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Re: [ccp4bb] units of f0, f', f''

[Morten Kjeldgaard]

On 01/03/2010, at 20.44, Dale Tronrud wrote:


Morten Kjeldgaard wrote:


On 01/03/2010, at 19.01, James Holton wrote:


personal discourse.  If I review a paper that lists electron density
in "1/A^3", I will tell the authors to fix it.  If a reviewer  
tells me

to change my "electron/A^3" to "A^-3", then I will simply tell the
editor that the reviewer is mistaken.  Nothing I read on the BB is
going to convince me otherwise, and


Both are correct. "Electrons" is a nominal unit, you can omit it if  
you

wish. Mathematically, "electrons" never enter the electron density
equation, because the atomic scattering factor is dimensionless, so  
the

dimension of rho is given by the 1/V term.


  This is seriously close to a circular argument.  You can leave off
"electrons" because they weren't there in the scattering factor?  We
"unit lovers" are not proposing to put it in one place and not the  
other.


The ambiguity probably arises because some authors choose to tabulate  
the atomic form factor in units of  "electrons". If you use that unit  
in the electron density equation, rho gets a unit of "electrons per  
cubic Ångstrøm". Mathematically, the atomic form factor is an function  
that -- for a specific atom type -- specifies the scattering  
efficiency, and it has no unit. Whether you specify the unit  
"electrons" or not doesn't matter, since there is no other unit that  
makes sense for the problem at hand. What *is* important is to specify  
what basic unit of length you are using to compute the unit cell  
volume. Thus, electron density could in principle be given in meter  
**-3 which would be correct according the the SI standard (but  
admittedely weird to a crystallographer.)


The same is true when talking about population density... you can  
specify it as 10 per square mile or 10 humans per square mile or 10  
persons per square mile. It's all the same, "persons" and "humans" are  
nominal units for the number and you can optionally omit it.  
Specifically, concerning dimensionless quantities, read section 1.3 of  
"The International System of Units" [1].



 I'm puzzled by how you define "nominal" units.  Certainly it cannot
be related to whether the variable is declared int or float?  I don't
see a logical connection and I don't see an operational difference
between the units you consider nominal and those you do not.  This
distinction is at the heart of the discussion here: which units can
be dropped at will and which must be kept?


It doesn't necessarily need to be a counting variable (integer). The  
atom form factor is an example of a variable that has the nominal unit  
of "electrons". An angle can be measured in degrees, but if specified  
in radians, that unit is nominal and can be omitted (I have personally  
heard you say "the phase angle is pi" but never "the phase angle is pi  
radians".)



  If "countability" is the principal difference between the two
classes of units what do you think of the unit "mole" (and I don't
mean the animal that burrows underground ;-) ).  This is just a
count of molecules and yet it is used pretty consistently.  I
don't see people talking of the energy of a reaction in "Kcal" with
out the "per mole" always being there.  Are you in favor of reporting
reaction energies in "Kcal"?


This whole thing has to do with what units have been defined and  
standardized. One mole is a defined unit consisting of NA molecules,  
it's a basic unit in the SI system, and so when we work with  
properties of molecules, we need to use it. If we didn't have a  
definition for a mole, I suppose we would specify reaction energies  
"per molecule" in which case the unit would be implicitly understood  
and could be omitted. When we work with lengths, there are several  
standardized measures we can use, and we need to choose one, and we  
need to specify which one we are using. When working with volumes or  
areas, we need to derive the unit from the basic unit of length. This  
is specified and defined by whatever unit standard we choose to work  
with (SI, CGS, ...). So to answer your question:  being an SI man, I'm  
in favour of reporting Gibbs free energy in kJ/mol ;-)


Cheers,
Morten

[1] http://physics.nist.gov/Pubs/SP330/sp330.pdf

Re: [ccp4bb] units of f0, f', f''

[Ian Tickle]

Hi Silvia, I don't know about sophisticated, but it's certainly interminable!

Whether you need to modify your slides (actually only your 3rd slide
seems to be relevant to the discussion) obviously depends on which
definition you choose to along with.  If you use what I can call the
'dimensionless' definition you need do nothing, since you are already
using that definition, i.e. f is a ratio of amplitudes (or sqrt of
ratio of intensities), therefore any units must cancel out and the
result must be dimensionless and unitless, just as in the definition
of refractive index (as Marc pointed out).

If you accept the alternative where f is not dimensionless (it has
dimensions of an amplitude, i.e. length), you need to re-define f as
the amplitude (or sqrt of the intensity) of scattering by the atom,
i.e. the sqrt of the numerator in your equation for 'f^2'.  Then you
need to define a new unit of f (call it [f]) as the amplitude of
scattering by a free electron, i.e. the sqrt of the denominator of
your equation: this is what pretty well everyone is calling an
'electron' - though definitely not to be confused with a real
electron!  Finally f is expressed as a multiple of its unit in the
usual way: f = n[f] where 'n' is the numerical value of f (for
example: "f = 10 electrons" if n=10).  So to summarise, using this
definition f has dimensions of 'length' and units of 'electrons'.

Further for the 2nd definition, if you're tempted to abbreviate
'electrons' to 'e' as is often seen, you also have to remember that
'e' here has nothing to do with the conventional physicists'
definition, namely the charge on the electron (though it seems I'm the
only one here who thinks this is very confusing notation).  If you do
decide to go down this path I would recommend following the notation
in Bernhard Rupp's book: he uses the correct abbreviation for the
electron, namely 'e-' avoiding the confusion with 'e', but again don't
confuse this with the real electron!  As Gerard pointed out you could
equally well use the terms 'positron' and 'e+' since the sign is
irrelevant for scattering.

