Re: [ccp4bb] units of the B factor

2009-11-23 Thread Marc SCHILTZ
This is absolutely correct. Radian is in fact just another symbol for 1. Thus : 1 rad = 1 From the official SI documentation (http://www.bipm.org/en/si/si_brochure)(section 2.2 - table 3) : The radian and steradian are special names for the number one that may be used to convey information

Re: [ccp4bb] units of the B factor

2009-11-23 Thread Marc SCHILTZ
James Holton wrote: No No No! This is not what I meant at all! I am not suggesting the creation of a new unit, but rather that we name a unit that is already in widespread use. This unit is A^2/(8*pi^2) which has dimensions of length^2 and it IS the unit of B factor. That is, every PDB file

Re: [ccp4bb] units of the B factor

2009-11-23 Thread Ed Pozharski
On Sun, 2009-11-22 at 23:33 -0800, Dale Tronrud wrote: I could be describing my angle as 1.5 radians, 1.5 degrees, or 1.5 cycles (or 1.5 of the mysterious grad on my calculator). I thought that use of degrees is based on dividing a circle into 360 parts - roughly one per day (then in

Re: [ccp4bb] units of the B factor

2009-11-23 Thread James Holton
...@jiscmail.ac.uk] On Behalf Of Ian Tickle Sent: Sunday, November 22, 2009 10:57 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] units of the B factor Back to the original problem: what are the units of B and u_x^2? I haven't been able to work that out. The first wack is to say the B occurs

Re: [ccp4bb] units of the B factor

2009-11-23 Thread marc . schiltz
: Re: [ccp4bb] units of the B factor Back to the original problem: what are the units of B and u_x^2? I haven't been able to work that out. The first wack is to say the B occurs in the term Exp( -B (Sin(theta)/lambda)^2) and we've learned that the unit of Sin(theta)/lamda is 1

Re: [ccp4bb] units of the B factor

2009-11-23 Thread Clemens Grimm
Zitat von marc.schi...@epfl.ch: Dale Tronrud wrote: While it is true that angles are defined by ratios which result in their values being independent of the units those lengths were measured, common sense says that a number is an insufficient description of an angle. If I tell you I

Re: [ccp4bb] units of the B factor

2009-11-23 Thread James Holton
Marc SCHILTZ wrote: Hi James I must confess that I do not understand your point. If you read a value from the last column of a PDB file, say 27.34, then this really means : B = 27.34 Å^2 for this atom. And, since B=8*pi^2*U, it also means that this atom's mean square atomic displacement

Re: [ccp4bb] units of the B factor

2009-11-23 Thread Ian Tickle
Ed, For instance, if angles are measured in degrees and x1 sin x ~ pi * x / 180 sin x ~ x Your equations cannot simultaneously be true in fact the 1st one is obviously wrong, the 2nd is right. In the 1st case I think you meant (substituting 'x*deg' for 'x' in your correct 2nd equation):

Re: [ccp4bb] units of the B factor

2009-11-23 Thread mb1pja
coordinate systems! -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ian Tickle Sent: Sunday, November 22, 2009 10:57 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] units of the B factor Back to the original problem: what are the units

Re: [ccp4bb] units of the B factor

2009-11-23 Thread Ian Tickle
without them! Cheers -- Ian -Original Message- From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of James Holton Sent: 23 November 2009 16:35 To: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] units of the B factor Just because something

Re: [ccp4bb] units of the B factor

2009-11-23 Thread Douglas Theobald
[mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of James Holton Sent: 23 November 2009 16:35 To: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] units of the B factor Just because something is dimensionless does not mean it is unit-less. The radian and the degree are very good examples

Re: [ccp4bb] units of the B factor

2009-11-23 Thread James Holton
16:35 To: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] units of the B factor Just because something is dimensionless does not mean it is unit-less. The radian and the degree are very good examples of this. Remember, the word unit means one, and it is the quantity of something that we give

Re: [ccp4bb] units of the B factor

2009-11-23 Thread Ian Tickle
-Original Message- From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of James Holton Sent: 23 November 2009 19:07 To: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] units of the B factor So... how do you measure or report a solid angle without invoking

