Re: [ccp4bb] units of the B factor
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 easy to say that the B factor was 80 B. This There is already the unit barn (b) for area - about the cross section of an uranium nucleus, it is 1E-8 A^2 (100 fm^2). http://en.wikipedia.org/wiki/Barn_%28unit%29 So a Born would be somewhat more than a Megabarn. -Christoph -- | Dr Christoph Best b...@ebi.ac.uk http://www.ebi.ac.uk/~best | Project Leader Electron Microscopy Data Bank, PDB Europe | European Bioinformatics Institute, Cambridge, UK +44-1223-492649
Re: [ccp4bb] units of the B factor
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 starts to look at derived units that have started to come out of the radiation damage field like A^2/MGy, which relates how much the B factor of a crystal changes after absorbing a given dose. Or is it the atomic displacement after a given dose? Depends on which paper you are looking at. It seems to me that the units of B and u^2 cannot both be A^2 any more than 1 radian can be equated to 1 degree. You need a scale factor. Kind of like trying to express something in terms of 1/100 cm^2 without the benefit of mm^2. Yes, mm^2 have the dimensions of cm^2, but you can't just say 1 cm^2 when you really mean 1 mm^2! That would be silly. However, we often say B = 80 A^2, when we really mean is 1 A^2 of square atomic displacements. The B units, which are ~1/80th of a A^2, do not have a name. So, I think we have a new unit? It is A^2/(8pi^2) and it is the units of the B factor that we all know and love. What 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 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? -James Holton MAD Scientist
Re: [ccp4bb] units of the B factor
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 the radiation damage field like A^2/MGy, which relates how much the B factor of a crystal changes after absorbing a given dose. Or is it the atomic displacement after a given dose? Depends on which paper you are looking at. There is nothing wrong with this. In the case of derived units, there is almost never a univocal relation between the unit and the physical quantity that it refers to. As an example: from the unit kg/m^3, you can not tell what the physical quantity is that it refers to: it could be the density of a material, but it could also be the mass concentration of a compound in a solution. Therefore, one always has to specify exactly what physical quantity one is talking about, i.e. B/dose or u^2/dose, but this is not something that should be packed into the unit (otherwise, we will need hundreds of different units) It simply has to be made clear by the author of a paper whether the quantity he is referring to is B or u^2. It seems to me that the units of B and u^2 cannot both be A^2 any more than 1 radian can be equated to 1 degree. You need a scale factor. Kind of like trying to express something in terms of 1/100 cm^2 without the benefit of mm^2. Yes, mm^2 have the dimensions of cm^2, but you can't just say 1 cm^2 when you really mean 1 mm^2! That would be silly. However, we often say B = 80 A^2, when we really mean is 1 A^2 of square atomic displacements. This is like claiming that the radius and the circumference of a circle would need different units because they are related by the scale factor 2*pi. What matters is the dimension. Both radius and circumference have the dimension of a length, and therefore have the same unit. Both B and u^2 have the dimension of the square of a length and therefoire have the same unit. The scalefactor 8*pi^2 is a dimensionless quantity and does not change the unit. The B units, which are ~1/80th of a A^2, do not have a name. So, I think we have a new unit? It is A^2/(8pi^2) and it is the units of the B factor that we all know and love. What 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 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
[ccp4bb] {Spam?} Re: {Spam?} Re: [ccp4bb] units of the B factor
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 wrote: 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 the radiation damage field like A^2/MGy, which relates how much the B factor of a crystal changes after absorbing a given dose. Or is it the atomic displacement after a given dose? Depends on which paper you are looking at. There is nothing wrong with this. In the case of derived units, there is almost never a univocal relation between the unit and the physical quantity that it refers to. As an example: from the unit kg/m^3, you can not tell what the physical quantity is that it refers to: it could be the density of a material, but it could also be the mass concentration of a compound in a solution. Therefore, one always has to specify exactly what physical quantity one is talking about, i.e. B/dose or u^2/dose, but this is not something that should be packed into the unit (otherwise, we will need hundreds of different units) It simply has to be made clear by the author of a paper whether the quantity he is referring to is B or u^2. It seems to me that the units of B and u^2 cannot both be A^2 any more than 1 radian can be equated to 1 degree. You need a scale factor. Kind of like trying to express something in terms of 1/100 cm^2 without the benefit of mm^2. Yes, mm^2 have the dimensions of cm^2, but you can't just say 1 cm^2 when you really mean 1 mm^2! That would be silly. However, we often say B = 80 A^2, when we really mean is 1 A^2 of square atomic displacements. This is like claiming that the radius and the circumference of a circle would need different units because they are related by the scale factor 2*pi. What matters is the dimension. Both radius and circumference have the dimension of a length, and therefore have the same unit. Both B and u^2 have the dimension of the square of a length and therefoire have the same unit. The scalefactor 8*pi^2 is a dimensionless quantity and does not change the unit. The B units, which are ~1/80th of a A^2, do not have a name. So, I think we have a new unit? It is A^2/(8pi^2) and it is the units of the B factor that we all know and love. What 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 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.