Note that both definitions are perfectly internally self-consistent -
no dimensionality issues - so the choice is purely a matter of
definition, certainly neither can be said to be right or wrong, and
therefore the definitions are essentially totally arbitrary.  It
really comes down to whether you wish to change the definition you're
accustomed to, and whether you can live with the ambiguities in the
definition of 'electron' (and 'e' if you use it).  It seems to me that
it's this ambiguity that actually instigated this whole thread!

One point highlighted by your slides: you say that at zero scattering
angle f0 = Z (atomic number).  This is perfectly correct, however note
that Z being a pure number is never expressed as say 'Z = 10
electrons', always as just 'Z = 10' so if you express f in 'e-' units
you need to say 'f0 = Ze-', otherwise the equation is dimensionally
inconsistent.

Anyway I beginning to sound like Microsoft explaining how to install
their competitors' browsers in as fair a way as possible in order to
placate the European Commission, so I'll stop there!

Cheers

-- Ian

> On Mon, Mar 1, 2010 at 7:06 PM, Silvia Onesti 
>  wrote:
> I feel uneasy at entering this sophisticated discussion, but since it looks
> like the very interesting, learned but subtle and complex statements by Ian,
> Marc, Gerard & co seem unable to shake people assumptions that the atomic
> scattering factor is expressed in electrons, can I provide a couple of very
> basic slides that I have been using for teaching an undergraduate course?
>
> As far as I know that is the DEFINITION of the atomic scattering factor. The
> scattering-equivalent of one electron is just a convenient unit.  Analogous
> to saying that the charge of a proton is +1, rather than 1.6x10-19 Coulomb.
>
> Now I hope that the experts are not going to find other mistakes in my
> slides!
>
> Silvia
>
> 
> Silvia Onesti
>
> Sincrotrone Trieste S.C.p.A.
> SS 14 - km 163,5 - AREA Science Park, 34149 Basovizza, Trieste ITALY
>
> Email: silvia.one...@elettra.trieste.it
> Tel. +39 040 3758451
> Mob +39 366 6878001
>
> http://www.elettra.trieste.it/PEOPLE/index.php?n=SilviaOnesti.HomePage
> http://www.sissa.it/sbp/web_2008/research_structuralbio.html
> 
>
> On Mon, 1 Mar 2010 09:10:44 -0800
>  Ronald E Stenkamp  wrote:
>  Hi.
>   I'm a little reluctant to get into this discussion, but I'm greatly
> confused
> by
>  it all, and I think much of my confusion comes from trying to understand
> one
> of Ian's assumptions.
>   Why are the scattering factors viewed as dimensionless quantities?  In
>  the International Tables (for example, Table 6.1.1.1 in the blue books),
> the
>  scattering factors are given "in electrons".

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Re: [ccp4bb] units of f0, f', f''

[Ronald E Stenkamp]

Hi.

I'm a little reluctant to get into this discussion, but I'm greatly confused by
it all, and I think much of my confusion comes from trying to understand one of 
Ian's assumptions.

Why are the scattering factors viewed as dimensionless quantities?  In
the International Tables (for example, Table 6.1.1.1 in the blue books), the
scattering factors are given "in electrons".   In the text for that section,
the scattering factors are obtained from an integral (over space) of the
electron density.  So there's some consistency there between scattering factors
in units of electrons and electron density in electrons/(Angstrom**3).  What's
gained at this point by dropping the word "electron" from all of these
dimensions?

Ron




On Sat, 27 Feb 2010, Ian Tickle wrote:

