BioMAX

[ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Dependency of theta on n/d in Bragg's law

[Herman . Schreuder]

Dear Edward,

Now I am getting a little confused: If you look at a "higher order" 2n 
reflection, you will also get diffraction from the intermediate "1n" layers, so 
the structure factor you are looking at is in fact the "1n" structure factor. I 
think your original post was correct.

To summarize how I see it:
1) Braggs law has nothing to do with crystals or unit cells, it only describes 
diffraction from sets of planes.
2) However, to get constructive interference from all unit cells in the 
crystal, the periodicity of the set of planes must match the periodicity of the 
crystal, which means that only sets of planes with integer miller indices are 
allowed.

So the unit cell dictates which sets of planes are able to constructively 
diffract. However, there might not be anything physically present in the 
crystal with that periodicity. In this case the corresponding reflection will 
be weak or absent. This is the kind of information we use to calculate our 
wonderful electron density maps.

Best,
Herman



-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Edward 
A. Berry
Gesendet: Freitag, 23. August 2013 01:01
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] AW: [ccp4bb] Dependency of theta on n/d in Bragg's law

OK, I see my mistake. n has nothing to do with higher-order reflections or 
planes at closer spacing than unit cell dimensions.
n >1 implies larger d, like the double layer mentioned by the original poster, 
and those turn out to give the same structure factor as the
n=1 reflection so we only consider n=1 (for monochromatic).
The higher order reflection from closer spaced miller planes of course do not 
satisfy bragg lawat the same lambda and theta.
So I hope people will disregard my confused post (but I think the one before 
was somewhat in the right direction)

The higher order diffractions come from finding planes through the latticethat 
intersect a large number of points? no- planes corresponding to 0,0,5 in an 
orthorhombic crystal do not  all intersect lattice points, and anyway protein 
crystals aren't made of lattice points, they havecontinuous density.

Applying Braggs law to these closer-spaced miller planes will tell you that 
points in one plane will diffract in phase.
But since the protein in the five layers between the planes will be different, 
in fact the layers will not diffract in phase  and diffraction condition will 
not be met.

You could say OK, each of the 5 layesr will diffract with different amplitude 
and out of phase, but their vector-sum resultant will be the same as that of 
every other five layers, so diffraction from points through the whole crystal  
will interfere constructively.

Or you could say that this theta and lambda satisfy the bragg equation with d= 
c axis and n=5, so that points separated by cell dimensions, which are equal 
due to the periodicity of the crystal, will diffract in phase.
That would be a use for n>1 with monochromatic light.
The points separated by the small d-spacing scatter in phase, but that is 
irrelevant since they are not crystallographically equivalent. But they also 
scatter in phase (actually out of phase by 5 wavelengths) with points separated 
by one unit cell, because they satisfy braggs law with d=c and n=5 (for 0,0,5 
reflection still).
So then the higher-order reflections do involve n, but it is the small 
d-spacing that corresponds to n=1 and the unit cell spacing which corresponds 
to the higher n.
The latter results in the diffraction condition being met.
(or am I still confused?)
(and I hope I've got my line-wrapping under control now so this won't be so 
hard to read)






















Ethan Merritt wrote:
> On Thursday, August 22, 2013 02:19:11 pm Edward A. Berry wrote:
>> One thing I find confusing is the different ways in which d is used.
>> In deriving Braggs law, d is often presented as a unit cell 
>> dimension, and "n" accounts for the higher order miller planes within the 
>> cell.
>
> It's already been pointed out above, and you sort of paraphrase it 
> later, but let me give my spin on a non-confusing order of presentation.
>
> I think it is best to tightly associate n and lambda in your mind (and 
> in the mind of a student). If you solve the Bragg's law equation for 
> the wavelength, you don't get a unique answer because you are actually 
> solving for n*lambda rather than lambda.
>
> There is no ambiguity about the d-spacing, only about the wavelength 
> that d and theta jointly select for.
>
> That's why, as James Holton mentioned, when dealing with a white 
> radiation source you need to do something to get rid of the harmonics 
> of the wavelength you are interested in.
>
>> But then when you ask a student to use Braggs law to calculate the 
>> resolution of a spot at 150 mm from the beam center at given camera 
>> length and wavelength, without mentioning any unit cell, they ask, "do you 
>> mean the first order reflection?"
>
> I would ans

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[Gary Battle]

There are only a few places remaining for the wwPDB Workshop on 
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What, why and how?
--
The world of the PDB will be changing rapidly and profoundly over the 
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http://www.wwpdb.org/news/news_2013.html#22-May-2013 and 
http://wwpdb.org/workshop/wgroup.html). To help software developers in 
the area of structural biology to make the transition and begin 
supporting the mmCIF/PDBx format in their own programs, wwPDB 
(http://wwpdb.org/) is organising a programmers workshop. This two-day 
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---
The workshop will be held at the EMBL-EBI (http://ebi.ac.uk/) in 
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-
If you are selected as a participant, we expect you to pay for your own 
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--
This workshop is intended for "high-powered" software developers in any 
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- a brief description of the software program(s) or package(s) you have 
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- what programming language(s) you are specifically interested in;
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- any specific topics or questions you would like to see addressed in 
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If the workshop is oversubscribed, we will use the information and 
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On behalf of Gerard Kleywegt & Sameer Velankar
Protein Data Bank in Europe
A member of the Worldwide Protein Data Bank

--
Gary Battle
Protein Data Bank in Europe (PDBe)

http://www.facebook.com/proteindatabank
http://twitter.com/PDBeurope

Re: [ccp4bb] AW: [ccp4bb] Dependency of theta on n/d in Bragg's law

[Dom Bellini]

Hi,

Despite the not so large size of the pdf (256 kbs), the file does not want to 
get through.

