Re: [ccp4bb] units of f0, f', f''
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. Dale Tronrud Gerard Bricogne wrote: Dear all, Two slight confusions seem to have popped up intermittently in this thread, in messages other than those included here. The first one was related to the charge of the electron - even the colour code according to which its electron density should be displayed - and the other one to its mass, i.e. the assumption that the word "density" was to be taken literally as being in some way connected to a mass by unit volume. Regarding the first, the sign of the charge plays no role, as shown by the fact that the Thomson scattering formula involves the square of the electron charge. This could be seen as an instance of TCP invariance: a free positron would scatter X-rays to exactly the same degree as a free electron. If there is something that would deserve to be called a unit in the original context of this question, i.e. a unit for structure factors, it would be (as was pointed out by many contributors) the X-ray scattering power of a free electron (or positron). A pedantic name for such a unit could be "electron qua X-ray scatterer", which the general aversion to Latin would immediately shorten to "electron", thereby explaining the current practice. At least the pedantic name would have the merit of making it clear that we are not referring to the electron in relation to its charge, but in relation to its scattering behaviour towards X-rays. Regarding the second, the word "density" has long been freed from its original connection with mass. For instance one speaks about a "probability density", which is stripped of any physical association and is related to the notion of a measure in the theory of integration. One even encounters the expression "number density" independently of any notion of probability, to designate a concentration of things that can be counted (as opposed to measured). The meaning of density, as has again been explained by several contributors, is that the density of 'whatever' is the amount of 'whatever' per unit volume; so that integrating it over a specified region delivers a result in the unit in which 'whatever' is measured. Replacing 'whatever' by X-ray scattering power measured in units of "electron qua X-ray scatterer" - or just "electron" - would seem to make everything that has been said consistent. To get back to the original question: if the reference X-ray scatterer was taken to be the proton (or antiproton), then the numerical values of f0, f' and f" giving the strength of the anomalous scattering of *electrons* would obviously change, so there is indeed an underlying dimensionality to these numbers via Thomson's formula; but since crystallographers live off X-ray scattering from electrons, such a change of units would seem a rather daft idea, the possibility of which I would not expect to have occurred to any journal editor or reviewer while staring at Table I ... - so if we have such a natural unit for what we are looking at, f0, f', f" are, for all intents and purposes, pure numbers. I hope this long message is only minimally eristic, and rather more dialectical :-)) ... . With best wishes, Gerard. -- On Sun, Feb 28, 2010 at 07:19:48AM -0800, James Holton wrote: I suppose I could point out that the letter "e" has many more "universal" meanings that just denoting electric charge, such the base of the natural logarithm, the identity element in set theory, or even a musical note. But, today I found that "e" can also stand for "eristic", a new word I learned while reading the following web page: http://en.wikipedia.org/wiki/Flame_war -James Holton MAD Scientist 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
Re: [ccp4bb] linux question
On Feb 27, 2010, at 7:10 PM, David Roberts wrote: > I have a quick question about linux for all. Is there anybody running a > windows pc with linux on a bootable cd or bootable drive/flash drive/??? that > works for crystallography apps? I have a colleague who does molecular > dynamics calculations and he needs some conversion programs that are unix > based (not pc based - they just haven't been ported and that's not my area). > We have linux computers that he can use, but I thought in the end it might be > easiest if he could just boot up a linux flash drive to run his conversion, > then go back to his pc and windows. Something like "damn small linux" or ?? > > Any thoughts on this? Thanks > > Dave A slightly different approach would be to install Cygwin, and then you can do unixy things within windoze. http://www.cygwin.com/
Re: [ccp4bb] linux question
On Feb 28, 2010, at 5:11 PM, Damon Colbert wrote: > I have a persistent Kubuntu 8.10 .. it took a week to work out some > problems. The main one being that with limited space on the thumb drive, > one cannot do a complete update of Kubuntu. Therefore many libraries are > missing and dependancy errors crop up during crystallography software > installation. You might want to look at Xubuntu. It uses the rather more lightweight xfce4 windowing system, which is nice and simple and basic and lightweight and clean and responsive. I prefer it over kde and gnome, even on hardware that can easily handle the overhead of all the extra features.