>> I'm not aware that anyone has suggested the notation "rho e/Å^3".
>
> I think you misunderstood my point, I certainly didn't mean to imply that
> anyone had suggested or used that notation, quite the opposite in fact.  My
> point was that you said that you use the term 'electron density' to define
> two different things either at the same time or on different occasions, but
> that to resolve the ambiguity you use labels such as 'e/Å^3' or
> 'sigma/Å^3' attached to the values.  My point was that if I needed to use
> these quantities in equations then the rules of algebra require that
> distinguishable symbols (e.g. rho and rho') be assigned, otherwise I would
> be forced into the highly undesirable situation of labelling the symbols
> with their units in the equations in the way you describe in order to
> distinguish them.  Then in my 'Notation' section my definitions of rho &
> rho' would need to be different in some way, again in order to distinguish
> them: I could not simply call both of them 'electron density' as you appear
> to be doing.
>
> The question of whether your units of electron density are '1/Å^3' or
> 'e/Å^3' clearly comes down to definition, nothing more.  If we can't agree
> on the definition then we are surely not going to agree on the units!
> Actually we don't need to agree on the definition: as long as I know what
> precisely your set of definitions is, I can make the appropriate adjustments
> to my units & you can do the same if you know my definitions; it just makes
> life so much easier if we can agree to use the same definitions!  Again it
> comes down to the importance of having a 'Notation' section so everyone
> knows exactly what the definitions in use are.  My definition of electron
> density is "number of electrons per unit volume" which I happen to find
> convenient and for which the appropriate units are '1/Å^3'.  In order for
> your choice of units 'e/Å^3' to be appropriate then your definition would
> have to be "electric charge per unit volume", then you need to include the
> conversion factor 'e' (charge on the electron) in order to convert from my
> "number of electrons" to your "electric charge", otherwise your values will
> all be very small (around 10^-19 in SI units).  I would prefer to call this
> quantity "electric charge density" since "electron density" to me implies
> "density of electrons" not "density of charge".  I just happen to think that
> it's easier to avoid conversion factors unless they're essential.
>
> Exactly the same thing of course happens with the scattering factor: I'm
> using what I believe is the standard definition (i.e. the one given in
> International Tables), namely the ratio of scattered amplitude to that for a
> free electron which clearly must be unitless.  So I would say 'f = 10' or
> whatever.  I take it that you would say 'f = 10e'.  Assuming that to be the
> case, then it means you must be using a different definition consistent with
> the inclusion of the conversion factor 'e', namely that the scattering
> factor is the equivalent point electric charge, i.e. the point charge that
> would scatter the same X-ray amplitude as the atom.  I've not seen the
> scattering factor defined in that way before: it's somewhat more convoluted
> than the standard definition but still usable.  The question remains of
> course - why would you not want to stick to the standard definitions?
>
> BTW I assume your 'sigma/Å^3' was a slip and you intended to write just
> 'sigma' since sigma(rho) must have the same units as rho (being its RMS
> value), i.e. 1/Å^3, so in your second kind of e.d. map rho/sigma(rho) is
> dimensionless (and therefore unitless).  However since rho and sigma(rho)
> have identical units I don't see how their ratio rho/sigma(rho) can have
> units of 'sigma', as you seem to imply if I've understood correctly?
>
>> What I'm more concerned about is when you assign a numerical value to
>> a quantity.  Take the equation E=MC^2.  The equation is true
>> regardless
>> of how you measure your energy, mass, and speed.  It is when you say
>> that M = 42 that it becomes important to unambiguously label 42 with
>> its units.  It is when you are given a mass equal to 42 newt

Re: [ccp4bb] units of f0, f', f''

[Gerard Bricogne]

Dear Ian,

 The iteration seems to be converging :-)) .
 
 Regarding your last paragraph, however, I do not think that we have to
forbid ourselves to call a spade a spade because of possible confusions that
might be caused by misleading abbreviations. If the unit is "an electron's
worth of scattering", its abbreviation to "electron" has to be accompanied
by a suitable annotation so that it does not get confused with some physical
attribute of an electron such as its charge. I don't think that anticipated
inadequacies of notation should stand in the way of correct terminology. If
necessary, we should draft a one-liner that could be added as a footnote to
every Table 1 (like the formula for the R-factor!) and would explain that
the word "electron", as used in the context of that Table, actually means
"an electron's worth of scattering"; and to show how important we are, we
could even have the exact wording reviewed and approved by the Computing
Commission of the IUCr! But this would start sounding like Russian history
in the 1920's ... .


 With best wishes,
 
  Gerard.

--
On Mon, Mar 01, 2010 at 04:14:57PM +, Ian Tickle wrote:
> Dear Gerard
> 
> I would certainly agree that in general, provided one takes sufficient
> care over dimensions and units, paradoxes can never appear.  However,
> in this particular case I was pointing out the dimensionality error of
> writing equations such as "f = 10e", and equivalent ones for the
> structure factor and electron density, given that 'f' is defined as a
> dimensionless ratio (as I believe it usually is).  Even if you
> replaced the 'e' with whatever unit represents an electron's ability
> to scatter X-rays (which would be the amplitude of the scattered
> wave), you still have the same problem.  I only focused on electric
> charge because 'e', the elementary unit of charge, was being posited
> as the unit of 'f'.
> 
> The alternative solution that you suggested of using the word
> 'electron' as an abbreviation for "an electron's worth of scattering",
> is likely to cause just as much confusion and probably would be
> further abbreviated to 'e' anyway, thus leading people to believe it
> represented the electronic charge!  The correct solution, as you, Marc
> and myself have pointed out, is to treat f as a pure number, with
> corresponding treatment of any other quantity that depends on f.
> 
> Cheers
> 
> -- Ian
> 
> 
> On Mon, Mar 1, 2010 at 1:13 PM, Gerard Bricogne  
> wrote:
> > Dear Ian,
> >
> >     Perhaps I should have made a more explicit connection to your message
> > in what I wrote yesterday. I do not think there is any paradox, or apples
> > vs. oranges problem, in this situation.
> >
> >     The structure factor is a count of "electrons as X-ray scatterers", so
> > that the Fourier synthesis computed from them is a number density for these
> > unit scatterers. The density can get clothed with a charge a-posteriori,
> > because we know what the charge of an electron is, but it is not that charge
> > as such that is sensed by the diffraction experiment: it is the complicated
> > combination of charge and mass and various physical constants that ends up
> > determining an electron's ability to scatter X-rays.
> >
> >     I think that if one bears this in mind at all times, paradoxes never
> > appear.

-- 

 ===
 * *
 * Gerard Bricogne g...@globalphasing.com  *
 * *
 * Global Phasing Ltd. *
 * Sheraton House, Castle Park Tel: +44-(0)1223-353033 *
 * Cambridge CB3 0AX, UK   Fax: +44-(0)1223-366889 *
 * *
 ===

Re: [ccp4bb] units of f0, f', f''

[Ethan Merritt]

On Monday 01 March 2010, Ian Tickle wrote:
> Dear Gerard
> 
> I would certainly agree that in general, provided one takes sufficient
> care over dimensions and units, paradoxes can never appear.  However,
> in this particular case I was pointing out the dimensionality error of
> writing equations such as "f = 10e", and equivalent ones for the
> structure factor and electron density, given that 'f' is defined as a
> dimensionless ratio (as I believe it usually is).