Re: [ccp4bb] units of the B factor
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 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 A^2/MGy, which relates how much the B factor of a crystal changes after absorbing a given dose. Or is it the atomic displacement after a given dose? Depends on which paper you are looking at. It seems to me that the units of B and u^2 cannot both be A^2 any more than 1 radian can be equated to 1 degree. You need a scale factor. Kind of like trying to express something in terms of 1/100 cm^2 without the benefit of mm^2. Yes, mm^2 have the dimensions of cm^2, but you can't just say 1 cm^2 when you really mean 1 mm^2! That would be silly. However, we often say B = 80 A^2, when we really mean is 1 A^2 of square atomic displacements. The B units, which are ~1/80th of a A^2, do not have a name. So, I think we have a new unit? It is A^2/(8pi^2) and it is the units of the B factor that we all know and love. What 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 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? -James Holton MAD Scientist
[ccp4bb] arp/warp failure on Debian testing
Hello, on two recently installed Linux boxes (PC, i7) with Debian testing (squeeze), arp warp classic does not run but produces the following log-file: --- 8 snip - #CCP4I VERSION CCP4Interface 2.0.5 #CCP4I SCRIPT LOG arp_warp #CCP4I DATE 20 Nov 2009 10:43:14 #CCP4I USER tg #CCP4I PROJECT aparp #CCP4I JOB_ID 3 #CCP4I SCRATCH /tmp/tg #CCP4I HOSTNAME hydra.sheldrick #CCP4I PID 4668 !--SUMMARY_END--/FONT/B #CCP4I TERMINATION STATUS 1 #CCP4I TERMINATION TIME 20 Nov 2009 10:43:44 #CCP4I TERMINATION OUTPUT_FILES /net/home/tg/others/ap/3_arp_warp.par aparp /net/home/tg/others/ap/1_wilson.loggraph aparp #CCP4I MESSAGE Task completed successfully ---8 snap -- The gui asks about the Wilson plot, and, when run as 'run and view com file' shows the script for mtzdump. That command executed in from the shell, produces the desired result without failure. On an older installation, but also Debian squeeze, arp warp runs normally. How could I further debug the arp-warp output? One guess would be that some library is missing, but I realised that the binaries are statically linked. The directory /tmp/tg exists and is writable on both computers. Cheers, Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
Re: [ccp4bb] units of the B factor
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 seem to be implying, but the *instantaneous* displacement (otherwise you then need another symbol for the instantaneous displacement!). See: http://www.iucr.org/resources/commissions/crystallographic-nomenclature/ adp (or Acta Cryst. (1996). A52, 770-781). My theory is that B became popular over U because it needs 1 fewer digit to express it to a given precision, and this was important given the limited space available in the 80-column PDB format. So a B of 20.00 to 4 sig figs requires 5 columns, whereas the equivalent U of 0.2500 to 4 sig figs requires 6 columns (personally I've got nothing against '.2500' but many compiler writers don't see it my way!). Interestingly the IUCr commission in their 1996 report did not address the question of units for B and U. Cheers -- Ian -Original Message- From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of James Holton Sent: 20 November 2009 07:14 To: CCP4BB@jiscmail.ac.uk Subject: units of the B factor 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 A^2/MGy, which relates how much the B factor of a crystal changes after absorbing a given dose. Or is it the atomic displacement after a given dose? Depends on which paper you are looking at. It seems to me that the units of B and u^2 cannot both be A^2 any more than 1 radian can be equated to 1 degree. You need a scale factor. Kind of like trying to express something in terms of 1/100 cm^2 without the benefit of mm^2. Yes, mm^2 have the dimensions of cm^2, but you can't just say 1 cm^2 when you really mean 1 mm^2! That would be silly. However, we often say B = 80 A^2, when we really mean is 1 A^2 of square atomic displacements. The B units, which are ~1/80th of a A^2, do not have a name. So, I think we have a new unit? It is A^2/(8pi^2) and it is the units of the B factor that we all know and love. What 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 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? -James Holton MAD Scientist Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing i.tic...@astex-therapeutics.com and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this 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 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 Science Park, Cambridge CB4 0QA under number 3751674
Re: [ccp4bb] units of the B factor
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 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 seem to be implying, but the *instantaneous* displacement (otherwise you then need another symbol for the instantaneous displacement!). See: http://www.iucr.org/resources/commissions/crystallographic-nomenclature/ adp (or Acta Cryst. (1996). A52, 770-781). My theory is that B became popular over U because it needs 1 fewer digit to express it to a given precision, and this was important given the limited space available in the 80-column PDB format. So a B of 20.00 to 4 sig figs requires 5 columns, whereas the equivalent U of 0.2500 to 4 sig figs requires 6 columns (personally I've got nothing against '.2500' but many compiler writers don't see it my way!). Interestingly the IUCr commission in their 1996 report did not address the question of units for B and U. Cheers -- Ian -Original Message- From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of James Holton Sent: 20 