Re: [ccp4bb] units of the B factor

2009-11-23 Thread James Holton
...@jiscmail.ac.uk] On Behalf Of Ian Tickle Sent: Sunday, November 22, 2009 10:57 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] units of the B factor Back to the original problem: what are the units of B and u_x^2? I haven't been able to work that out. The first wack is to say the B occurs

Re: [ccp4bb] units of the B factor

2009-11-23 Thread Frank von Delft
Holton Sent: 23 November 2009 19:07 To: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] units of the B factor So... how do you measure or report a solid angle without invoking the steradian? sterdegrees? Ian Tickle wrote: James, I think you misunderstood, no-one is suggesting that we

Re: [ccp4bb] units of the B factor

2009-11-23 Thread Ed Pozharski
Ian, On Mon, 2009-11-23 at 17:34 +, Ian Tickle wrote: Ed, For instance, if angles are measured in degrees and x1 sin x ~ pi * x / 180 sin x ~ x Your equations cannot simultaneously be true in fact the 1st one is obviously wrong, the 2nd is right. In the 1st case I think you

Re: [ccp4bb] units of the B factor

2009-11-23 Thread Scott Pegan
Nice Scott On Mon, Nov 23, 2009 at 1:07 PM, Ed Pozharski epozh...@umaryland.eduwrote: Ian, On Mon, 2009-11-23 at 17:34 +, Ian Tickle wrote: Ed, For instance, if angles are measured in degrees and x1 sin x ~ pi * x / 180 sin x ~ x Your equations cannot simultaneously be

Re: [ccp4bb] units of the B factor

2009-11-23 Thread marc . schiltz
James, I don't think that you are re-phrasing me correctly. At least I can not understand how your statement relates to mine. You simply have to tell us whether a value of 27.34 read from the last column of a PDB file means : (1) B = 27.34 Å^2 , as I (and hopefully some others) think, or

Re: [ccp4bb] units of the B factor

2009-11-23 Thread marc . schiltz
Not at all ! If I want to compute the sinus of 15 degrees, using the series expansion, I write X = 15 degrees = 15 * pi/180 = 0.2618 because, 1 degree is just a symbol for the unitless, dimensionless number pi/180. I plug this X into the series expansion and get the right result. Marc

Re: [ccp4bb] units of the B factor

2009-11-23 Thread marc . schiltz
-- Ian -Original Message- From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of James Holton Sent: 23 November 2009 16:35 To: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] units of the B factor Just because something is dimensionless does not mean it is unit

Re: [ccp4bb] units of the B factor - resolved?

2009-11-23 Thread James Holton
I would like to apologize to everyone for creating such a busy thread (an what could perhaps be construed as an occasionally belligerent tone), but I really do want to know the right answer to this! I am trying to model radiation damage from first principles, and in such models you cannot

Re: [ccp4bb] units of the B factor

2009-11-23 Thread Douglas Theobald
be better off without them! Cheers -- Ian -Original Message- From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of James Holton Sent: 23 November 2009 16:35 To: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] units of the B factor Just because

Re: [ccp4bb] units of the B factor

2009-11-23 Thread marc . schiltz
Quoting James Holton jmhol...@lbl.gov: Now the coefficients of a Taylor polynomial are themselves values of the derivatives of the function being approximated. Each time you take a derivative of f(x), you divide by the units (and therefore dimensions) of x. So, Pete's coefficients below: 1,

Re: [ccp4bb] units of the B factor - resolved?

2009-11-23 Thread Lijun Liu
James, I could not help typing something! Consider a circle of radius R, its circumstance L is then 2*Pi*R. Both R and L have the same unit, the 2*Pi angle is unitless. SI defines the unit of angle to be Ran just because this unitless number is different because it is obtained by the length of

Re: [ccp4bb] units of the B factor

2009-11-23 Thread Ian Tickle
angle then you absolutely must state that, but I would advise sticking to the SI unit. Cheers -- Ian -Original Message- From: James Holton [mailto:jmhol...@lbl.gov] Sent: 23 November 2009 19:53 To: Ian Tickle Subject: Re: [ccp4bb] units of the B factor .. and if you have 1234