In my experience, f' and f" are given in units of e, just as f itself is,
and "e" is read out loud as "electrons".

Ethan



> Even if you
> replaced the 'e' with whatever unit represents an electron's ability
> to scatter X-rays (which would be the amplitude of the scattered
> wave), you still have the same problem.  I only focused on electric
> charge because 'e', the elementary unit of charge, was being posited
> as the unit of 'f'.
> 
> The alternative solution that you suggested of using the word
> 'electron' as an abbreviation for "an electron's worth of scattering",
> is likely to cause just as much confusion and probably would be
> further abbreviated to 'e' anyway, thus leading people to believe it
> represented the electronic charge!  The correct solution, as you, Marc
> and myself have pointed out, is to treat f as a pure number, with
> corresponding treatment of any other quantity that depends on f.
> 
> Cheers
> 
> -- Ian
> 
> 
> On Mon, Mar 1, 2010 at 1:13 PM, Gerard Bricogne  
> wrote:
> > Dear Ian,
> >
> > Perhaps I should have made a more explicit connection to your message
> > in what I wrote yesterday. I do not think there is any paradox, or apples
> > vs. oranges problem, in this situation.
> >
> > The structure factor is a count of "electrons as X-ray scatterers", so
> > that the Fourier synthesis computed from them is a number density for these
> > unit scatterers. The density can get clothed with a charge a-posteriori,
> > because we know what the charge of an electron is, but it is not that charge
> > as such that is sensed by the diffraction experiment: it is the complicated
> > combination of charge and mass and various physical constants that ends up
> > determining an electron's ability to scatter X-rays.
> >
> > I think that if one bears this in mind at all times, paradoxes never
> > appear.
> 

Re: [ccp4bb] units of f0, f', f''

[Ian Tickle]

Dear Gerard

I would certainly agree that in general, provided one takes sufficient
care over dimensions and units, paradoxes can never appear.  However,
in this particular case I was pointing out the dimensionality error of
writing equations such as "f = 10e", and equivalent ones for the
structure factor and electron density, given that 'f' is defined as a
dimensionless ratio (as I believe it usually is).  Even if you
replaced the 'e' with whatever unit represents an electron's ability
to scatter X-rays (which would be the amplitude of the scattered
wave), you still have the same problem.  I only focused on electric
charge because 'e', the elementary unit of charge, was being posited
as the unit of 'f'.

The alternative solution that you suggested of using the word
'electron' as an abbreviation for "an electron's worth of scattering",
is likely to cause just as much confusion and probably would be
further abbreviated to 'e' anyway, thus leading people to believe it
represented the electronic charge!  The correct solution, as you, Marc
and myself have pointed out, is to treat f as a pure number, with
corresponding treatment of any other quantity that depends on f.

Cheers

-- Ian


On Mon, Mar 1, 2010 at 1:13 PM, Gerard Bricogne  wrote:
> Dear Ian,
>
>     Perhaps I should have made a more explicit connection to your message
> in what I wrote yesterday. I do not think there is any paradox, or apples
> vs. oranges problem, in this situation.
>
>     The structure factor is a count of "electrons as X-ray scatterers", so
> that the Fourier synthesis computed from them is a number density for these
> unit scatterers. The density can get clothed with a charge a-posteriori,
> because we know what the charge of an electron is, but it is not that charge
> as such that is sensed by the diffraction experiment: it is the complicated
> combination of charge and mass and various physical constants that ends up
> determining an electron's ability to scatter X-rays.
>
>     I think that if one bears this in mind at all times, paradoxes never
> appear.

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opportunities to work on X-ray crystallography of selected GPCRs in order to 
visualize the specific signaling confirmations of these receptors. The project 
is primarily based in the Lefkowitz laboratory at Duke university 
(http://www.lefkolab.org/), however, it involves a close collaboration with Dr. 
Brian Kobilka's lab at Stanford University 
(http://med.stanford.edu/kobilkalab). The project activities include construct 
design and characterization, protein expression and purification, and 
structural determination of target receptors. 
 We are seeking highly motivated recent 
graduates with PhD in structural biology who have a track record of solving 
X-ray crystal structures of proteins and protein complexes. Experience with 
protein crystallization, data collection, structure determination and 
interpretation are essential. Additional expertise in membrane protein 
crystallography is desired but not absolutely required. 
Interested candidates can send their CV to Dr. 
Lefkowitz (lefko...@receptor-biol.duke.edu).
_

Arun K. Shukla, Ph.D.
Lab- Dr. Robert J. Lefkowitz
HHMI/Duke University Medical Center
Durham, NC 27710
Phone: 919-684-4730 (Office)
Email: arun.shu...@receptor-biol.duke.edu
_

Re: [ccp4bb] units of f0, f', f''

[Morten Kjeldgaard]

On 01/03/2010, at 13.55, Boaz Shaanan wrote:

As for equilibrium constants, I'm somewhat puzzled by your remark on  
their lack of units (I'm a chemist by the way). Is the equilibrium  
constant (or dissociation constant) of the reaction A+B<->AB  
identical to that of the reaction: A+2B <--> AB2 ? I didn't think  
so. I could of course misunderstand your statement, so please  
correct me.


