Re: [ccp4bb] Summary: Phasing statistics

2010-04-16 Thread Marc SCHILTZ
from SHELXE. These all looked quite convincing, so hopefully my referees will be happy.] -- Marc SCHILTZ http://lcr.epfl.ch

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

2010-02-27 Thread marc . schiltz
Quoting Dale Tronrud : P.S. to respond out-of-band to Dr. Schiltz: On the US flag I see 7 "red stripes", 6 "white stripes", and 50 "stars". If I state "I see 7" I have conveyed no useful information. Yes, but cast in a mathematical equations one would write : Number of red stripes = 7 N

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

2010-02-26 Thread marc . schiltz
Quoting Dale Tronrud : I've held off on getting involved in this as long as I could, but you are so definitive in your comment. I could make the same argument that the unit of electron density is "1" because, after all, the volume is just the count of the number of Å^3 and a count is not a

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

2010-02-26 Thread marc . schiltz
I fully agree with Ian and would again point to the authoritative documentation : http://www.bipm.org/en/si/derived_units/2-2-3.html The quantities f^0, f' and f" are unitless, i.e. simply numbers (or rather: their unit is the number one, which is usually omitted). The unit of the electron

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

2010-02-26 Thread Marc SCHILTZ
what again ? -- Marc SCHILTZ http://lcr.epfl.ch

Re: [ccp4bb] units of the B factor

2009-11-23 Thread marc . schiltz
Quoting James Holton : 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, -1/6, and 1/12

Re: [ccp4bb] units of the B factor

2009-11-23 Thread marc . schiltz
I would believe that the official SI documentation has precedence over Wikipedia. In the SI brochure it is made quite clear that Radian is just another symbol for the number one and that it may or may no be used, as is convenient. Therefore, stating alpha = 15 (without anything else) is per

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
e and refine U's) rarely see values as low as U = 0.00438 Å^2. Cheers Marc Quoting 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 = 27.3

Re: [ccp4bb] units of the B factor

2009-11-23 Thread marc . schiltz
his email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd onl

Re: [ccp4bb] units of the B factor

2009-11-23 Thread Marc SCHILTZ
cles per second or radians per second? The dimension of an angular frequency can not be "cycles per second", because that contradicts the definition of this quantity, which is defined to be an angle per time. Again, there is no need to specifically pack this information into the unit (althoug

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 abo

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] units of the B factor

2009-11-20 Thread Marc SCHILTZ
urpose. However, within a system of units (whichever is adopted), the number of different units should be kept reasonably small. Cheers Marc Sounds familiar... phx Marc SCHILTZ wrote: Hi James, James Holton wrote: Many textbooks describe the B factor as having units of square Angst

Re: [ccp4bb] units of the B factor

2009-11-20 Thread Marc SCHILTZ
uot;B", which will make it easy to say that the B factor was "80 B". This might be very handy indeed if, say, you had an editor who insists that all reported values have units? Anyone disagree or have a better name? Good luck in submitting your proposal to the General Conference on Weights and Measures. -- Marc SCHILTZ http://lcr.epfl.ch

Re: [ccp4bb] phasing with se-met at low resolution

2009-05-13 Thread Marc SCHILTZ
background). So if the fall-off due to overall thermal motion etc as described by Kevin causes the S/N ratio to dip much below 1 then the anomalous signal won't help you. Cheers -- Ian -Original Message- From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk]

Re: [ccp4bb] phasing with se-met at low resolution

2009-05-13 Thread Marc SCHILTZ
Kevin Cowtan wrote: Marc SCHILTZ wrote: I agree with everything but would like to add the following: if we assume an overall atomic displacement parameter, the drop-off in both the anomalous and non-anomalous scattering is the same. Therefore, the ratio of anomalous differences over mean

Re: [ccp4bb] phasing with se-met at low resolution

2009-05-13 Thread Marc SCHILTZ
effectively small atomic radii (only inner shell being effective). FOR HIGH ANGLE REFLECTIONS ANOMALOUS DATA BECOMES IMPORTANT. Raja -- Marc SCHILTZ http://lcr.epfl.ch

Re: [ccp4bb] Reason for Neglected X-ray Fluorescence

2009-04-25 Thread marc . schiltz
Quoting Jacob Keller : Also, in your selenium crystal example, I think there would still be an anomalous signal, because there would always be regular scattering as well as the anomalous effect. Isn't that true? It is certainly not correct to state that there is no anomalous scattering in

Re: [ccp4bb] Reason for Neglected X-ray Fluorescence

2009-04-25 Thread marc . schiltz
Quoting Jacob Keller : Aha, so I have re-invented the wheel! But I never made sense of why f' is negative--this is beautiful! Just to make sure: you are saying that the real part of the anomalous scattering goes negative because those photons are sneaking out of the diffraction pattern through a