Since a reasonable amount of people seem to have liked a copy for their 
students, following some smart suggestions I have put the booklet on Dropbox.

Here's the link: https://www.dropbox.com/s/gljckhw7ui6df6c/Booklet.pdf?m

Best,

D

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dom 
Bellini
Sent: 22 August 2013 23:38
To: ccp4bb
Subject: Re: [ccp4bb] AW: [ccp4bb] Dependency of theta on n/d in Bragg's law

Dear Community,

I have attached a short booklet written some 6 years ago during rainy evenings 
to teach principle of crystal diffraction with biologist students in mind, 
never used it as I don't have students, but I now believe its mission was this 
thread ;-)

It uses lots of real space diffraction examples, easily to picture them in the 
head, so to stick with the students for good. It was written with the 
philadelphia philosophy of "explain it to me as if I was a 5 yo".

I hope it can save some students the time of going to look for many different 
sources as it is probably a nice summary of the diffraction process.

A short answer, same as many of the other answers but in different words, to 
the original post would be: each hkl family of planes generates one and only 
one structure factor or diffraction spot without any contributions from other 
families (talking of monochromatic experiments). Perhaps doubts may arise due 
to the fact that, e.g., every other 002 plane superpose/aligns with one 001 
plane, but since their spacing d is half of the other and lambda is fixed, from 
2d sin(theta)=lambda it will result that 002, despite perfectly superposing 
with (same inclination of) 001, will reflect in a different direction with 
sin(theta) twice as that for 001. Despite 001 and 002 superpose/align with one 
another the diffraction angle changes because it is not a real reflection 
phenomenon (as if they were mirrors), keeping in mind that the planes are only 
imaginary and a way to help us to visualize the process.

Probably many people from the bb that could have given a better explanation 
than mine might have been put off by the length of the email that might have 
been required. Since I had already written it and ready to go I decided to 
attach it with the best of intentions.

Hopefully it may turn up to be useful for some one.

D




From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Ethan Merritt 
[merr...@u.washington.edu]
Sent: 22 August 2013 22:57
To: ccp4bb
Subject: Re: [ccp4bb] AW: [ccp4bb] Dependency of theta on n/d in Bragg's law

On Thursday, August 22, 2013 02:19:11 pm Edward A. Berry wrote:
> One thing I find confusing is the different ways in which d is used.
> In deriving Braggs law, d is often presented as a unit cell dimension, 
> and "n" accounts for the higher order miller planes within the cell.

It's already been pointed out above, and you sort of paraphrase it later, but 
let me give my spin on a non-confusing order of presentation.

I think it is best to tightly associate n and lambda in your mind (and in the 
mind of a student). If you solve the Bragg's law equation for the wavelength, 
you don't get a unique answer because you are actually solving for n*lambda 
rather than lambda.

There is no ambiguity about the d-spacing, only about the wavelength that d and 
theta jointly select for.

That's why, as James Holton mentioned, when dealing with a white radiation 
source you need to do something to get rid of the harmonics of the wavelength 
you are interested in.

> But then when you ask a student to use Braggs law to calculate the 
> resolution of a spot at 150 mm from the beam center at given camera 
> length and wavelength, without mentioning any unit cell, they ask, "do you 
> mean the first order reflection?"

I would answer that with "Assume a true monochromatic beam, so n is necessarily 
equal to 1".

> Yes, it would be the first order reflection from planes whose spacing 
> is the answer i am looking for, but going back to Braggs law derived 
> with the unit cell it would be a high order reflection for any reasonable 
> sized protein crystal.

For what it's worth, when I present Bragg's law I do it in three stages.
1) Explain the periodicity of the lattice (use a 2D lattice for clarity).
2) Show that a pair of indices hk defines some set of planes (lines)
   through the lattice.
3) Take some arbitrary set of planes and use it to draw the Bragg construction.

This way the Bragg diagram refers to a particular set of planes, d refers to 
the resolution of that set of planes, and n=1 for a monochromatic X-ray source. 
 The unit cell comes back into it only if you try to interpret the Bragg 
indices belonging to that set of planes.

Ethan


> Maybe the mistake is in bringing the unit cell into the derivation in 
> the first place, just define it in terms o

[ccp4bb] sin(theta_hkl)=n*lambda/(2*d_hkl)

[Robert Blessing]

A point to bear in mind is that only planes with co-prime h k l indices are 
"lattice planes" that pass through lattice points.  Planes with indices that 
are composite numbers nh nk nl are "virtual lattice planes" that do not pass 
through lattice points.

Bob


Robert H. Blessing, Ph.D.

 Hauptman-Woodward Medical Research Institute, Inc.

and

 State University of New York

at Buffalo


Hauptman-Woodward Institute

700 Ellicott Street

Buffalo, New York 14203, USA

 Phone716-898-8613

 Fax 716-898-8660

 eMail  bless...@hwi.buffalo.edu

 Internet  http://www.hwi.buffalo.edu

[ccp4bb] in summary

[Pietro Roversi]

Yes, thank you Bob! and therefore, as first pointed out in this thread
by Loes Kroon-Batenburg, and as explainedin  (among other places)
the Ladd and Palmer book that Dom Bellini pointed me to,
the indices 001, 010 etc. for example, will index first order diffraction 
maxima,
while 002, 020 etc. will be the indices for the second order diffraction maxima
from the same sets of lattice planes.