The equilibrium constant is defined as a ratio of the products of the  
chemical activities on the right and left sides of the equilibrium,  
and chemical activities themselves are dimensionless. In practical  
work, we use concentrations, which do have dimensions, but are  
multiplied by an activity factor which is usually ignored because it  
is very close to 1. For this reason, it appears that K has a unit, but  
it's only nominal.


Cheers,
Morten

Re: [ccp4bb] units of f0, f', f''

[Gerard Bricogne]

Dear Ian,

 Perhaps I should have made a more explicit connection to your message
in what I wrote yesterday. I do not think there is any paradox, or apples
vs. oranges problem, in this situation.

 The structure factor is a count of "electrons as X-ray scatterers", so
that the Fourier synthesis computed from them is a number density for these
unit scatterers. The density can get clothed with a charge a-posteriori,
because we know what the charge of an electron is, but it is not that charge
as such that is sensed by the diffraction experiment: it is the complicated
combination of charge and mass and various physical constants that ends up
determining an electron's ability to scatter X-rays. 

 I think that if one bears this in mind at all times, paradoxes never
appear.


 With best wishes,
 
  Gerard.

--
On Sun, Feb 28, 2010 at 02:40:15PM -, Ian Tickle wrote:
> 
> > Yes, I think this is exactly the point. 'Electrons' gives the whole 
> > thing a consistent meaning. 
> 
> The big problem with statements like 'f = 10e' or 'rho = 1.5e/Å^3' is of 
> course that they are dimensionally invalid, and I'm surprised that people are 
> not doing such simple checks!  For example I think we've all agreed that 'f' 
> is defined as the ratio of two amplitudes and is therefore dimensionless, 
> whereas 'e' is universally defined as the electronic charge, which in SI 
> units has the value 1.602176487×10^−19 coulombs, but obviously has the 
> dimensions of electric charge (time*electric current in terms of the base SI 
> dimensions).  So we have a real apples & oranges situation!
> 
> You could of course get around this by redefining 'f' as I suggested 
> previously, as the free point equivalent charge, but to avoid confusion we 
> should call it something else, so let's say:
> 
> Notation
> 
> f: "atomic scattering factor", defined as the ratio of scattered amplitude 
> for an atom to that for a free electron (dimensionless).
> g: "atomic scattering free point equivalent charge", defined as the free 
> point charge which scatters with the same amplitude as the atom (dimensions 
> of electric charge).
> 
> Now we can validly write 'g = 10e' since we have dimensions of charge on both 
> sides.
> 
> This again highlights the importance of 1) rigorously defining all quantities 
> in use, and 2) that the definition and the dimensions are linked: you cannot 
> arbitrarily change the dimensions of some quantity without also changing its 
> definition, or vice versa; and in particular you can't mix the definition of 
> 'f' with the units of 'g', which is what seems to be happening here!
> 
> This logical inconsistency can only be resolved by recognising that 'f' is a 
> pure number so removing the 'e' unit.  The same argument obviously applies to 
> anything derived from 'f' such as the structure factor and the electron 
> density.
> 
> Cheers
> 
> -- Ian
> 
> 
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Re: [ccp4bb] units of f0, f', f''

[Morten Kjeldgaard]

Let me give my input to the confusion :-)

Things that can be counted are integers, and have no unit. They may,  
however, have a _nominal_ unit, which can be "stripes", "apples",  
"pieces of fruit". Those units are solely used for clarity. For  
example, I can have 13 pieces of fruit, but that may be 5 oranges and  
8 bananas, or 12 apples and 1 kiwi, so to avoid confusion, I'd better  
name those units; they become nominal (nomen == name).


Some things cannot be counted. Like the height of the tree outside my  
window. I would say its height is 12, and Dale would say its height is  
37. The height of the tree is a continuous variable, and so it needs  
to be measured in some unit. Therefore, the height of the tree can't  
be specified as just "12"; it is indeed "12 m" or "37 feet".


It so happens that we think of electrons as particles, so on one hand,  
you might imagine that you can "count" electrons. We can argue whether  
or not that is true; someone might claim that electrons are  
delocalized, and can only be positioned via some kind of probability  
function. Perhaps it would make more sense to count the number of  
protons in the atomic nucleii of the unit cell, since those are used  
to compute the number of electrons anyway.


I always enjoy asking students what the unit of an equilibrium  
constant is, and they always answer "molar" or "micromolar squared" or  
"milimolar to the minus first" ... etc. That is of course wrong;  
equilibrium constants are dimensionless, but are almost always given  
nominal units for clarity, especially by biologists.


Cheers,
Morten

[ccp4bb] MAX-lab beamtime Deadline March 12th 2010

[Thomas Ursby]

CALL FOR PROPOSALS for beam time at MAX-lab, Lund, Sweden.

Researchers using synchrotron radiation are invited to submit proposals
for beam time for experiments to be carried out during the time period
July 2010 to June 2011.

The available facilities include beamlines for MX and SAXS, see below.

Please note that the tunable station I911-3 will be upgraded during 2010 
with a completely new experimental set-up including a EMBL/ESRF 
microdiffractometer and a CATS sample changing robot.


Information on how to prepare and submit proposals as well as
descriptions of the other experimental facilities available at MAX-lab
can be found at http://www.maxlab.lu.se

It is also possible to apply for Fast Access MX beam time at any time
though it is recommended to submit normal proposals if possible.

It is not possible to submit block allocation proposals for MX this year 
(ie all groups with block allocations do not need to resubmit this year).