Re: [ccp4bb] linux question
I have a persistent Kubuntu 8.10 on a 16Gb flash drive, on which I have been running the likes of Coot, iMosflm and CCP4. I have used my setup to process two datasets via MolRep. There are plenty of resources on the internet telling you how to set it up. e.g http://www.pendrivelinux.com/ http://www.linux-usb.org/ https://wiki.kubuntu.org/LiveUsbPendrivePersistent It was relatively quick to set up, but it took a week to work out some problems. The main one being that with limited space on the thumb drive, one cannot do a complete update of Kubuntu. Therefore many libraries are missing and dependancy errors crop up during crystallography software installation. It's not too difficult a problem to deal with if you are familiar with installing apps on linux. And by partitioning your drive with FAT32, and two ext3 partitions (one for the root, and one labelled "casper-rw") before creating the linux boot-stick, you can have a bootable linux usb stick with the ability to share files with a windows machine (fat32 partition) and enough space to install those behemoth crystallography apps. And I managed to do all this with minimal linux experience. (The only issue I haven't yet resolved is with graphics drivers. Its a trivial task to install the appropriate drivers, but it seems every time I boot up Kubuntu, I have to run 'x-config' and restart the x-server to get the Nvidia drivers to work, which is necessary for Coot, at least. An inconvenience every time I start linux, but not impossible). Im not familiar with setting up or running virtual machines / emulators, but they might be a simpler, more versatile option? But at least you can run graphical applications with ease (pymol and coot run well once the nvidia drivers are working).
Re: [ccp4bb] linux question
On 2/27/2010 10:10 PM, David Roberts wrote: I have a quick question about linux for all. Is there anybody running a windows pc with linux on a bootable cd or bootable drive/flash drive/??? that works for crystallography apps? I have a colleague who does molecular dynamics calculations and he needs some conversion programs that are unix based (not pc based - they just haven't been ported and that's not my area). We have linux computers that he can use, but I thought in the end it might be easiest if he could just boot up a linux flash drive to run his conversion, then go back to his pc and windows. Something like "damn small linux" or ?? Alternatively, he can install some xterm emulator for windows (like putty) then use it to connect to the real linux machines you already have. Any thoughts on this? Thanks Dave
Re: [ccp4bb] units of f0, f', f''
Dear all, Two slight confusions seem to have popped up intermittently in this thread, in messages other than those included here. The first one was related to the charge of the electron - even the colour code according to which its electron density should be displayed - and the other one to its mass, i.e. the assumption that the word "density" was to be taken literally as being in some way connected to a mass by unit volume. Regarding the first, the sign of the charge plays no role, as shown by the fact that the Thomson scattering formula involves the square of the electron charge. This could be seen as an instance of TCP invariance: a free positron would scatter X-rays to exactly the same degree as a free electron. If there is something that would deserve to be called a unit in the original context of this question, i.e. a unit for structure factors, it would be (as was pointed out by many contributors) the X-ray scattering power of a free electron (or positron). A pedantic name for such a unit could be "electron qua X-ray scatterer", which the general aversion to Latin would immediately shorten to "electron", thereby explaining the current practice. At least the pedantic name would have the merit of making it clear that we are not referring to the electron in relation to its charge, but in relation to its scattering behaviour towards X-rays. Regarding the second, the word "density" has long been freed from its original connection with mass. For instance one speaks about a "probability density", which is stripped of any physical association and is related to the notion of a measure in the theory of integration. One even encounters the expression "number density" independently of any notion of probability, to designate a concentration of things that can be counted (as opposed to measured). The meaning of density, as has again been explained by several contributors, is that the density of 'whatever' is the amount of 'whatever' per unit volume; so that integrating it over a specified region delivers a result in the unit