I feel now reconciled with Bragg's law (although for obvious reasons
I like Ewald's constructions much better) and this is happening
just in time for next year's 2014 IUCr celebrations :-)

Thank you all contributors to the thread!

Regards

Pietro

Sent from my Desktop

Dr. Pietro Roversi
Oxford University Biochemistry Department - Glycobiology Division
South Parks Road
Oxford OX1 3QU England - UK
Tel. 0044 1865 275339

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Robert Blessing 
[bless...@hwi.buffalo.edu]
Sent: 23 August 2013 15:52
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] sin(theta_hkl)=n*lambda/(2*d_hkl)

A point to bear in mind is that only planes with co-prime h k l indices are 
"lattice planes" that pass through lattice points.  Planes with indices that 
are composite numbers nh nk nl are "virtual lattice planes" that do not pass 
through lattice points.

Bob


Robert H. Blessing, Ph.D.

 Hauptman-Woodward Medical Research Institute, Inc.

and

 State University of New York

at Buffalo


Hauptman-Woodward Institute

700 Ellicott Street

Buffalo, New York 14203, USA

 Phone716-898-8613

 Fax 716-898-8660

 eMail  bless...@hwi.buffalo.edu

 Internet  http://www.hwi.buffalo.edu

Re: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Dependency of theta on n/d in Bragg's law

[Edward A. Berry]

I think we are just discussing different ways of saying the same thing now.
But that can be interesting, too.  If not, read no farther.

herman.schreu...@sanofi.com wrote:

Dear Edward,

Now I am getting a little confused: If you look at a "higher order" 2n reflection, you will also 
get diffraction from the intermediate "1n" layers, so the structure factor you are looking at is in 
fact the "1n" structure factor. I think your original post was correct.


Yes- I think the original poster's question about diffraction from
the 2n planes, and whether that contributes to diffraction in the
1n reflection, has been answered- physically they are the same thing.

My question now is whether it is useful to consider Braggs-law "n" to
have values other than one, and whether it is useful to tie Braggs law
to the unit cell, or better to derive it for a set of equally spaced
planes (as I think it originally was derived) and later put conditions
on when those planes will diffract.

In addition to Bragg's law one also talks about the "Bragg condition",
as somewhat related to the "diffraction condition" although maybe that
is closer to "Laue condition".
But anyway, the motivation for presenting Braggs law is to decide where
(as a function of lambda and theta) diffraction will be observed.
And in a continuos crystal (admittedly not what Braggs law was derived
for, but what the students are interested in) you don't get diffraction
without periodicity, and the spacing of the planes has to be related to
the unit cell for braggs law to help (as you say, periodicity of the planes
must match periodicity of the crystal).

When Bragg's condition is met, points separated by d scatter in phase.
Diffraction occurs when d matches the periodicity of the material, so that
crystallographically-equivalent-by-translation points scatter in phase,
and the resultants from each unit layer (1-D unit cell) scatter in phase.

If we are just considering equal planes separated by d with nothing between,
then the periodicity is just d, and bragg condition gives diffraction
condition.
If we are considering a crystal with continuous density, if d is equal to
a unit cell dimension and the planes are perpendicular to that axis, then
then the periodicity is d and brags law gives the (1-dimensional) diffraction
condition.
If d is some arbitrary spacing not related to periodicity of the matter,
brag condition still tells you that points separated by d along S scatter
in phase but if d has no relation to the periodicity, diffraction conditions
are not met and the different slabs thickness d will not scatter in phase.
If d is an integral submultiple of the periodicity, we get diffraction.
What is the best way to explain this?
1. if points separated by d scatter in phase (actually out of phase by one 
wavelength),
then spots separated by an integral multiple n of d will scatter in phase
(out of phase by n wavelengths). Now if n*d is the unit cell spacing, spots
separated by nd will be crystallographically equivalent, and scatter in
phase (actually out of phase by n wavelengths).
  But this is more elegantly expressed by using braggs law with d' =  the unit
cell spacing, nd, and n'= n. The right hand side of braggs law is calculating
the phase difference, and the left hand is saying this must be = n lambda.
That's what n is there for!

2. the periodicity of the set of planes must match the periodicity of the 
crystal-
if d is a submultiple of the unit cell spacing, points separated by d will 
scatter in
phase, but there is no relation between what exists at those points, so they 
will
not interfere constructively. each slab of thickness d will have resultant phase
(and amplitude) different from the slab above or below it.
But if d is an integral submultiple of unit cell spacing, there will be
periodicity to these slabs- the sixth slab will have the same content as
the first (or the fifth will be the same as the zero'th may be more comfortable)
so each stack of five slabs will interfere constructively with the 5 slabs above
it and so on throughout the crystal.
And as in the answer to original poster's question, it is the same diffraction
whether you consider it to be the first order diffraction of planes with d=c/5
or the fifth-order diffraction from the unit cell spacing.

I think these are equivalent in terms of the underlying physics
so this is semantics, or choosing the most intuitive explanation.
I will consider introducing Bragg's law for arbitrary planes in space
and introducing diffraction condition later with Laue condition.
And of course I should look again at some of the excellent textbooks
that are available in coming up with a plan.