*** The proposal deadline is March 12th, 2010 ***
___
MACROMOLECULAR CRYSTALLOGRAPHY

Beam time for macromolecular crystallography is available at:

* Beamline I911-2: Fixed-wavelength (1.04 Å): 165mm marccd, mardtb,
marccs sample changer

* Beamline I911-3: Tunable 0.7-2.0 Å, suitable for MAD/SAD: 225mm
marmosaic detector, Roentec fluorescence detector.
The new experimental set-up with a microdiffractometer will be available 
for the coming period. The CATS sample changing robot will be 
commissioned during the autumn 2010 and is expected to come in user 
operation during autumn.


* Beamline I911-5: Fixed-wavelength (0.91 Å): 165mm marccd, mardtb

All beamlines are equipped with user-friendly data collection software.

For more information, see the beamline web site:
http://www.maxlab.lu.se/beamlines/bli911

or information about the stations:

I911-2
http://www.maxlab.lu.se/beamline/max-ii/i911/i911-2.html
I911-3
http://www.maxlab.lu.se/beamline/max-ii/i911/i911-3.html
I911-5
http://www.maxlab.lu.se/beamline/max-ii/i911/i911-5.html

___
SAXS

Beam time is also available at the SAXS station at beamline I711. The 
set-up is further described at:


http://www.maxlab.lu.se/beamline/max-ii/i711/i711.html
___
ACCESSIBILITY AND SUPPORT
MAX-lab is situated in Lund, 50 km or 30 minutes by car from Copenhagen
airport (with less than 2 hour flights from e.g. London, Paris,
Strasbourg, Munich, Budapest, Helsinki,...). Trains leave the airport
every 20 to 40 minutes (44 minutes to Lund).
Users from EU countries and associated states can apply for financial
support through the project "Integrating Activity on Synchrotron and
Free Electron Laser Science (IA-SFS)" within the Sixth Framework
Programme (more information can be found in the beam time application
instructions).
___

<>

Re: [ccp4bb] units of f0, f', f''

[Morten Kjeldgaard]

On 01/03/2010, at 08.02, Dale Tronrud wrote:


Dear X-ray Community,

  I'm sorry to have dragged you all along on this journey.  There is
something to Ian and Marc's arguments but I have been unable to  
understand

their point.  That is my failure and I don't wish to subject the rest
of you to continued argument.  Ian, Marc, and I should get together
in a bar somewhere and hash this out.


That sounds like fun! Can we come? :-)

PS: Enjoyed the journey!

Cheers,
Morten

--
Morten Kjeldgaard, asc. professor, MSc, PhD
BiRC - Bioinformatics Research Center, Aarhus University
C. F. Møllers Alle, Building 1110, DK-8000 Århus C, Denmark.
Lab +45 8942 3130 * Fax +45 8942 3077 * Home +45 8618 8180

[ccp4bb] Second Announcement: EMBO Course on Macromolecular Complexes

[Carlo Petosa]

Dear colleagues,

We are organizing an EMBO Practical Course on the Structural Characterization
of  Macromolecular Complexes.  The course is primarily intended for Ph.D.
students and postdocs engaged in challenging structural projects involving
macromolecular complexes.

WHEN:  31 May - 5 June, 2010

WHERE: Grenoble, France

TOPICS INCLUDE:
  - expression & purification of multi-subunit complexes
  - biophysical & biochemical characterization of complexes
  - bioinformatic & experimental analysis of interaction networks
  - combining different structural methods (EM, NMR, SAXS, crystallography)

SPEAKERS INCLUDE:
  Radu Aricescu (Oxford U.)
  Imre Berger (EMBL Grenoble)
  Martin Blackledge (IBS Grenoble)
  John Briggs (EMBL Heidelberg)
  Gianni Cesareni (U. Rome)
  Kai Johnsson (EPFL Lausanne)
  Par Nordlund (Karolinska Institute, Stockholm)
  Andreas Plückthun (U. Zurich)
  Vladimir Rybin  (EMBL Heidelberg)
  Christophe Romier  (IGBMC Illkirch)
  Michael Sattler  (Tech. U. Munich)
  Christiane Schaffitzel  (EMBL Grenoble)
  Patrick Schulz  (IGBMC Illkirch)
  Bertrand Séraphin  (IGBMC Illkirch)
  Montserrat Soler-López (IRB Barcelona)
  Dmitri Svergun (EMBL Hamburg)
  Song Tan  (Pennsylvania State U.)

APPLICATION DEADLINE: 15 March 2010

A maximum of 20 participants will be selected to attend the course.

For more details please visit:   http://cwp.embo.org/pc10-20/index.html


Best regards,
Carlo Petosa, Darren Hart, Elspeth Gordon,
Guy Schoehn, Winfried Weissenhorn


Carlo Petosa, Ph.D.
Institut de Biologie Structurale
41 rue Jules Horowitz
38027 Grenoble Cedex 1, France
Tel. +33 438 78 40 24   Fax +33 438 78 54 94

Re: [ccp4bb] Molrep error - bug 3790

[Charles Ballard]

Dear Jonathan

this sounds like a known issue with the version on molrep that was  
released with ccp4 version 6.1.1 (so if you are having the problem  
with 6.1.3 then it has got back in).   For some reason we did not get  
to the bottom of the file path gets doubled up, /home/caruthej/bo3/ 
ccp4/bo3P1_11_molrep_/home/caruthej/bo3/ccp4/ 
bo3P1_11_molrep_trfn_scr.crd , we have the /home twice.  The  
suggested work around is to upgrade to 6.1.3 .  If you do not wish to  
upgrade fully at this point just download the new version and replace  
the molrep in $CCP4/bin