November 2009 07:14 To: CCP4BB@jiscmail.ac.uk Subject: units of the B factor 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 A^2/MGy, which relates how much the B factor of a crystal changes after absorbing a given dose. Or is it the atomic displacement after a given dose? Depends on which paper you are looking at. It seems to me that the units of B and u^2 cannot both be A^2 any more than 1 radian can be equated to 1 degree. You need a scale factor. Kind of like trying to express something in terms of 1/100 cm^2 without the benefit of mm^2. Yes, mm^2 have the dimensions of cm^2, but you can't just say 1 cm^2 when you really mean 1 mm^2! That would be silly. However, we often say B = 80 A^2, when we really mean is 1 A^2 of square atomic displacements. The B units, which are ~1/80th of a A^2, do not have a name. So, I think we have a new unit? It is A^2/(8pi^2) and it is the units of the B factor that we all know and love. What 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 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? -James Holton MAD Scientist Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing i.tic...@astex-therapeutics.com and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this 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 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 Science Park, Cambridge CB4 0QA under number 3751674
Re: [ccp4bb] {Spam?} Re: {Spam?} Re: [ccp4bb] units of the B factor
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 that you misunderstood me. Å and atmospheres are units which really refer to physical quantities of different dimensions. So, of course, there must be different units for them (by the way: atmosphere is not an accepted unit in the SI system - not even a tolerated non SI unit, so a conscientious editor of an IUCr journal would not let it go through. On the other hand, the Å is a tolerated non SI unit). But in the case of B and U, the situation is different. These two quantities have the same dimension (square of a length). They are related by the dimensionless factor 8*pi^2. Why would one want to incorporate this factor into the unit ? What advantage would it have ? The physics literature is full of quantities that are related by multiples of pi. The frequency f of an oscillation (e.g. a sound wave) can be expressed in s^-1 (or Hz). The same oscillation can also be charcterized by its angular frequency \omega, which is related to the former by a factor 2*pi. Yet, no one has ever come up to suggest that this quantity should be given a new unit. Planck's constant h can be expressed in J*s. The related (and often more useful) constant h-bar = h/(2*pi) is also expressed in J*s. No one has ever suggested that this should be given a different unit. The SI system (and other systems as well) has been specially crafted to avoid the proliferation of units. So I don't think that we can (should) invent new units whenever it appears convenient. It would bring us back to times anterior to the French revolution. Please note: I am not saying that the SI system is the definite choice for every purpose. The nautical system of units (nautical mile, knot, etc.) is used for navigation on sea and in the air and it works fine for this purpose. 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 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 A^2/MGy, which relates how much the B factor of a crystal changes after absorbing a given dose. Or is it the atomic displacement after a given dose? Depends on which paper you are looking at. There is nothing wrong with this. In the case of derived units, there is almost never a univocal relation between the unit and the physical quantity that it refers to. As an example: from the unit kg/m^3, you can not tell what the physical quantity is that it refers to: it could be the density of a material, but it could also be the mass concentration of a compound in a solution. Therefore, one always has to specify exactly what physical quantity one is talking about, i.e. B/dose or u^2/dose, but this is not something that should be packed into the unit (otherwise, we will need hundreds of different units) It simply has to be made clear by the author of a paper whether the quantity he is referring to is B or u^2. It seems to me that the units of B and u^2 cannot both be A^2 any more than 1 radian can be equated to 1 degree. You need a scale factor. Kind of like trying to express something in terms of 1/100 cm^2 without the benefit of mm^2. Yes, mm^2 have the dimensions of cm^2, but you can't just say 1 cm^2 when you really mean 1 mm^2! That would be silly. However, we often say B = 80 A^2, when we really mean is 1 A^2 of square atomic displacements. This is like claiming that the radius and the circumference of a circle would need different units because they are related by the scale factor 2*pi. What matters is the dimension. Both radius and circumference have the dimension of a length, and therefore have the same unit. Both B and u^2 have the dimension of the square of a length and therefoire have the same unit. The scalefactor 8*pi^2 is a dimensionless quantity and does not change the unit. The B units, which are ~1/80th of a A^2, do not have a name. So, I think we have a new unit? It is A^2/(8pi^2) and it is the units of the B factor that we all know and love. What 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 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
