Re: [ccp4bb] video that explains, very simply, what Structural Molecular Biology is about
Dear Fred A really nice video that would be great for giving non-crystallographers (including colleagues and 1st year students, and perhaps also friends and family) an overview of what we do. Thank you for pointing it out - and of course very many thanks to Dominique Sauter for making it. I am sure it will prove very popular. bet wishes Pete (Pete Artymiuk) On 11 Nov 2009, at 09:44, Vellieux Frederic wrote: > Dear all, > > Thought I'd share this with you: > > I located this through Ms Ines Kahlaoui, from the Beja Higher Institute of > Biotechnology in Tunisia (Ines has to teach and locates videos on the > internet, which she then downloads and uses for teaching). Ines located this > jewel: > > http://video.google.com/videoplay?docid=7084929825683486794&ei=M3b5SvXqD6em2AK3jY33CQ&q=Plongee+coeur+vivant# > > > This is the French version (explains everything about Structural Molecular > Biology, but for the maths :-( , but also shows what we crystallographers > have known for a long time, since the first colour E&S graphics workstations > in fact, that the electron are blue :-) ). > > Both French and English versions can be downloaded from > > http://cj.sauter.free.fr/xtal/Film/ > > No rights associated with the movie, and the Strasbourg group intends to > release a higher quality version on DVD soon. Please contact them about > that... I am only sharing what I thought was good for educational purposes. > 18 minutes of your life, but worth it I think. So feel free to share this. > > Wish you all a nice day, > > Fred.
Re: [ccp4bb] video that explains, very simply, what Structural Molecular Biology is about
... and thanks also to Ines Kahlaoui who pointed it out to you! On 11 Nov 2009, at 09:44, Vellieux Frederic wrote: > Dear all, > > Thought I'd share this with you: > > I located this through Ms Ines Kahlaoui, from the Beja Higher Institute of > Biotechnology in Tunisia (Ines has to teach and locates videos on the > internet, which she then downloads and uses for teaching). Ines located this > jewel: > > http://video.google.com/videoplay?docid=7084929825683486794&ei=M3b5SvXqD6em2AK3jY33CQ&q=Plongee+coeur+vivant# > > > This is the French version (explains everything about Structural Molecular > Biology, but for the maths :-( , but also shows what we crystallographers > have known for a long time, since the first colour E&S graphics workstations > in fact, that the electron are blue :-) ). > > Both French and English versions can be downloaded from > > http://cj.sauter.free.fr/xtal/Film/ > > No rights associated with the movie, and the Strasbourg group intends to > release a higher quality version on DVD soon. Please contact them about > that... I am only sharing what I thought was good for educational purposes. > 18 minutes of your life, but worth it I think. So feel free to share this. > > Wish you all a nice day, > > Fred.
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 = > (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
how does the equation cos(x)= (exp(ix) + exp(-ix))/2 and the sine equivalent fit into this? Clearly exponentials are not restricted to angles ... indicating that x (and by implication angles) have no dimensions. Marc Schiltz's previously cited Taylor expansion demonstrates this even better: sin(x) = x/1! - x^3/3! + x^5/5! . etc to infinity If you assume for a moment that x does have a dimension, lets call it [X], then the equation is dimensionally unbalanced [?] = [X]^1 - [X]^3 + [X]^5.. etc and is therefore invalid. It only makes sense if x, and its sine, are dimensionless Pete On 23 Nov 2009, at 16:42, marc.schi...@epfl.ch wrote: > Dale Tronrud wrote: >>While it is true that angles are defined by ratios which result in >> their values being independent of the units those lengths were measured, >> common sense says that a number is an insufficient description of an >> angle. If I tell you I measured an angle and its value is "1.5" you >> cannot perform any useful calculation with that knowledge. > > > I disagree: you can, for instance, put this number x = 1.5 (without units) > into the series expansion for sin X : > > x - x^3/(3!) + x^5/(5!) - x^7/(7!) + ... > > and compute the value of sin(1.5) to any desired degree of accuracy > (four terms will be enough to get an accuracy of 0.0001). Note that > the x in the series expansion is just a real number (no dimension, no > unit). > > > > Yes it's >> true that the confusion does not arise from a mix up of feet and meters. >> I would have concluded my angle was 1.5 in either case. >> >>The confusion arises because there are differing conventions for >> describing that "unitless" angle. I could be describing my angle as >> 1.5 radians, 1.5 degrees, or 1.5 cycles (or 1.5 of the mysterious >> "grad" on my