Sorry for the problem

Charles Ballard
CCP4

On 26 Feb 2010, at 19:31, Jonathan Marvin Caruthers wrote:


All:



Can anyone help me out here?  I'm trying to get Molrep to run but  
it seems to be crashing while trying to open some file after it's  
done the rotation function search.  I'm getting the following error:


**

  Number of RF peaks :  30
 thetaphi chialphabeta   gamma   
RfRf/sigma
 Sol_RF   144.61  -44.03  112.01  272.52   71.21  180.58 
0.3240E+05 10.69
 Sol_RF   262.99  136.68  133.64   93.36  109.980.00 
0.3154E+05 10.40
 Sol_RF   3   111.50 -133.69  138.32   92.40  120.82  179.79 
0.2804E+05  9.25
 Sol_RF   4   139.89   46.56  102.16  273.12   60.170.00 
0.2556E+05  8.43
 Sol_RF   5   147.85   44.94   96.78  271.31   46.891.43 
0.1701E+05  5.61
 Sol_RF   6   119.97 -108.35  162.70   88.58  117.83  125.29 
0.1673E+05  5.52
 Sol_RF   756.80  141.24  140.27  107.82  103.815.34 
0.1650E+05  5.44
 Sol_RF   855.15  142.30  142.33  111.46  101.916.87 
0.1601E+05  5.28
 Sol_RF   954.36  143.15  143.09  113.35  100.887.05 
0.1563E+05  5.16
 Sol_RF  10   115.41 -108.41  160.88   93.02  125.92  129.84 
0.1562E+05  5.15
 Sol_RF  1155.10  137.38  127.36   96.53   94.641.77 
0.1554E+05  5.13
 Sol_RF  12   142.36   34.36  113.03  254.24   61.235.51 
0.1539E+05  5.08
 Sol_RF  13   115.81 -141.38  155.86   64.78  123.37  167.54 
0.1516E+05  5.00
 Sol_RF  14   147.45   78.25  143.98  279.34   61.55  302.85 
0.1501E+05  4.95
 Sol_RF  15   116.29 -141.01  153.70   66.80  121.63  168.82 
0.1500E+05  4.95
 Sol_RF  1675.23  164.12  119.33   97.66  113.14  309.42 
0.1461E+05  4.82
 Sol_RF  17   150.03   57.40   91.74  285.64   42.03  350.83 
0.1450E+05  4.78
 Sol_RF  1849.18  -35.04   85.65  266.17   61.92  156.24 
0.1437E+05  4.74
 Sol_RF  19   139.72   66.72  124.31  281.42   69.74  327.98 
0.1434E+05  4.73
 Sol_RF  2060.59  -24.12   79.57  268.13   67.75  136.36 
0.1434E+05  4.73
 Sol_RF  21   118.54 -105.41  168.98   86.00  121.95  116.82 
0.1429E+05  4.71
 Sol_RF  22   109.08 -138.84  156.70   73.40  135.51  171.08 
0.1422E+05  4.69
 Sol_RF  2337.48  -33.22   75.56  268.37   43.78  154.81 
0.1417E+05  4.67
 Sol_RF  24   118.00 -105.87  171.24   83.39  123.37  115.14 
0.1411E+05  4.65
 Sol_RF  25   119.13 -105.81  169.16   85.22  120.83  116.84 
0.1410E+05  4.65
 Sol_RF  26   117.07 -130.56  136.98   90.32  111.87  171.45 
0.1403E+05  4.63
 Sol_RF  27   142.78   18.10  126.65  230.35   65.43   14.15 
0.1400E+05  4.62
 Sol_RF  28   135.68   14.72  139.96  221.71   82.06   12.27 
0.1399E+05  4.62
 Sol_RF  29   146.60   71.15  139.06  275.24   62.10  312.94 
0.1397E+05  4.61
 Sol_RF  3058.45  -20.76   81.24  273.41   67.39  134.93 
0.1392E+05  4.59

  Final number of peaks :  30
 INFO:Relations between peaks see in molrep.doc
  NCS_model (from Model Self rotation Function): 1
  Program will use NCS =: 1
 Sol_
 Sol_--- Multi-copy Search ---
 Sol_
 Sol_ Resmin,Resmax :   77.324.00
 Sol_ Radius_giration:  30.442
  Radius_max :  56.282
 Sol_ Chi,Delta  :   0.000  10.000
 Sol_ Dist_min,max,Dpar_max  :30.442  1000.000  1000.000
 Sol_
 Sol_--- First monomer search ---
 Sol_
 Sol_ RF TF   Tf/sigTFcntrst PKind PKmax PKmin   Rfac  Scor  
Scor_max Cntrst
 Open failed: Unit:   8, File: /home/caruthej/bo3/ccp4/ 
bo3P1_11_molrep_/home/caruthej/bo3/ccp4/ 
bo3P1_11_molrep_trfn_scr.crd (logical: /home/caruthej/bo3/ccp4/ 
bo3P1_11_molrep_/home/caruthej/bo3/ccp4/bo3P1_11_molrep_trfn_scr.crd)
 MOLREP(ccp4):   Open failed: File: /home/caruthej/bo3/ccp4/ 
bo3P1_11_molrep_/home/caruthej/bo3/ccp4/bo3P1_11_molrep_trfn_scr.crd

Times: User:  82.2s System:1.2s Elapsed: 1:35


** 
*

* Information from CCP4Interface script
** 
*
The program run with command: /usr/local/ccp4-6.1.0/ccp4-6.1.0/bin/ 
molrep PATH_SCR "/home/caruthej/bo3/ccp4/bo3P1_11_molrep_" PATH_OUT  
"/home/caruthej/bo3/ccp4/bo3P1_11_molrep_" HKLIN "/home/caruthej/ 
bo3/P1/ccp4/merged.mtz" MODEL "/hom

Re: [ccp4bb] about comparing Rwork and Rfree factors of different refinement trials

[Eleanor Dodson]

Dirk is right. It isnt so much a GUI bug as a feature!