But when a colleague studying 2D crystals in cryo-EM gloats:
"I got diffraction out to the fifth order", we don't want to pour
cold water by saying, "sorry, those are first order diffraction from
from planes at 1/5 spacing!" even though it means the same thing in
terms of resolution. (OK, order of diffraction doesn't h

[ccp4bb] Refinement of crystals containing a mixture in the asymmetric unit

[Paul Paukstelis]

Greetings,

We have been working on a few DNA crystals in which the asymmetric unit 
contains a stoichiometric (or nearly so) mixture of two similar but 
distinct oligonucleotides. The resolution is medium to low (2.7-2.8) but 
for a few of these there are some hints from the density for two 
different bases at the same position. I'm curious what the best way to 
approach refinement would be in this case. Alternate conformation 
doesn't really work since the residues have different nucleobases. 
Having two complete chains with 0.5 occupancy is overkill since there 
are only 2 (or 4) positions in which the sequence differs. I tried just 
adding a second chain for the varying residues at 0.5 occupancy and 
adding link records to the original chain, however this doesn't seem to 
respect geometry of the phosphodiester for the flanking residues. I 
would appreciate suggestions or any examples in the PDB that might set 
me in the right direction.


--paul

Re: [ccp4bb] Refinement of crystals containing a mixture in the asymmetric unit

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Paul,

have you actually tried using the 'alternate location indicator' with
two different residues? I would not be surprised if that would work
with refmac.

Best,
Tim

On 08/23/2013 05:39 PM, Paul Paukstelis wrote:
> Greetings,
> 
> We have been working on a few DNA crystals in which the asymmetric
> unit contains a stoichiometric (or nearly so) mixture of two
> similar but distinct oligonucleotides. The resolution is medium to
> low (2.7-2.8) but for a few of these there are some hints from the
> density for two different bases at the same position. I'm curious
> what the best way to approach refinement would be in this case.
> Alternate conformation doesn't really work since the residues have
> different nucleobases. Having two complete chains with 0.5
> occupancy is overkill since there are only 2 (or 4) positions in
> which the sequence differs. I tried just adding a second chain for
> the varying residues at 0.5 occupancy and adding link records to
> the original chain, however this doesn't seem to respect geometry
> of the phosphodiester for the flanking residues. I would appreciate
> suggestions or any examples in the PDB that might set me in the
> right direction.
> 
> --paul
> 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

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Re: [ccp4bb] Refinement of crystals containing a mixture in the asymmetric unit

[Pavel Afonine]

Hi Paul,
I would have them both in PDB file with different non-blanc altLocs and
arbitrary starting occupancies and that will work in refinement (in
phenix.refine for sure, can't tell for other programs).
Pavel



On Fri, Aug 23, 2013 at 8:39 AM, Paul Paukstelis
wrote:

> Greetings,
>
> We have been working on a few DNA crystals in which the asymmetric unit
> contains a stoichiometric (or nearly so) mixture of two similar but
> distinct oligonucleotides. The resolution is medium to low (2.7-2.8) but
> for a few of these there are some hints from the density for two different
> bases at the same position. I'm curious what the best way to approach
> refinement would be in this case. Alternate conformation doesn't really
> work since the residues have different nucleobases. Having two complete
> chains with 0.5 occupancy is overkill since there are only 2 (or 4)
> positions in which the sequence differs. I tried just adding a second chain
> for the varying residues at 0.5 occupancy and adding link records to the
> original chain, however this doesn't seem to respect geometry of the
> phosphodiester for the flanking residues. I would appreciate suggestions or
> any examples in the PDB that might set me in the right direction.
>
> --paul
>

[ccp4bb] Suitability of RaptorX models for molecular replacement

[Dimitris Ladakis]

Dear members of CCP4bb
I've used RaptorX to generate a structural model for molecular replacement, 
since there isn't any structure on PDB similar enough that i could use instead.
I am trying to find out if this is a common practice within the community and 
if people have managed to get molecular replacement to work from predicted 
models like that.
The program produced 5 different models and I got p values around 2.9e^(-3) to 
4.85e^(-3) and a uGDT around 76. Are there any other descriptors that would 
indicate the suitability of the models obtained?Your guidance would be as 
always highly appreciatedKind regardsDimitrisUniversity of Kent UK

  

[ccp4bb] cryoprotection

[Uday Kumar]

Hello

Can anyone suggest a cryoprotectant for the following crystallization condition

0.2-0.4M sodium formate

~20% PEG 3350

0-25 mM Nickel

0-100 mM Malonate

Thank you

with regards
uday

Re: [ccp4bb] cryoprotection

[Bosch, Juergen]

increase your PEG3350 >27% and keep the other components at their current 
concentration. You can also add glycerol or ethylene glycol into the mix.

If you have multiple crystals then try various variants.

Jürgen

On Aug 23, 2013, at 1:52 PM, Uday Kumar wrote:

Hello

Can anyone suggest a cryoprotectant for the following crystallization condition

0.2-0.4M sodium formate

~20% PEG 3350

0-25 mM Nickel

0-100 mM Malonate

Thank you

with regards
uday

..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-2926
http://lupo.jhsph.edu

Re: [ccp4bb] cryoprotection

[Alexander D. Scouras]

I've had good success transferring crystals grown in

200 mM NaOAc pH 5.5 / 10% PEG 

Into a solution for room temperature diffraction (in ~6 steps, peg first, then 
buffers) :

100 mM NaOAc / 100 mM Malonate / 30% PEG

And from there into a cryo solution in 4-5 steps) that was:

100 mM NaOAc / 100 mM Malonate / 30% PEG / 20% Ethylene Glycol


Crystals have been solved to at least 1.4A resolution with mosaicity in the 
0.2-0.3 range. 