Re: [ccp4bb] Reason for Neglected X-ray Fluorescence

2009-04-23 Thread Marc SCHILTZ
Compton wrote in the quoted paper [read the sentence just after his equation (9)]. -- Marc SCHILTZ http://lcr.epfl.ch

Re: [ccp4bb] Reason for Neglected X-ray Fluorescence

2009-04-23 Thread Marc SCHILTZ
astic scattering. which probably contributed to his Nobel four years later. This is a classic example of the confusion that can arise from the particle-wave duality. It seems to me that the confusion here is between energy and momentum. -- Marc SCHILTZ http://lcr.epfl.ch

Re: [ccp4bb] Reason for Neglected X-ray Fluorescence

2009-04-22 Thread marc . schiltz
Quoting Ethan Merritt : On Wednesday 22 April 2009 09:23:19 Jacob Keller wrote: Hello All, What is the reason that x-ray fluorescence is neglected in our experiments? Obviously it is measureable, as in EXAFS experiments to determine anomalous edges, but should it not play a role in the int

Re: [ccp4bb] Crick-Magdoff and anomalous

2009-03-24 Thread Marc SCHILTZ
omalous signal, based on slightly different assumptions. And the generalization of their formulae is given in : Flack, H. D. & Shmueli, U. (2007). Acta Cryst. A63, 257-265. In a follow-up paper, their derivations were extended to all spacegroups, also taking account of special reflections.

Re: [ccp4bb] structure (factor) amplitude

2009-01-12 Thread marc . schiltz
; the quantity which von Laue would have called "lattice factor" (and they call "formfactor" the quantity which von Laue called "structure factor") . Seems that there will be little agreement -- Marc SCHILTZ http://lcr.epfl.ch Ian Tickle wrote: OK, limi

Re: [ccp4bb] structure (factor) amplitude

2009-01-12 Thread Marc SCHILTZ
a "rotation trace". Mal nommer les choses, c'est ajouter au malheur des hommes. A.Camus. -- Marc SCHILTZ http://lcr.epfl.ch

Re: [ccp4bb] Reading the old literature / truncate / refinement programs

2008-11-26 Thread Marc SCHILTZ
hod for estimating S, and therefore consider it beneficial if the RMS error on the "parameter" S is reduced. Is this really what you think ? Best regards Marc -- Marc SCHILTZ http://lcr.epfl.ch

Re: [ccp4bb] Reading the old literature / truncate / refinement programs

2008-10-06 Thread marc . schiltz
le to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Sci

Re: [ccp4bb] truncate ignorance

2008-09-10 Thread Marc SCHILTZ
Well, I was pointing to the Sivia & David (1994) paper because I thought it might be helpful in the discussion about how to convert intensities to amplitudes. The paper is probably not so well known in the PX community, so I decided that I would advertise it on this BB. However, since I am not one

Re: [ccp4bb] truncate ignorance

2008-09-08 Thread marc . schiltz
scussed on page 710 (final part of section 5). The authors seem to be more in favor of using F's. Marc Schiltz Quoting Jacob Keller <[EMAIL PROTECTED]>: Does somebody have a .pdf of that French and Wilson paper? Thanks in advance, Jacob *

Re: [ccp4bb] Is anomalous signal a different wavelength?

2007-05-31 Thread marc . schiltz
quot; and "anomalous scattering" are synonyms and it is almost a matter of taste which term one prefers. Both are perfectly acceptable. The x-ray physics and crystallography communities (except protein crystallography) have shifted from the usage of "anomalous scattering" to "resonant scattering". But then, as you write, if we want to keep the MAD SAD SIRAS etc acronyms we are tied to "anomalous". Marc Schiltz

Re: [ccp4bb] Is anomalous signal a different wavelength?

2007-05-31 Thread Marc SCHILTZ
adequate term since the X-ray phenomena under discussion involve resonant interactions of photons with matter and are actually not at all 'anomalous'. -- Marc SCHILTZ http://lcr.epfl.ch

Re: [ccp4bb] Advice on img proc software

2007-02-19 Thread Marc SCHILTZ
. You need to have Java running on you computer. There are other interesting applets on that page, e.g. "diffractOgram", which illustrates the Ewald construction. I use many of these applets for teaching purposes. best regards Marc Schiltz Bernhard Rupp wrote: Dear All: I am

Re: [ccp4bb] relation between wavelength and inter-atomic distances

2007-01-25 Thread Marc SCHILTZ
presence of so-called diffraction fringes (Born & Wolf, section 8.1), i.e. a variation of the intensity as a function of scattering angle. This can only occur if the wavelength is of the same order or shorter than the size of the aperture. Wikipedia is great, but use it with care..