calculator). > > > > These are just symbols for dimensionless factors : > > 1 rad = 1 > 1 degree = pi/180 > 1 grad = pi/200 > > Thus : > > 1.5 rad = 1.5 > 1.5 degree = 0.0268 > 1.5 grad = 0.0236 > > and all these numbers (which have no units !!!) can be put into the > series expansions for trigonometric functions. > > In my opinion, it is actually best not to use the symbol rad. As we can > see from this discussion, it mostly creates confusion. > > > > For me to communicate my result to you >> I would need to also tell you the convention I'm using, and you will >> have to perform a conversion to transform my value to your favorite >> convention. If it looks like a unit, and it quacks like a unit, I >> think I'm free to call it a unit. >> >>I think you will agree that if we fail to pass the convention >> along with it value our space probe will crash on Mars just as hard >> as if we had confused feet and meters. >> >>The result of a Sin or Cos calculation can be treated as "unitless" >> only because there is 100% agreement on how these results should be >> represented. Everyone agrees that the Sin of a right angle is 1. > > > This is not a simple matter of agreement (or convention), it is > contained in the very definition of the sine function. > > >> If I went off the deep end I could declare that the Sin of a right >> angle is 12 and I could construct an entirely self-consistent description >> of physics using that convention. > > > I challenge you to draw a right triangle on paper where the length of > one of the sides measures 12 times the length of the hypotenuse. > > Of course, you can say that your "crazy Tronrud Sin" is defined > differently, but then we are really speaking about something else. You > can define whatever crazy quantity you want. But the need for a function > which describes the ratio of the length of a side of a right triangle > to the length of its hypotenuse will inevitably arise at some point in > physics and mathematics. And the "crazy Tronrud Sin" will not do this > job. So the proper sine and cosine functions will eventually have to > be invented. > > > > > In that case I would have to be >> very careful to keep track of when I was working with traditional >> Sin's and when with "crazy Tronrud Sin's". When switching between >> conventions I would have to careful to use the conversion factor of >> 12 "crazy Tronrud Sin's"/"traditional Sin" and I'd do best if I >> put a mark next to each value indicating which convention was used >> for that particular value. Sounds like units to me. >> >>Of course no one would create "crazy Tronrud Sin's" because the >> pain created by the confusion of multiple conventions is not compensated >> by any gain. When it comes to angles, however, that ship has sailed. >> While mathematicians have very good reasons for preferring the radian >> convention you are never going to convince a physicist to change from >> Angstrom/cycle to Angstrom/radian when measuring wavelengths. You >> will also fail to convince a crystallographer to measure fractional >> coordinates in radians. We are going to have to live in a
Re: [ccp4bb] microsoft 3-button wheel mouse with OS X 10.5
Dear Bill William Scott wrote Aqua simply behaves by slightly different rules. Although I am a slobbering OS X fan, this lack of customizability to me, as well as a lack of focus-follows-mouse, it a negative. To get focus-follows-mouse in Aqua, type the following in your Terminal window: defaults write com.apple.Terminal FocusFollowsMouse -string YES and then logout and log in again or quit and restart Terminal. I had thought I originally got that useful hint from your own fabulous PX on OSX pages but clearly not. best wishes Pete Artymiuk On 20 Jan 2008, at 15:39, William Scott wrote: Hi David: david lawson (JIC) wrote: Dear All, Sorry for the slightly off-topic subject. We have recently bought a few iMacs for crystallography. I'm not keen on the supplied "mighty mouse" May I have them? so I have switched to using a microsoft 3-button wheel mouse. I would like to configure it so that it behaves as it would with other unix systems such as RH Linux. You managed to use "Microsoft", "behaved" and "Linux" (albeit RH) all in one sentence without a hint of irony. i.e. (1) double-clicking with LH button on a file name selects ALL of the file name, not just up to the first full stop. Although your choice of Microsoft products shows dedication to a company with a firm reputation for placing the customizability needs of its customers ahead of its own desire to make profits, the first thing to realize is that you should never ever ever install their drivers. Ever. So if you did, take them out, now, and reboot. I'll wait. It is still early Sunday morning here. (2) clicking the scroll wheel pastes the selected text AND it can be done multiple times without re-selecting. When