-Alex




On Aug 23, 2013, at 10:52 AM, Uday Kumar  wrote:

> Hello
> 
> Can anyone suggest a cryoprotectant for the following crystallization 
> condition
> 
> 0.2-0.4M sodium formate
> 
> ~20% PEG 3350
> 
> 0-25 mM Nickel
> 
> 0-100 mM Malonate
> 
> Thank you
> 
> with regards
> uday

[ccp4bb] 3D printing structures?

[Ronnie]

An off-topic question-now that 3D printing is becoming more common, has anyone 
tried to print protein structures other than just the surface representation 
like in this tutorial? 
http://www.instructables.com/id/3D-Print-a-Protein-Modeling-a-Molecular-Machine/

Is it possible to print a ribbon representation for example?

Thanks!

Ronnie

Re: [ccp4bb] 3D printing structures?

[Miller, Mitchell D.]

Hi Ronnie,
 
I have not tried it, but a quick google search for
protein ribbon 3d printer
turns up the following in the results list-- 
http://ironchefsynbio.wordpress.com/tag/3d-printer/ 
http://www.lib.ua.edu/sites/default/files/rodgers/Rodgers%203D%20Printing%20Molecular%20X-ray%20Data_V1.pdf
http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-May/008821.html 
http://www.cgl.ucsf.edu/Outreach/technotes/ModelGallery/index.html

Regards,
Mitch

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ronnie
Sent: Friday, August 23, 2013 11:16 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] 3D printing structures?

An off-topic question-now that 3D printing is becoming more common, has anyone 
tried to print protein structures other than just the surface representation 
like in this tutorial? 
http://www.instructables.com/id/3D-Print-a-Protein-Modeling-a-Molecular-Machine/

Is it possible to print a ribbon representation for example?

Thanks!

Ronnie

Re: [ccp4bb] 3D printing structures?

[Edward A. Berry]

Along the same lines, does anyone have a program for converting Raster-3D format
such as Molscript puts out, into one of the formats readable by a 3D printer?
eab

Ronnie wrote:

An off-topic question-now that 3D printing is becoming more common, has anyone 
tried to print protein structures other than just the surface representation 
like in this tutorial? 
http://www.instructables.com/id/3D-Print-a-Protein-Modeling-a-Molecular-Machine/

Is it possible to print a ribbon representation for example?

Thanks!

Ronnie

[ccp4bb] Twinabs-cell_now

[Mahesh Lingaraju]

hello everyone

Can anyone point to me where i could obtain the programs twinabs, cell_now
? i cannot seem to locate them by simple googling.

Thanks

mahesh

Re: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Dependency of theta on n/d in Bragg's law

[Jrh]

Dear Edward,
Re your em colleagues:-
We are indeed happy to understand their diffraction to 5th order, by which we 
mean the d/5 reflection (1st order) because the two are simply different 
viewpoints.

Just one loose end:-
The remarkable thing is that the diffraction from a crystal is largely empty. 
We focus on the spots, true, but the largely empty diffraction space from a 
crystal in a sense is a most useful aspect about the W L Bragg equation.

Finally, just to mention, when I saw the laser light diffraction from a 
periodic ruled grating for the first time i thought:- it is magnificent. I rank 
it alongside the spectral lines in an atom's emission spectrum, such as the 
sodium D lines ie as i saw in my physics teaching lab. The red shifted hydrogen 
spectra of Hubble himself, available to view in the museum of the astronomical 
observatory in Los Angeles, are of course in a yet different, higher, league of 
where we are in the (expanding) universe. 

Yours sincerely,
John

Prof John R Helliwell DSc FInstP CPhys FRSC CChem F Soc Biol.
Chair School of Chemistry, University of Manchester, Athena Swan Team.
http://www.chemistry.manchester.ac.uk/aboutus/athena/index.html
 
 

On 23 Aug 2013, at 16:34, "Edward A. Berry"  wrote:

> I think we are just discussing different ways of saying the same thing now.
> But that can be interesting, too.  If not, read no farther.
> 
> herman.schreu...@sanofi.com wrote:
>> Dear Edward,
>> 
>> Now I am getting a little confused: If you look at a "higher order" 2n 
>> reflection, you will also get diffraction from the intermediate "1n" layers, 
>> so the structure factor you are looking at is in fact the "1n" structure 
>> factor. I think your original post was correct.
>> 
> Yes- I think the original poster's question about diffraction from
> the 2n planes, and whether that contributes to diffraction in the
> 1n reflection, has been answered- physically they are the same thing.
> 
> My question now is whether it is useful to consider Braggs-law "n" to
> have values other than one, and whether it is useful to tie Braggs law
> to the unit cell, or better to derive it for a set of equally spaced
> planes (as I think it originally was derived) and later put conditions
> on when those planes will diffract.
> 
> In addition to Bragg's law one also talks about the "Bragg condition",
> as somewhat related to the "diffraction condition" although maybe that
> is closer to "Laue condition".
> But anyway, the motivation for presenting Braggs law is to decide where
> (as a function of lambda and theta) diffraction will be observed.
> And in a continuos crystal (admittedly not what Braggs law was derived
> for, but what the students are interested in) you don't get diffraction
> without periodicity, and the spacing of the planes has to be related to
> the unit cell for braggs law to help (as you say, periodicity of the planes
> must match periodicity of the crystal).
> 
> When Bragg's condition is met, points separated by d scatter in phase.
> Diffraction occurs when d matches the periodicity of the material, so that
> crystallographically-equivalent-by-translation points scatter in phase,
> and the resultants from each unit layer (1-D unit cell) scatter in phase.
> 
> If we are just considering equal planes separated by d with nothing between,
> then the periodicity is just d, and bragg condition gives diffraction
> condition.
> If we are considering a crystal with continuous density, if d is equal to
> a unit cell dimension and the planes are perpendicular to that axis, then
> then the periodicity is d and brags law gives the (1-dimensional) diffraction
> condition.
> If d is some arbitrary spacing not related to periodicity of the matter,
> brag condition still tells you that points separated by d along S scatter
> in phase but if d has no relation to the periodicity, diffraction conditions
> are not met and the different slabs thickness d will not scatter in phase.
> If d is an integral submultiple of the periodicity, we get diffraction.
> What is the best way to explain this?
> 1. if points separated by d scatter in phase (actually out of phase by one 
> wavelength),
> then spots separated by an integral multiple n of d will scatter in phase
> (out of phase by n wavelengths). Now if n*d is the unit cell spacing, spots
> separated by nd will be crystallographically equivalent, and scatter in
> phase (actually out of phase by n wavelengths).
>  But this is more elegantly expressed by using braggs law with d' =  the unit
> cell spacing, nd, and n'= n. The right hand side of braggs law is calculating
> the phase difference, and the left hand is saying this must be = n lambda.
> That's what n is there for!
> 
> 2. the periodicity of the set of planes must match the periodicity of the 
> crystal-
> if d is a submultiple of the unit cell spacing, points separated by d will 
> scatter in
> phase, but there is no relation between what exists at those points, so they 
> will
> not interfere