[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! 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 obnoxious, but because they're handy for a large number of people in their specific situations. Hi Frank, I think that you misunderstood me. Å and atmospheres are units which really refer to physical quantities of different dimensions. So, of course, there must be different units for them (by the way: atmosphere is not an accepted unit in the SI system - not even a tolerated non SI unit, so a conscientious editor of an IUCr journal would not let it go through. On the other hand, the Å is a tolerated non SI unit). But in the case of B and U, the situation is different. These two quantities have the same dimension (square of a length). They are related by the dimensionless factor 8*pi^2. Why would one want to incorporate this factor into the unit ? What advantage would it have ? The physics literature is full of quantities that are related by multiples of pi. The frequency f of an oscillation (e.g. a sound wave) can be expressed in s^-1 (or Hz). The same oscillation can also be charcterized by its angular frequency \omega, which is related to the former by a factor 2*pi. Yet, no one has ever come up to suggest that this quantity should be given a new unit. Planck's constant h can be expressed in J*s. The related (and often more useful) constant h-bar = h/(2*pi) is also expressed in J*s. No one has ever suggested that this should be given a different unit. The SI system (and other systems as well) has been specially crafted to avoid the proliferation of units. So I don't think that we can (should) invent new units whenever it appears convenient. It would bring us back to times anterior to the French revolution. Please note: I am not saying that the SI system is the definite choice for every purpose. The nautical system of units (nautical mile, knot, etc.) is used for navigation on sea and in the air and it works fine for this purpose. 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 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 A^2/MGy, which relates how much the B factor of a crystal changes after absorbing a given dose. Or is it the atomic displacement after a given dose? Depends on which paper you are looking at. There is nothing wrong with this. In the case of derived units, there is almost never a univocal relation between the unit and the physical quantity that it refers to. As an example: from the unit kg/m^3, you can not tell what the physical quantity is that it refers to: it could be the density of a material, but it could also be the mass concentration of a compound in a solution. Therefore, one always has to specify exactly what physical quantity one is talking about, i.e. B/dose or u^2/dose, but this is not something that should be packed into the unit (otherwise, we will need hundreds of different units) It simply has to be made clear by the author of a paper whether the quantity he is referring to is B or u^2. It seems to me that the units of B and u^2 cannot both be A^2 any more than 1 radian can be equated to 1 degree. You need a scale factor. Kind of like trying to express something in terms of 1/100 cm^2 without the benefit of mm^2. Yes, mm^2 have the dimensions of cm^2, but you can't just say 1 cm^2 when you really mean 1 mm^2! That would be silly. However, we often say B = 80 A^2, when we really mean is 1 A^2 of square atomic displacements. This is like claiming that the radius and the circumference of a circle would need different units because they are related by the scale factor 2*pi. What matters is the dimension. Both radius and circumference have the dimension of a length, and therefore have the same unit. Both B and u^2 have the dimension of the square of a length and therefoire have the same unit. The scalefactor 8*pi^2 is a dimensionless quantity and does not change the unit. The B units, which are ~1/80th of a A^2, do not have a name. So, I think we have a new unit? It is A^2/(8pi^2) and it is the units of the B factor that we all know and love. What 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 easy to say that the B
Re: [ccp4bb] {Spam?} Re: {Spam?} Re: [ccp4bb] {Spam?} Re: {Spam?} Re: [ccp4bb] units of the B factor
But in this case you are no longer defining distances but some other arbitrary
quantity, like vendors do when they convert a small computer speaker into a
rockband PA by using PMPO instead of music power.
Herman
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@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!
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 obnoxious, but because they're handy for a large number of
people in their specific situations.
Hi Frank,
I think that you misunderstood me. Å and atmospheres are units which
really refer to physical quantities of different dimensions. So, of
course, there must be different units for them (by the way: atmosphere
is not an accepted unit in the SI system - not even a tolerated non SI
unit, so a conscientious editor of an IUCr journal would not let it go
through. On the other hand, the Å is a tolerated non SI unit).
But in the case of B and U, the situation is different. These two
quantities have the same dimension (square of a length). They are
related by the dimensionless factor 8*pi^2. Why would one want to
incorporate this factor into the unit ? What advantage would it have ?
The physics literature is full of quantities that are related by
multiples of pi. The frequency f of an oscillation (e.g. a sound wave)
can be expressed in s^-1 (or Hz). The same oscillation can also be
charcterized by its angular frequency \omega, which is related to the
former by a factor 2*pi. Yet, no one has ever come up to suggest that
this quantity should be given a new unit. Planck's constant h can be
expressed in J*s. The related (and often more useful) constant h-bar =
h/(2*pi) is also expressed in J*s. No one has ever suggested that this
should be given a different unit.