in which 'whatever' is measured. Replacing 'whatever' by X-ray scattering power measured in units of "electron qua X-ray scatterer" - or just "electron" - would seem to make everything that has been said consistent. To get back to the original question: if the reference X-ray scatterer was taken to be the proton (or antiproton), then the numerical values of f0, f' and f" giving the strength of the anomalous scattering of *electrons* would obviously change, so there is indeed an underlying dimensionality to these numbers via Thomson's formula; but since crystallographers live off X-ray scattering from electrons, such a change of units would seem a rather daft idea, the possibility of which I would not expect to have occurred to any journal editor or reviewer while staring at Table I ... - so if we have such a natural unit for what we are looking at, f0, f', f" are, for all intents and purposes, pure numbers. I hope this long message is only minimally eristic, and rather more dialectical :-)) ... . With best wishes, Gerard. -- On Sun, Feb 28, 2010 at 07:19:48AM -0800, James Holton wrote: > I suppose I could point out that the letter "e" has many more "universal" > meanings that just denoting electric charge, such the base of the natural > logarithm, the identity element in set theory, or even a musical note. > But, today I found that "e" can also stand for "eristic", a new word I > learned while reading the following web page: > > http://en.wikipedia.org/wiki/Flame_war > > -James Holton > MAD Scientist > > > 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' s
Re: [ccp4bb] Molrep error -
Dear Jon -- it looks to me that it is trying to open a file that does not exist because of the path name... I'm not an expert in MolRep, but you defined PATH_SCR and PATH_OUT with the same names; the problem might then be that it tried to open a file located in the PATH_SCR/ PATH_OUT... (or the opposite). Perhaps if you try the following it could work: /usr/local/ccp4-6.1.0/ccp4-6.1.0/bin/molrep PATH_SCR "/home/caruthej/ bo3/ccp4/" PATH_OUT "bo3P1_11_molrep_" HKLIN "/home/caruthej/bo3/P1/ ccp4/merged.mtz" MODEL "/home/caruthej/bo3/P1/cns/model.pdb" Sorry if it doesn't help. Kind regards. -- Leo -- On 27 Feb 2010, at 04:31, Jonathan Marvin Caruthers wrote: 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 "/home/caruthej/bo3/P1/cns/model.pdb" Chavas Leonard, Ph.D. Assistant Professor Structural Biology Research Center Photon Factory High Energy Research Organization (KEK) 305-0801 Tsukuba Oho 1-1 Japan Tel: +81(0)29-864-5642 (4901) Fax: +81(0)29-864-2801 e-mail: leonard.cha...@kek.jp Science Advisory Board (BIT Life Sciences) Editorial Board (JAA) http://pfweis.kek.jp/~leo
[ccp4bb] Senior Scientist position in structural biology/immunology with applications in T cell and NK cell receptor recognition of MHC class I and class II complexes in Stockholm, Sweden
Dear group members, I would like to bring to the following opening to your attention: ANNOUNCEMENT TITLE: Senior Scientist position in structural biology/immunology with applications in T cell and NK cell receptor recognition of MHC class I and class II complexes in Stockholm, Sweden DEADLINE FOR APPLICATIONS: 10 April 2010 TYPE OF POSITION: Senior Scientist INSTITUTION/DEPARTMENT: Center for Infectious Medicine (CIM), Department of Medicine, F59 Karolinska University Hospital in Huddinge, Karolinska Institutet CONTACT PERSON: Adnane Achour, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, S-171 77 Stockholm, Sweden. e-mail address: adnane.ach...@ki.se, Phone: +46-8-5248 6216, Fax: +46-8-30 42 76, website: http://www.ki.se/cim DESCRIPTION/REQUIREMENTS: A senior scientist position is available for an enthusiastic individual for a period of at least four years within the laboratory of Assoc. Prof. Adnane Achour at the Center for Infectious Medicine (CIM), Karolinska Institutet in Stockholm, Sweden. The candidate should be a good team-player, with excellent knowledge of X-ray crystallography and deep proven insights in TCR/MHC interaction. She/he will co-supervise both PhD students and post-doctoral fellows in the group and will be responsible for the expression, purification, crystallization and structural analysis of proteins that are involved in the structure of the T cell and NK cell synapse. The prime targets of this project are T and NK cell receptors and a large array of MHC class I and class II alleles as well as other co-receptors. Site directed mutagenesis studies will be combined with a wide array of biochemical and immunological assays, as well as imaging, in order to assess the molecular mechanisms underlying the modulation of T cell activation in cancer and infection-related