When you press restart for any job the previous parameters are loaded 
into the script.


Usually this saves you work, but if you are changing from TLS with 
initial B fixed to 20 to restrained refinement it is undesirable to keep 
that fixed B! You can change it by clicking the appropriate widget but 
it is easy to miss..


I guess a cleverer GUI would recognise that you are not really 
restarting a job... just using a short cut to get the correct mtz etc 
entered..


 Eleanor


Dirk Kostrewa wrote:
Could this be a long-standing bug in the ccp4i Refmac GUI? Some time 
ago, I sent a bug report to the ccp4 developers: if you did TLS 
refinement, you got an additional tab where you should set the B-factor 
to a uniform value. In the next round of refinement, where you read in 
the refined TLS parameters from the previous run, this tab vanished, but 
the B-factor was nevertheless still set to the same uniform value, which 
resulted in high starting R-factors for the first cycle!


I haven't tested this recently, but if you display the actual Refmac 
command script from the GUI, it should be obvious whether this bug is 
still there or not.


Best regards,

Dirk.

Am 25.02.10 17:54, schrieb Jan Schoepe:

What I tried for instance was in refmac:
1.) 20 cycles TLS followed by 10 cycles restrained refinement which 
gave Rwork=24%/Rfree=33%.
Afterwards I did 0-1 cycles restrained refinement with output from 
prev. run (pdb file, mtz file, tls file) as input for that. Result: 
33%/44%.
2.) I omitted the restrained refinement, else same as above. Result 
was 26%/32% after TLS and 31%/38% after restrained refinement...




--- gbirr...@bidmc.harvard.edu // schrieb 
am *Do, 25.2.2010:

*

*
Von: gbirr...@bidmc.harvard.edu 
Betreff: RE: [ccp4bb] about comparing Rwork and Rfree factors of
different refinement trials
An: j.scho...@yahoo.de
Datum: Donnerstag, 25. Februar, 2010 17:12 Uhr

*
* *
*You can fix the TLS parameters as well. *
*Zero cycles of Refmac and fixed TLS*
*Will this work in your case?*
* *
* *
* *

*Gabriel Birrane**
Beth Israel Deaconess Medical Center
RN348
99 Brookline Ave
Boston, MA 02215 *

* *
*
*



**From:* Jan Schoepe [mailto:j.scho...@yahoo.de]
*Sent:* Thursday, February 25, 2010 11:06 AM
*To:* Birrane,Gabriel (Bidmc-Research Fellow)
*Subject:* RE: [ccp4bb] about comparing Rwork and Rfree factors of
different refinement trials

*
In principle yes, but I doubt that this works properly, especially
after TLS refinement.

--- gbirr...@bidmc.harvard.edu //
schrieb am *Do, 25.2.2010:
*

*
Von: gbirr...@bidmc.harvard.edu 
Betreff: RE: [ccp4bb] about comparing Rwork and Rfree factors
of different refinement trials
An: j.scho...@yahoo.de
Datum: Donnerstag, 25. Februar, 2010 16:04 Uhr

*
*


You can do zero cycles of refinement in Refmac. This will just
give you the statistics as Refmac calculates them without
any refinement. Is this what you are looking for?



From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of
Jan Schoepe [j.scho...@yahoo.de]
Sent: Thursday, February 25, 2010 9:38 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] about comparing Rwork and Rfree factors of
different refinement trials

Dear all,

I do have a question about comparing Rfree and Rwork factors
of different refinement trials whereas I always started with
the same pdb file and structure factors (phasing by MR).
Means I had a protein structure which was (not just by me)
refined several times in different ways also with different
programs and also accordingly got different R factors for each
finally refined structure.
Could anyone suggest if there is something like a "standard
run" which makes all these R factors (or "derivatives" since
this run should change the R factors) better comparable?
(E.g. it did not work for me to do a 1 cycle rigid body
refinement in refmac hoping that the R factors are measured
well and the structure does not change much. In fact, the R
factors increased dramatically, lets say Rfree from 30% to 40%.)

Many thanks for your suggestions!
Jan


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Re: [ccp4bb] Refmac ligand refinement question

[Eleanor Dodson]

Katarina Moravcevic wrote:

Dear all,

I am refining a structure of a protein in a complex with phosphorylated
ligand (inositol ring).  My problem is that after restrained refinement with
Refmac, the ring is distorted in geometrically impossible ways. Could
anybody advise me on how to deal with this problem?  Ideally, I would just
like to keep the ring as is and let the phosphates move around.

Thanks in advance

K


I suspect the problem is with the dictionary.

Do you want to send coordinates of ligand and dictionary - it is hard to 
diagnose problem without that information

Eleanr