The SI system (and other systems as well) has been specially crafted
to avoid the proliferation of units. So I don't think that we can
(should) invent new units whenever it appears convenient. It would
bring us back to times anterior to the French revolution.
Please note: I am not saying that the SI system is the definite choice
for every purpose. The nautical system of units (nautical mile, knot,
etc.) is used for navigation on sea and in the air and it works fine
for this purpose. 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
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 A^2/MGy, which relates how much
the B factor of a crystal changes after absorbing a given dose. Or
is it the atomic displacement after a given dose? Depends on which
paper you are looking at.
There is nothing wrong with this. In the case of derived units,
there is almost never a univocal relation between the unit and the
physical quantity that it refers to. As an example: from the unit
kg/m^3, you can not tell what the physical quantity is that it
refers to: it could be the density of a material, but it could also
be the mass concentration of a compound in a solution. Therefore,
one always has to specify exactly what physical quantity one is
talking about, i.e. B/dose or u^2/dose, but this is not something
that should be packed into the unit (otherwise, we will need
hundreds of different units)
It simply has to be made clear by the author of a paper whether the
quantity he is referring to is B or u^2.
It seems to me that the units of B and u^2 cannot both be A^2
any more than 1 radian can be equated to 1 degree. You need a
scale factor. Kind of like trying to express something in terms of
1/100 cm^2 without the benefit of mm^2. Yes, mm^2 have the
dimensions of cm^2, but you can't just say 1 cm^2 when you really
mean 1 mm^2! That would be silly. However, we often say B = 80
A^2, when we really mean is 1 A^2 of square atomic displacements.
This is like claiming that the radius and the circumference of a
circle would need different units because they are related by the
scale factor 2*pi.
What matters is the dimension. Both radius and circumference have
the dimension of a length, and therefore have the same unit. Both B
and u^2 have the dimension of the
[ccp4bb] Scientific programmer position at MRC LMB Cambridge UK
Scientific Programmer MRC Laboratory of Molecular Biology Cambridge £20,074 – £27,271 per annum A two year position is available for a programmer to continue the development of a new Graphical User Interface for a widely used program package to process X-ray diffraction data from crystals of biological macromolecules. The interface is written in Tcl/Tk and C. Applicants should have a degree in a relevant area and experience in programming in a scientific environment. Familiarity with Tcl/Tk and C would be a distinct advantage. For informal enquiries please email: and...@mrc-lmb.cam.ac.uk Your salary will be supported by a flexible pay and reward policy, 30 days annual leave entitlement, an optional MRC final salary pension scheme and excellent on-site sports and social facilities. This position is subject to pre-employment screening. If you would like to receive this advert in large print, Braille, audio, or electronic format/ hard copy, please contact the Recruitment team at the MRC Shared Service Centre on the telephone number below or recruitm...@ssc.mrc.ac.uk Applications for this role must now be made online at http://jobs.mrc.ac.uk inputting reference LMB09/609. If you do not have internet access or experience technical difficulties please call 01793 301157. Closing date 7th December 2009 For further information about the MRC please visit www.mrc.ac.uk.
[ccp4bb] X-ray facility scientist at MRC LMB Cambridge, UK
X-Ray Facility Scientist MRC Laboratory of Molecular Biology Cambridge £26,022 - £31,758 per annum We wish to recruit an Investigator Scientist to join the MRC Laboratory of Molecular Biology X-ray facility in Cambridge, UK. You will provide support for a range of projects involving X-ray crystallographic data collection both in-house and at synchrotrons. You would also be responsible for optimising the performance of the in- house X-ray facilities, liaising with maintenance engineers and helping to train new users. The position requires extensive travel to synchrotrons both in UK and abroad. You should have a PhD in a relevant subject and experience in X-ray crystallographic data collection. For informal enquiries please email: and...@mrc-lmb.cam.ac.uk Your salary will be supported by a flexible pay and reward policy, 30 days annual leave entitlement, an optional MRC final salary pension scheme and excellent on-site sports and social facilities. This position is subject to pre-employment screening. If you would like to receive this advert in large print, Braille, audio, or electronic format/ hard copy, please contact the Recruitment team at the MRC Shared Service Centre on the telephone number below or recruitm...@ssc.mrc.ac.uk Applications for this role must now be made online at http://jobs.mrc.ac.uk inputting reference LMB09/608. If you do not have internet access or experience technical difficulties please call 01793 301157. Closing date 7th December 2009 For further information about the MRC please visit www.mrc.ac.uk. The Medical Research Council is an Equal Opportunities Employer
Re: [ccp4bb] arp/warp failure on Debian testing