projects. Determination of crystallization conditions as well as the determination and interpretation of three-dimensional structures of several of these proteins, alone and in complex , should be undertaken by the candidate in close collaboration with other members of the research groups. The Achour structural biology research group at CIM is well equipped for all aspects of modern structural biology, with state-of-the-art laboratories for molecular biology, recombinant expression in bacterial and eukaryotic systems, biochemistry and X-ray crystallography. Excellent synchrotron access is available at BESSY and ESRF. Applicants must have a PhD, and experience in recombinant expression, protein purification, crystallization and X-ray crystallography. Furthermore, the applicants must have published record of previous work on TCR/MHC interactions. Information on our previous work in this field can be found by searching PubMed and via the CIM website (ki.se/cim). APPLICATION PROCEDURE: The application should include a CV (including in particular any experience relevant to the position announced) as well as the names and contact details of 2 references. The applicants should also submit a list of publications and submitted manuscripts. Adnane Achour, Associate Professor fax:+46-8-30 42 76 tel;work:+46-8-5248 6216 Center for Infectious Medicine; Department of Medicine, Karolinska University Hospital Huddinge Karolinska Institute 141 86 Stockholm, Sweden url: http://ki.se/cim <>
Re: [ccp4bb] How to save LSQ output in coot
james09 pruza wrote: Dear all, I just wonder, How to save the LSQ output in coot. It is not clear what you mean by "output". The transformed coordinates can be saved with File -> Save Coordinates... The rotation matrix in both orthogonal and fractional form is written to the terminal. Paul.
[ccp4bb] How to save LSQ output in coot
Dear all, I just wonder, How to save the LSQ output in coot. Thanks in advance. J...
Re: [ccp4bb] linux question
The simplest solution is to install your favorite linux distro in a virtual machine. I use Sun's VirtualBox to install Ubuntu on my WinXP machine. Performance is reasonable even in the virtual environment. I use VBox to test install CCP4 and other crystallography software in Ubuntu before installing on my lab servers. I have also used Vbox to test windows crystallography software running in Wine under virtual Ubuntu on a WinXP machine. The only thing you won't be able to do well in a virtual machine is high-performance graphical stuff like Pymol, Coot, etc. They will run, but slowly with emulated graphics. Cheers. On 2/27/2010 10:10 PM, David Roberts wrote: I have a quick question about linux for all. Is there anybody running a windows pc with linux on a bootable cd or bootable drive/flash drive/??? that works for crystallography apps? I have a colleague who does molecular dynamics calculations and he needs some conversion programs that are unix based (not pc based - they just haven't been ported and that's not my area). We have linux computers that he can use, but I thought in the end it might be easiest if he could just boot up a linux flash drive to run his conversion, then go back to his pc and windows. Something like "damn small linux" or ?? Any thoughts on this? Thanks Dave
Re: [ccp4bb] units of f0, f', f''
What I meant of course was that the electronic charge (note: not the same thing at all as "electric charge") is universally given the symbol 'e', but with e-mail being what it is one usually doesn't take the time to consider such logical niceties as whether 'A implies B' is equivalent to 'B implies A'. Of course, all the letters of the Roman and Greek alphabets are already heavily overloaded, maybe we should consider using symbols from Chinese, Japanese, Cyrillic, Arabic, Sanskrit ... in our equations. Cheers -- Ian > -Original Message- > From: owner-ccp...@jiscmail.ac.uk > [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of James Holton > Sent: 28 February 2010 15:20 > To: CCP4BB@jiscmail.ac.uk > Subject: Re: [ccp4bb] units of f0, f', f'' > > I suppose I could point out that the letter "e" has many more > "universal" meanings that just denoting electric charge, such > the base > of the natural logarithm, the identity element in set theory, > or even a > musical note. But, today I found that "e" can also stand for > "eristic", > a new word I learned while reading the following web page: > > http://en.wikipedia.org/wiki/Flame_war > > -James Holton > MAD Scientist > > > 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 > > > > > > 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 > > > > > > Disclaimer This communication is confidential and may contain