[ccp4bb] In situ data collection

[Theresa Hsu]

Dear all

Could I get some personal reviews on the CrystalHarp plates? Has anyone used it 
for actual data collection and structure solution in situ? How does it compare 
with X-ray 'transparent' plates?

Thank you.

Theresa

Re: [ccp4bb] 3D printing structures?

[Joel Sussman]

Output should be in VRML formal
RasMol, PyMol & Jmol all have options to write out VRML format files.
Sometimes you need add additional 'struts' to give additional structural 
support, Jmol has option of adding these struts.
best regards,
Joel

On 23 Aug 2013, at 21:33, Edward A. Berry 
mailto:ber...@upstate.edu>> wrote:

Along the same lines, does anyone have a program for converting Raster-3D format
such as Molscript puts out, into one of the formats readable by a 3D printer?
eab

Ronnie wrote:
An off-topic question-now that 3D printing is becoming more common, has anyone 
tried to print protein structures other than just the surface representation 
like in this tutorial? 
http://www.instructables.com/id/3D-Print-a-Protein-Modeling-a-Molecular-Machine/

Is it possible to print a ribbon representation for example?

Thanks!

Ronnie

Re: [ccp4bb] 3D printing structures?

[Edward A. Berry]

Thanks, yes, i should have checked out the link on the original post before 
asking.
Free programs "blender" or "meshlab" convert vmrl to .stl files which 
3d-printers
including makerbot read.  
eab


Joel Sussman wrote:

Output should be in *VRML* formal
RasMol, PyMol & Jmol all have options to write out VRML format files.
Sometimes you need add additional 'struts' to give additional structural 
support, Jmol has option of adding these struts.
best regards,
Joel

On 23 Aug 2013, at 21:33, Edward A. Berry mailto:ber...@upstate.edu>> wrote:


Along the same lines, does anyone have a program for converting Raster-3D format
such as Molscript puts out, into one of the formats readable by a 3D printer?
eab

Ronnie wrote:

An off-topic question-now that 3D printing is becoming more common, has anyone 
tried to print protein structures other than just the surface representation 
like in this tutorial? 
http://www.instructables.com/id/3D-Print-a-Protein-Modeling-a-Molecular-Machine/

Is it possible to print a ribbon representation for example?

Thanks!

Ronnie

Re: [ccp4bb] 3D printing structures?

[Artem Evdokimov]

As a proud owner of the fdm 3d printer I would like to mention that if you
go from vrml to stl and then into slic3r you have to drastically refuce
polygon count or else slic3r chokes trying to process the file.

Cjeets,

Artem
On Aug 23, 2013 5:54 PM, "Edward A. Berry"  wrote:

> Thanks, yes, i should have checked out the link on the original post
> before asking.
> Free programs "blender" or "meshlab" convert vmrl to .stl files which
> 3d-printers
> including makerbot read.  eab
>
> Joel Sussman wrote:
>
>> Output should be in *VRML* formal
>> RasMol, PyMol & Jmol all have options to write out VRML format files.
>> Sometimes you need add additional 'struts' to give additional structural
>> support, Jmol has option of adding these struts.
>> best regards,
>> Joel
>>
>> On 23 Aug 2013, at 21:33, Edward A. Berry > ber...@upstate.edu>> wrote:
>>
>>  Along the same lines, does anyone have a program for converting
>>> Raster-3D format
>>> such as Molscript puts out, into one of the formats readable by a 3D
>>> printer?
>>> eab
>>>
>>> Ronnie wrote:
>>>
 An off-topic question-now that 3D printing is becoming more common, has
 anyone tried to print protein structures other than just the surface
 representation like in this tutorial? http://www.instructables.com/**
 id/3D-Print-a-Protein-**Modeling-a-Molecular-Machine/

 Is it possible to print a ribbon representation for example?

 Thanks!