Hi Tim, First, we do not have access to Debian squeeze so I am afraid I cant say much about it. The gui asks about the Wilson plot, and, when run as 'run and view com file' shows the script for mtzdump. The 'run and view command file' will not work with the way that ARP/ wARP Classic (ab)uses ccp4i. That command executed in from the shell, produces the desired result without failure. Could you please clarify which is 'that commend'? Is that something like warp_tracing.sh my_cp4i_par_file_from_above.par or auto_tracing [parameters] On an older installation, but also Debian squeeze, arp warp runs normally. How could I further debug the arp-warp output? One guess would be that some library is missing, but I realised that the binaries are statically linked. Indeed, arp/warp is statically built. But, since the command line run its not the executables. I suspect semething with Tcl/Tk versions maybe. The directory /tmp/tg exists and is writable on both computers. If you send me what exactly you tried from the commend line I am sure we will be able to debug it. A. Cheers, Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A P please don't print this e-mail unless you really need to Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791
Re: [ccp4bb] {Spam?} Re: {Spam?} Re: [ccp4bb] {Spam?} Re: {Spam?} Re: [ccp4bb] units of the B factor
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 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 that you misunderstood me. Å and atmospheres are units which really refer to physical quantities of different dimensions. So, of course, there must be different units for them (by the way: atmosphere is not an accepted unit in the SI system - not even a tolerated non SI unit, so a conscientious editor of an IUCr journal would not let it go through. On the other hand, the Å is a tolerated non SI unit). But in the case of B and U, the situation is different. These two quantities have the same dimension (square of a length). They are related by the dimensionless factor 8*pi^2. Why would one want to incorporate this factor into the unit ? What advantage would it have ? The physics literature is full of quantities that are related by multiples of pi. The frequency f of an oscillation (e.g. a sound wave) can be expressed in s^-1 (or Hz). The same oscillation can also be charcterized by its angular frequency \omega, which is related to the former by a factor 2*pi. Yet, no one has ever come up to suggest that this quantity should be given a new unit. Planck's constant h can be expressed in J*s. The related (and often more useful) constant h-bar = h/(2*pi) is also expressed in J*s. No one has ever suggested that this should be given a different unit. The SI system (and other systems as well) has been specially crafted to avoid the proliferation of units. So I don't think that we can (should) invent new units whenever it appears convenient. It would bring us back to times anterior to the French revolution. Please note: I am not saying that the SI system is the definite choice for every purpose. The nautical system of units (nautical mile, knot, etc.) is used for navigation on sea and in the air and it works fine for this purpose. 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 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 A^2/MGy, which relates how much the B factor of a crystal changes after absorbing a given dose. Or is it the atomic displacement after a given dose? Depends on which paper you are looking at. There is nothing wrong with this. In the case of derived units, there is almost never a univocal relation between the unit and the physical quantity that it refers to. As an example: from the unit kg/m^3, you can not tell what the physical quantity is that it refers to: it could be the density of a material, but it could also be the mass concentration of a compound in a solution. Therefore, one always has to specify exactly what physical quantity one is talking about, i.e. B/dose or u^2/dose, but this is not something that should be packed into the unit (otherwise, we will need hundreds of different units) It simply has to be made clear by the author of a paper whether the quantity he is referring to is B or u^2. It seems to me that the units of B and u^2 cannot both be A^2 any more than 1 radian can be equated to 1 degree. You need a scale factor. Kind of like trying to express something in terms of 1/100 cm^2 without the benefit of mm^2. Yes, mm^2 have the dimensions of cm^2, but you can't just say 1 cm^2 when you really mean 1 mm^2! That would be silly. However, we often say B = 80 A^2, when we really mean is 1 A^2 of square atomic displacements. This is like claiming that the radius and the circumference of a circle would need different units because they are related by the scale factor 2*pi. What matters is the dimension. Both radius and circumference have the dimension of a length, and therefore have the same unit. Both B and u^2 have the dimension of the square of a length and therefoire have the same unit. The scalefactor 8*pi^2 is a dimensionless quantity and does not change the unit. The B units, which are ~1/80th of a A^2, do not have a name. So, I think we have a new unit? It is A^2/(8pi^2) and it is the units of the B factor that we all know and love. What should we call it? I nominate the Born after Max Born who did so much fundamental and far-reaching work on the nature
Re: [ccp4bb] ... docking question