Re: [ccp4bb] units of the B factor

2009-11-23 Thread Artem Evdokimov
to propose, insinuate, proselytize or enforce it in any way, for now... Artem -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Dale Tronrud Sent: Monday, November 23, 2009 1:33 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] units of the B factor

Re: [ccp4bb] units of the B factor

2009-11-22 Thread Ian Tickle
Interesting that the IUCr committee report that Ian pointed out stated we recommend that the use of B be discouraged. Hmm... Good luck with that! You seem to be implying, if I understand you correctly, that the IUCr report recommends that the use of the equivalent isotropic B be

Re: [ccp4bb] units of the B factor

2009-11-22 Thread Ian Tickle
Back to the original problem: what are the units of B and u_x^2? I haven't been able to work that out. The first wack is to say the B occurs in the term Exp( -B (Sin(theta)/lambda)^2) and we've learned that the unit of Sin(theta)/lamda is 1/Angstrom and the argument of

Re: [ccp4bb] units of the B factor

2009-11-22 Thread Artem Evdokimov
sides of a right triangle -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ian Tickle Sent: Sunday, November 22, 2009 10:57 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] units of the B factor Back to the original problem: what are the units

Re: [ccp4bb] units of the B factor

2009-11-22 Thread Dale Tronrud
as 499 sec. Those people in general relativity are great at manipulating coordinate systems! -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ian Tickle Sent: Sunday, November 22, 2009 10:57 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] units

Re: [ccp4bb] units of the B factor

2009-11-21 Thread James Stroud
To avoid the creation of a cumbersome new unit everyone will need to keep track of, can we just come up with a prefix that means 0.013 of something? Perhaps we could give it the symbol b and then we could say the B-factor is 20 bA^2.* James *Seemed like 76.92 b humor units when I wrote

Re: [ccp4bb] units of the B factor

2009-11-21 Thread Dale Tronrud
This question by the Mad Scientist (here after the MS) has provoked me to give the topic a lot of thought. I think I can provide some direction towards the solution, but I'm not adept enough with The Optical Principles of the Diffraction of X-rays (Which people on this BB should refer to

Re: [ccp4bb] units of the B factor

2009-11-20 Thread Christoph Best
On Thu, 19 Nov 2009 23:13:53 -0800, James Holton jmhol...@lbl.gov said: should we call it? I nominate the Born after Max Born who did so much fundamental and far-reaching work on the nature of disorder in crystal lattices. The unit then has the symbol B, which will make it

Re: [ccp4bb] units of the B factor

2009-11-20 Thread Frank von Delft
I second that... are there committees that ratify these things? phx James Holton wrote: Many textbooks describe the B factor as having units of square Angstrom (A^2), but then again, so does the mean square atomic displacement u^2, and B = 8*pi^2*u^2. This can become confusing if one

Re: [ccp4bb] units of the B factor

2009-11-20 Thread Marc SCHILTZ
Hi James, James Holton wrote: Many textbooks describe the B factor as having units of square Angstrom (A^2), but then again, so does the mean square atomic displacement u^2, and B = 8*pi^2*u^2. This can become confusing if one starts to look at derived units that have started to come out of

[ccp4bb] {Spam?} Re: {Spam?} Re: [ccp4bb] units of the B factor

2009-11-20 Thread Frank von Delft
Hi Marc Not at all, one uses units that are convenient. By your reasoning we should get rid of Å, atmospheres, AU, light years... They exist not to be obnoxious, but because they're handy for a large number of people in their specific situations. Sounds familiar... phx Marc SCHILTZ

Re: [ccp4bb] units of the B factor

2009-11-20 Thread Adam Ralph
I think that you should suggest a new unit of 10^(-11) m, a JHm perhaps. If it is convenient to have B in A^2 then u^2 should be in JHm^2. Adam On Thu, 19 Nov 2009, James Holton wrote: Many textbooks describe the B factor as having units of square Angstrom (A^2), but then again, so does

Re: [ccp4bb] units of the B factor

2009-11-20 Thread Ian Tickle
Hi James If we're going to sort out the units we need to get the terminology right too. The mean square atomic displacement already has a symbol U = u^2 (or to be precise Ueq as we're talking about isotropic displacements here), and u is conventionally not defined as the RMS displacement as you