Re: [ccp4bb] units of f0, f', f''
I suppose I could point out that the letter "e" has many more "universal" meanings that just denoting electric charge, such the base of the natural logarithm, the identity element in set theory, or even a musical note. But, today I found that "e" can also stand for "eristic", a new word I learned while reading the following web page: http://en.wikipedia.org/wiki/Flame_war -James Holton MAD Scientist 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 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 f0, f', f''
Thanks, I was actually joking because I was a little annoyed about the discussion, but then I realized that this discussion is great, (now I will not forget the units of electron density) and it's still not resolved. You said the charge/mass ratio and the density of that, but other people said the electron density is number of electrons (not charge) divided by volume (1/A^3). Maia H. Raaijmakers wrote: Maia, Usually we live in a macroscopic world and usually gravity is the most important force. In x-ray diffraction the charge/mass ratio is the most important paramater (and the density of that). Hans Maia Cherney schreef: Hi all, Usually density means mass divided by volume. The mass of an electron is known. Then it will be no arguments. Maia
Re: [ccp4bb] units of f0, f', f''
> 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 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] linux question
You may want to consider CD-bootable Puppy Linux (http://en.wikipedia.org/wiki/Puppy_Linux). HTH, Nadir -- Pr. Nadir T. Mrabet Structural & Molecular Biochemistry INSERM U-954 UHP - Nancy 1, School of Medicine 54505 Vandoeuvre-les-Nancy Cedex France Tel : +33 (0)3.83.68.32.73 Fax : +33 (0)3.83.68.32.79 E-mail : nadir.mra...@medecine.uhp-nancy.fr Selon David Roberts : > I have a quick question about linux for all. Is there anybody running a > windows pc with linux on a bootable cd or bootable drive/flash drive/??? that > works for crystallography apps? I have a colleague who does molecular > dynamics calculations and he needs some conversion programs that are unix > based (not pc based - they just haven't been ported and that's not my area). > We have linux computers that he can use, but I thought in the end it might be > easiest if he could just boot up a linux flash drive to run his conversion, > then go back to his pc and windows. Something like "damn small linux" or ?? > > Any thoughts on this? Thanks > > Dave >
Re: [ccp4bb] linux question
An alternative to VMWare is virtualbox (www.virtualbox.org) which is available for free for several operating systems. Tim On Sat, Feb 27, 2010 at 10:47:42PM -0500, Jim Fairman wrote: > I think a good option would be to use VMWare Player to run a flavor of Linux > within Windows (http://www.vmware.com/products/player/). Using VMware > player, you can run any flavor of linux or windows within a window in your > native OS (be it windows, mac, or any flavor of linux). I use it to run > Ubuntu in a window inside of Windows 7 for CCP4, phenix, etc and it works > pretty flawless so far. You can also run as many different linuxes as you > want within your native OS (ie: If you want to try out Suse, Ubuntu, Red Hat > and CentOS you can install all 4 of them on your system using VMWare within > your native OS). > > On Sat, Feb 27, 2010 at 10:10 PM, David Roberts wrote: > > > I have a quick question about linux for all. Is there anybody running a > > windows pc with linux on a bootable cd or bootable drive/flash drive/??? > > that works for crystallography apps? I have a colleague who does molecular > > dynamics calculations and he needs some conversion programs that are unix > > based (not pc based - they just haven't been ported and that's not my area). > > We have linux computers that he can use, but I thought in the end it might > > be easiest if he could just boot up a linux flash drive to run his > > conversion, then go back to his pc and windows. Something like "damn small > > linux" or ?? > > > > Any thoughts on this? Thanks > > > > Dave > > > > > > -- > Jim Fairman, Ph D. > Post-Doctoral Fellow > National Institutes of Health - NIDDK > Cell: 1-865-748-8672 > Lab: 1-301-594-9229 > E-mail: fairman@gmail.com james.fair...@nih.gov -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
Re: [ccp4bb] units of f0, f', f''
Maia, Usually we live in a macroscopic world and usually gravity is the most important force. In x-ray diffraction the charge/mass ratio is the most important paramater (and the density of that). Hans Maia Cherney schreef: > Hi all, > > Usually density means mass divided by volume. The mass of an electron is > known. Then it will be no arguments. > > Maia >