On 19 Nov 2009, at 09:34, Anastassis Perrakis wrote: Dear all, I am risking life and limb here, and possibly wining a first row seat to 'Morten's Inferno' for modelers! I want a software that will do some docking of a flexible ligand to a rigid protein model. Consensus google search suggested me to use AutoDock 4/Vina. (I am looking for free software). However, what I want to do is 'non-standard': I know from a crystallographic structure (b) the position of a Vanadate, which has to be (give or take) the position of my phosphate atom in my substrate (I have a phosphodiesterase). Thus this point should get fixed in space (no translation, or ideally restrained translation of some sort), while rotation around it should be allowed, plus that point should be the 'root' of the torsion tree of the ligand to allow it to change conformation around it. AutoDock (but not Vina) seems to be able to do it in simulated annealing mode, by setting the translation to 0. Hi Anastassis, I suggest you to stick with Autodock4 for a quick and dirty trick. Define your ligand as a flexible residue, choose the phosphorus atom as the root and put it in the rigid part of the docking (i.e. with the receptor). Then perform a run using the do_local_only option in the dpf file (you have to comment out ga_run in the dpf). It is equivalent to a minimization. That should do the trick. Florian
Re: [ccp4bb] {Spam?} Re: {Spam?} Re: [ccp4bb] {Spam?} Re: {Spam?} Re: [ccp4bb] units of the B factor
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 attachment: p_dumas.vcf
Re: [ccp4bb] {Spam?} Re: {Spam?} Re: [ccp4bb] {Spam?} Re: {Spam?} Re: [ccp4bb] units of the B factor
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 convert anything into anything else (related to it by a scale factor) using Google, e.g.: http://www.google.com/search?hl=enq=2+fortnights+in+msec http://www.google.com/search?hl=enq=7+furlongs+in+mm http://www.google.com/search?hl=enq=7+square+angstrom+in+cm%5E2 To answer your question: http://www.google.com/search?hl=enq=1+inches%5E2*gallons*pounds%5E-3 So: 1 inches^2*gallons*pounds^-3 = 2.61687719 10^-5 m^5 / kg^3 (assuming US gallons! If you meant imperial gallons, the answer is 3.14273976 10^-5 m^5 / kg^3). (2) With respect to the subject of this thread, can I have my spam, spam, spam, spam and units with eggs, please? (http://www.youtube.com/watch?v=cFrtpT1mKy8) --dvd ** Gerard J. Kleywegt Dept. of Cell Molecular Biology University of Uppsala Biomedical Centre Box 596 SE-751 24 Uppsala SWEDEN http://xray.bmc.uu.se/gerard/ mailto:ger...@xray.bmc.uu.se ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. **
[ccp4bb] Warren Fund update - more books - lower threshold
Dear All, Great news: The Publisher, Garland Science, has kindly offered up to 5 additional books, so I will lower the winning threshold to 100 tickets. That means we have already a second round winner (announced later on the web page) and all entries posted past 1925 PST on Nov 19 play already in the 3rd round! Let's not get complacent now, because first it is not for winning that you donate but to keep Pymol and Warren's work and memory going, and second, the fine print said: we need to REACH 100 tickets for each book. Less than 100 in any given round, and the money just goes to Warren's fund by Dec 15 and NO book 8-( Best, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org http://www.ruppweb.org/ - People can be divided in three classes: The few who make things happen The many who watch things happen And the overwhelming majority who have no idea what is happening. -
[ccp4bb] warning message: bound resonance
Hi, Since the newest upgrade of analysis, I get this warning message once in a while: Dimensions 1 and 3 are directly bound but resonance 7LysCd is already bound to 7LysHdb not 7LysHda Continue with assignement? I understand what it means and I'm ok with that. I'm wondering if there's a way to avoid this message or to inactivate this. My problem is that I tried to produce a synthetic list on a carbon HSQC and this message appears every time it assigns a peak... I have hundreds of peaks! It's just annoying... Thanks, Julien
Re: [ccp4bb] warning message: bound resonance
'Allo! 'Allo! I suspect that you are looking for the CCPN mailing list rather than the CCP4 one. You have just confused thousands of innocent crystallographers! --dvd On Fri, 20 Nov 2009, Julien Litt?rature wrote: Hi, Since the newest upgrade of analysis, I get this warning message once in a while: Dimensions 1 and 3 are directly bound but resonance 7LysCd is already bound to 7LysHdb not 7LysHda Continue with assignement? I understand what it means and I'm ok with that. I'm wondering if there's a way to avoid this message or to inactivate this. My problem is that I tried to produce a synthetic list on a carbon HSQC and this message appears every time it assigns a peak... I have hundreds of peaks! It's just annoying... Thanks, Julien Best wishes, --Gerard ** Gerard J. Kleywegt Dept. of Cell Molecular Biology University of Uppsala Biomedical Centre Box 596 SE-751 24 Uppsala SWEDEN http://xray.bmc.uu.se/gerard/ mailto:ger...@xray.bmc.uu.se ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. **
Re: [ccp4bb] warning message: bound resonance
And a few guilty ones. - === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu On Fri, 2009-11-20 at 22:24 +0100, Gerard DVD Kleywegt wrote: 'Allo! 'Allo! I suspect that you are looking for the CCPN mailing list rather than the CCP4 one. You have just confused thousands of innocent crystallographers! --dvd
[ccp4bb] Warren DeLano Memorial Fund - 2nd winner
Second Winner: Tara Davis, UCSC -congratulations! http://www.ruppweb.org/Garland/Warren_raffle.htm 77 to go for #3 I'll stop these annoying updates to the bb now - you can follow on twitter or face book using the Icons on my home page http://www.ruppweb.org/ Thx, BR - Bernhard Rupp b...@ruppweb.org http://www.ruppweb.org/ - The hard part about playing chicken is to know when to flinch -
[ccp4bb] hairpin formation in gene
Dear bb-ers, I am trying to have a gene synthesized and found out that it forms an 11-bp hairpin. Does that complicate expression? Would it be better to try and disrupt it by altering codon usage to improve expression? Thank you in advance, Sangeetha.