Re: [ccp4bb] units of the B factor

2009-11-20 Thread mb1pja
Of course, for SI political correctness we should be using nm^2 anyway. This would add more confusion to a situation that most people don't worry about anyway. Pete On 20 Nov 2009, at 11:05, Ian Tickle wrote: Hi James If we're going to sort out the units we need to get the terminology

Re: [ccp4bb] {Spam?} Re: {Spam?} Re: [ccp4bb] units of the B factor

2009-11-20 Thread Marc SCHILTZ
Frank von Delft wrote: Hi Marc Not at all, one uses units that are convenient. By your reasoning we should get rid of Å, atmospheres, AU, light years... They exist not to be obnoxious, but because they're handy for a large number of people in their specific situations. Hi Frank, I think

[ccp4bb] {Spam?} Re: {Spam?} Re: [ccp4bb] {Spam?} Re: {Spam?} Re: [ccp4bb] units of the B factor

2009-11-20 Thread Frank von Delft
Eh? m and Å are related by the dimensionless quantity 10,000,000,000. Vive la révolution! Marc SCHILTZ wrote: Frank von Delft wrote: Hi Marc Not at all, one uses units that are convenient. By your reasoning we should get rid of Å, atmospheres, AU, light years... They exist not to be

Re: [ccp4bb] {Spam?} Re: {Spam?} Re: [ccp4bb] {Spam?} Re: {Spam?} Re: [ccp4bb] units of the B factor

2009-11-20 Thread Herman . Schreuder
...@jiscmail.ac.uk] On Behalf Of Frank von Delft Sent: Friday, November 20, 2009 1:11 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] {Spam?} Re: {Spam?} Re: [ccp4bb] {Spam?} Re: {Spam?} Re: [ccp4bb] units of the B factor Eh? m and Å are related by the dimensionless quantity 10,000,000,000. Vive la révolution

Re: [ccp4bb] {Spam?} Re: {Spam?} Re: [ccp4bb] {Spam?} Re: {Spam?} Re: [ccp4bb] units of the B factor

2009-11-20 Thread Marc SCHILTZ
Yes, but Å is really only just tolerated. It has evaded the Guillotine - for the time being ;-) Frank von Delft wrote: Eh? m and Å are related by the dimensionless quantity 10,000,000,000. Vive la révolution! Marc SCHILTZ wrote: Frank von Delft wrote: Hi Marc Not at all, one uses

Re: [ccp4bb] {Spam?} Re: {Spam?} Re: [ccp4bb] {Spam?} Re: {Spam?} Re: [ccp4bb] units of the B factor

2009-11-20 Thread Philippe DUMAS
What a funny pleasant piece of discussion ! Given any physical quantity Something, having any kind of dimension (even as awful as inches^2*gallons*pounds^-3) Would it exist any room for a discussion about the dimension of 2*Something ? And what about 1*Something ? Philippe Dumas

Re: [ccp4bb] {Spam?} Re: {Spam?} Re: [ccp4bb] {Spam?} Re: {Spam?} Re: [ccp4bb] units of the B factor

2009-11-20 Thread Gerard DVD Kleywegt
What a funny pleasant piece of discussion ! Given any physical quantity Something, having any kind of dimension (even as awful as inches^2*gallons*pounds^-3) Would it exist any room for a discussion about the dimension of 2*Something ? And what about 1*Something ? (1) You can always

Re: [ccp4bb] units of the B factor

2009-11-20 Thread James Holton
No No No! This is not what I meant at all! I am not suggesting the creation of a new unit, but rather that we name a unit that is already in widespread use. This unit is A^2/(8*pi^2) which has dimensions of length^2 and it IS the unit of B factor. That is, every PDB file lists the B

[ccp4bb] units of the B factor

2009-11-19 Thread James Holton
Many textbooks describe the B factor as having units of square Angstrom (A^2), but then again, so does the mean square atomic displacement u^2, and B = 8*pi^2*u^2. This can become confusing if one starts to look at derived units that have started to come out of the radiation damage field like