 Ronnie

>>>
>>

[ccp4bb] Purification of a protein

[Jahan Alikhajeh]

Dear Friends,

I have been trying to purify a protein (27 kDa) which has a sumo plus 6 His-tag 
at N-ter giving totaly a 45 kDa protein.
This protein does not express without sumo tag and has a poly basic tail (Arg 
and Lys) at its N-ter. It does polymerize at acidic pHs.
When I tried to purify it with chelating Ni-NTA, it did not bind to the column. 
I thought perhaps His-tag hided somewhere in the protein and is not accessible 
thus, I repeated the experiments at 8 M urea. It did not make any difference; 
very low binding to the column with high amount of unbound protein in FT. Your 
advice is highly appreciated.

Regards,
Jahan

Re: [ccp4bb] Purification of a protein

[Roger Rowlett]

Why not adopt a classical purification strategy? IEX-HIC-GEC. His-tag not
required. With your protein strongly basic, anion exchange seems like a
likely first step. After IEX, hydrophobic interaction or salt precipitation
followed by gel exclusion is normally enough for well-expressed proteins.

Roger Rowlett
On Aug 23, 2013 9:27 PM, "Jahan Alikhajeh"  wrote:

> Dear Friends,
>
> I have been trying to purify a protein (27 kDa) which has a sumo plus 6
> His-tag at N-ter giving totaly a 45 kDa protein.
> This protein does not express without sumo tag and has a poly basic tail
> (Arg and Lys) at its N-ter. It does polymerize at acidic pHs.
> When I tried to purify it with chelating Ni-NTA, it did not bind to the
> column. I thought perhaps His-tag hided somewhere in the protein and is not
> accessible thus, I repeated the experiments at 8 M urea. It did not make
> any difference; very low binding to the column with high amount of unbound
> protein in FT. Your advice is highly appreciated.
>
> Regards,
> Jahan
>
>
>

Re: [ccp4bb] Purification of a protein

[Mahesh Lingaraju]

i am not sure this would work as his protein seems to be degraded by the n
end degradation pathway. i feel like it almost needs to be expressed as a
fusion protein with some stabilizing sequence


On Fri, Aug 23, 2013 at 10:08 PM, Roger Rowlett wrote:

> Why not adopt a classical purification strategy? IEX-HIC-GEC. His-tag not
> required. With your protein strongly basic, anion exchange seems like a
> likely first step. After IEX, hydrophobic interaction or salt precipitation
> followed by gel exclusion is normally enough for well-expressed proteins.
>
> Roger Rowlett
> On Aug 23, 2013 9:27 PM, "Jahan Alikhajeh"  wrote:
>
>> Dear Friends,
>>
>> I have been trying to purify a protein (27 kDa) which has a sumo plus 6
>> His-tag at N-ter giving totaly a 45 kDa protein.
>> This protein does not express without sumo tag and has a poly basic tail
>> (Arg and Lys) at its N-ter. It does polymerize at acidic pHs.
>> When I tried to purify it with chelating Ni-NTA, it did not bind to the
>> column. I thought perhaps His-tag hided somewhere in the protein and is not
>> accessible thus, I repeated the experiments at 8 M urea. It did not make
>> any difference; very low binding to the column with high amount of unbound
>> protein in FT. Your advice is highly appreciated.
>>
>> Regards,
>> Jahan
>>
>>
>>
>

Re: [ccp4bb] Refinement of crystals containing a mixture in the asymmetric unit

[Paul Paukstelis]

As an update, this approach did not work in Refmac, but as Pavel 
suggested it worked fine with phenix.refine.


--paul

On 08/23/2013 11:51 AM, Tim Gruene wrote:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Paul,

have you actually tried using the 'alternate location indicator' with
two different residues? I would not be surprised if that would work
with refmac.

Best,
Tim

On 08/23/2013 05:39 PM, Paul Paukstelis wrote:

Greetings,

We have been working on a few DNA crystals in which the asymmetric
unit contains a stoichiometric (or nearly so) mixture of two
similar but distinct oligonucleotides. The resolution is medium to
low (2.7-2.8) but for a few of these there are some hints from the
density for two different bases at the same position. I'm curious
what the best way to approach refinement would be in this case.
Alternate conformation doesn't really work since the residues have
different nucleobases. Having two complete chains with 0.5
occupancy is overkill since there are only 2 (or 4) positions in
which the sequence differs. I tried just adding a second chain for
the varying residues at 0.5 occupancy and adding link records to
the original chain, however this doesn't seem to respect geometry
of the phosphodiester for the flanking residues. I would appreciate
suggestions or any examples in the PDB that might set me in the
right direction.

--paul

- -- 
- --

Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

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Re: [ccp4bb] 3D printing structures?

[Edward A. Berry]

Great! we can all send our .stl and slic3r files to Artem for rendering!

I want to make individual subunits of a multisubunit protein,
or domains of a protein like Src, and be able to fit them
together to make the complex or multidomain protein.
Topology constraints may require slicing some subunits in half
and fitting with snaptogether pins so they can encircle another
subunit. In other cases flexibility of the plastic may allow
inserting subunits, or no deformation may be required.

The surfaces we usually make have a radius of a water molecule
added on the outside, which would cause problems where two surfaces
are in vdw contact, so I'm thinking of using space-filling model.
eab


Artem Evdokimov wrote:

As a proud owner of the fdm 3d printer I would like to mention that if you go 
from vrml to stl and then into slic3r you have to drastically refuce polygon 
count or else slic3r chokes trying to process the file.