Re: [ccp4bb] units of the B factor
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 factor as a multiple of THIS fundamental quantity, not A^2. If the unit were simply A^2, then the PDB file would be listing much smaller numbers (U, not B). (Okay, there are a few PDBs that do that by mistake, but not many.) As Marc pointed out, a unit and a dimension are not the same thing: millimeters and centimeters are different units, but they have the same dimension: length. And, yes, dimensionless scale factors like milli and centi are useful. The B factor has dimension length^2, but the unit of B factor is not A^2. For example, if we change some atomic B factor by 1, then we are actually describing a change of 0.013 A^2, because this is equal to 1.0 A^2/(8*pi^2). What I am suggesting is that it would be easier to say that the B factor changed by 1.0, and if you must quote the units, the units are B, otherwise we have to say: the B factor changed by 1.0 A^2/(8*pi^2). Saying that a B factor changed by 1 A^2 when the actual change in A^2 is 0.013 is (formally) incorrect. The unfortunate situation however is that B factors have often been reported with units of A^2, and this is equivalent to describing the area of 80 football fields as 80 and then giving the dimension (m^2) as the units! It is better to say that the area is 80 football fields, but this is invoking a unit: the football field. The unit of B factor, however does not have a name. We could say 1.0 B-factor units, but that is not the same as 1.0 A^2 which is ~80 B-factor units. Admittedly, using A^2 to describe a B factor by itself is not confusing because we all know what a B factor is. It is that last column in the PDB file. The potential for confusion arises in derived units. How does one express a rate-of-change in B factor? A^2/s? What about rate-of-change in U? A^2/s? I realized that this could become a problem while comparing Kmetko et. al. Acta D (2006) and Borek et. al. JSR (2007). Both very good and influential papers: the former describes damage rates in A^2/MGy (converting B to U first so that A^2 is the unit), and the latter relates damage to the B factor directly, and points out that the increase in B factor from radiation damage of most protein crystals is almost exactly 1.0 B/MGy. This would be a great rule of thumb if one were allowed to use B as a unit. Why not? 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! I agree that I should have used U instead of u^2 in my original post. Actually, the u should have a subscript x to denote that it is along the direction perpendicular to the Bragg plane. Movement within the plane does not change the spot intensity, and it also does not matter if the x displacements are instantaneous, dynamic or static, as there is no way to tell the difference with x-ray diffraction. It just matters how far the atoms are from their ideal lattice points (James 1962, Ch 1). I am not sure how to do a symbol with both superscripts and subscripts AND inside brackets that is legible in all email clients. Here is a try: B = 8*pi*usubx/sub^2. Did that work? I did find it interesting that the 8*pi^2 arises from the fact that diffraction occurs in angle space, and so factors of 4*pi steradians pop up in the Fourier domain (spatial frequencies). In the case of B it is (4*pi)^2/2 because the second coefficient of a Taylor series is 1/2. Along these lines, quoting B in A^2 is almost precisely analogous to quoting an angular frequency in Hz. Yes, the dimensions are the same (s^-1), but how does one interpret the statement: the angular frequency was 1 Hz. Is that cycles per second or radians per second? That's all I'm saying... -James Holton MAD Scientist 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 obnoxious, but because they're handy for a large number of people in their specific situations. Hi Frank, I think that you misunderstood me. Å and atmospheres are units which really refer to physical quantities of different dimensions. So, of course, there must be different units for them (by the way: atmosphere is not an accepted unit in the SI system - not even a tolerated non SI unit, so a conscientious editor of an IUCr journal would not let it go through. On the other hand, the Å is a tolerated non SI unit). But in the case of B and U, the situation is different. These two quantities have the same dimension (square of a length). They are related by the