Cjeets,

Artem

On Aug 23, 2013 5:54 PM, "Edward A. Berry" mailto:ber...@upstate.edu>> wrote:

Thanks, yes, i should have checked out the link on the original post before 
asking.
Free programs "blender" or "meshlab" convert vmrl to .stl files which 
3d-printers
including makerbot read.  eab

Joel Sussman wrote:

Output should be in *VRML* formal
RasMol, PyMol & Jmol all have options to write out VRML format files.
Sometimes you need add additional 'struts' to give additional 
structural support, Jmol has option of adding these struts.
best regards,
Joel

On 23 Aug 2013, at 21:33, Edward A. Berry mailto:ber...@upstate.edu> >> wrote:

Along the same lines, does anyone have a program for converting 
Raster-3D format
such as Molscript puts out, into one of the formats readable by a 
3D printer?
eab

Ronnie wrote:

An off-topic question-now that 3D printing is becoming more common, 
has anyone tried to print protein structures other than just the surface 
representation like in this tutorial? 
http://www.instructables.com/__id/3D-Print-a-Protein-__Modeling-a-Molecular-Machine/ 


Is it possible to print a ribbon representation for example?

Thanks!

Ronnie

Re: [ccp4bb] Why MAD didn't work but SAD works well

[James Holton]

My "default" MAD strategy is to do single-image inverse beam with round 
robin wavelength changes.  That is:

energy  phi
peak   0
peak 180
remote   0
remote 180
peak1
peak  181
remote1
etc

with one image taken for each line above.   I do this until a full 
"sphere" is collected for each wavelength (720 images) with an exposure 
time short enough so that the final dose is less than 5 MGy.  On ALS 
8.3.1 that's about 1 second/image.  The 5 MGy comes from the half-dose 
of the fastest-decaying SeMet site I have ever seen (Holton, 2007).  
Once the initial 5 MGy pass is done, then I quadruple the exposure time 
and move the detector a little closer to the sample for another 
"sphere".  Moving the detector is to try and put the spots on "fresh" 
pixels and average over the systematic error associated with using 
exactly the same part of the detector over and over again.  This becomes 
important for Bijvoet ratios less than ~2%.   It is also a good idea to 
always do a full "sphere" for the same reason: never use the same pixel 
twice.


  The quadrupling of the exposure time is mainly for expediency. Given 
that any rad dam reaction will be essentially exponential, but with an 
unknown half-dose, the best way to sample the curve is with a geometric 
series of exposure times.  Doubling the exposure time increases 
signal/noise by not more than 40%, which seems hardly worth it.  
Quadrupling the exposure doubles the S/N for counting statistics.  So: 
1s, 4s, 16s, and then the crystal is usually pretty dead (at ~0.5 
MGy/min).  This then gives the user the "opportunity" to do RIP using 
the long exposures as the "native".  Or, if there is little damage, they 
can just merge everything together and get the best signal.  The 
influence of read-out noise (if any) also gets effectively washed out in 
the longer exposures.


Now, what I call "peak" is actually a compromise between the usual 
"peak" and the "inflection".  What I do is split the difference between 
these two for an "inf-eak" or "pea-lection" wavelength. From a 
signal-vs-damage point of view this seems to be optimal in my hands.  
Two wavelengths are about twice as good as one, even if the f" and f' to 
the remote are only 80% of what they would be at their maxima.  Three 
wavelengths are "better" than two, but only ~20% better.  I judge this 
by looking at map correlations and the number of sites I can leave 
unmodeled in a 3-wavelength dataset and still get the same map quality 
as a 2-wavelength dataset.  I call such a 2-wavelength dataset "DAD", or 
sometimes Bijvoet Anomalous and Dispersive Anomalous Scattering (BADAS).


The only time using the same pixel twice could actually be an advantage 
is if you could somehow put the same spot on the same pixel at two 
different wavelengths.  You can "sort of" do this by moving the detector 
by a distance proportional to the change in wavelength.  Doesn't work 
exactly because the Ewald sphere is curved and the detector isn't, but 
you can get some spots "close".  This might be why Gonzalez et al. 
(2007) noticed that using inflection-and-remote tended to perform better 
than using just the peak.  I haven't done an experiment of my own to 
show this is due to pixel calibration, however.


Of course, for most "test crystals" it doesn't really matter how you 
collect the data because the anomalous signal is so strong relative to 
pixel calibration, or almost any other source of error for that matter.  
The problem with differentiating the efficacy of one strategy over 
another is that the transition between "solvable" and "unsolvable" is 
very very sharp.  Basically, phase improvement methods either make your 
phases better or they don't, and then you iterate.  But, in a rad 
dam-limited world (such as a very very small "test" crystal), the best 
strategy will prevail. The minimum crystal size you should need if you 
do everything right is what is reported by this web page:

http://bl831.als.lbl.gov/xtalsize.html

As for the terms, "inverse beam" I think came from Stout and Jensen in 
their description of absorption corrections.  It is supposed to be a 
variation on "normal beam" (which is where the x-ray beam is 
perpendicular to the spindle).  But like most things, the widespread use 
of the term arises because a popular piece of software (BLU-ICE) chose 
to put those words next to a button on the GUI.


The term "round robin" I take from a simple load-distribution technique 
in computer science where each CPU, network card, etc takes turns 
getting the next job.  This way each of the things being switched up 
gets the same amount of "exposure" with minimal granularity.  
Apparently, this name is derived from competitive sporting events where 
the athletes do pretty much the same thing.


One final word to the wise: My strategy of single-image-round-robin is 
not appropriate to all beamlines! Some shutters are better than others 
(even the electronic "shutter" used for shutterle