you've gotten rid of the drivers, this should now work. In Apple's Terminal program (as of 10.5) and iTerm (as of 1215), you just set the preference to do middle-button-paste and left-button select, and Blair's your uncle. Unfortunately, in pretty much every other application I can think of on OS X, this, sadly, does not work, and there is nothing Steve Gates will let you do about it. (2) I would like these functions to work in terminal windows, the ccp4i gui and web pages (and probably a few other things I haven't thought of yet!) AND be able to transfer the selected text between applications. I'd like to be at my ideal high-school weight, be paid more than a postdoc, and, well ... Getting the OS X gui to play nice with X11 is sometimes challenging. With the exception of Terminal and iTerm, you have to explicitly put stuff in the copy/paste buffer (command-C) before it is in the system clipboard. Then you can paste to X11 programs with a middle-button click, but this only works if you uninstalled that viral driver. Going from X11 to aqua programs requires selecting the text in the usual X11 manner but explicitly issuing the paste command (command- p). If you are using KDE X11 applications, you are really in for headaches. To get whole-string selection in iTerm or Terminal, there is a preference setting that allows you to input which characters you want to have considered parts of a "word" for click-to-select purposes. Unfortunately, pretty much every other application lacks this customizability, and I know of no system-wide preference setting that would enable you to do this globally. Aqua simply behaves by slightly different rules. Although I am a slobbering OS X fan, this lack of customizability to me, as well as a lack of focus-follows-mouse, it a negative. If you really need the canonical linux behavior, you can install gnome, xfce4, KDE, enlightenment, or any number of other window managers via fink. I've found KDE buggy and the XFCE4 is way out of date. Gnome is probably the best bet, and there is a major effort now to bring it completely up to date in fink. I have installed the microsoft intellipoint drivers that seem to give more control over configuring the various buttons through "system preferences", but I still can't get what I want. Therein lies the problem, I am afraid. OS X will behave better using the default settings. It may be possible to tinker around with the driver, including separate settings in X11, to recover canonical behavior, but for purposes of sanity, uninstall them first, get everything working as best as possible, verify middle-button-paste works in X11, verify X11 coot and pymol do the right thing, and then if you need additional functionality, reinstall the drivers, verify things like coot and pymol still use the middle button correctly, or adjust until they do, and only then try customizing. Best of luck! Bill Any help would be much appreciated. Many thanks Dave Lawson --- Dr. David M. Lawson Biological Chemistry Dept., John Innes Centre, Norwich, NR4 7UH, UK. Tel: +44-(0)1603-450725 Fax: +44-(0)1603-450018 Email: [EMAIL PROTECTED] Web: h
Re: [ccp4bb] cross-section view of (protein) molecules in pymol?
Dear Jacob If you do want brainless and are not fastidious, you can fake a similar solid-looking cutaway surface using Rasmol display your coordinates in rasmol Centre on an atom you wish to see lying in the cutaway surface by typing set picking centre and clicking on it. Make a space filling representation with cpk (or cpk 600 if you want the spheres bigger and overlapping) and finally do slab 50 (or slab 55) to cut away the front part of the molecule. You can then use rasmol's simple commands to modify the colours and represntation of different parts of the structure OK, not a real vdW surface, no electrostatics, no finesse, but possibly OK for a seminar if not a publication, and certainly br/ painless best wishes Pete Pete Artymiuk University of Sheffield On 14 Mar 2009, at 02:25, Ethan A Merritt wrote: On Friday 13 March 2009, Jacob Wong wrote: Dear all, http://www.nature.com/nature/journal/v458/n7234/fig_tab/nature07819_F3.html Just came across this figure Fig. 3b) and would like to know what is the general and easiest way to make things like this, as a "non- brainer". Thank you, -Jacob I don't know of any way to not engage a brain in the process, but that particular figure could be made by 1) create electrostatic coloured surface in GRASP or MSMS or 2) export surface as a file and convert it to Raster3D 3) define a bounding plane (some point on the plane + a surface normal) 4) render the surface in Raster3D, clipped by the bounding plane Example: top figure in http://skuld.bmsc.washington.edu/raster3d/examples/examples.html I have been slowly working to put together a less brain-involving pathway, ideally involving some smallish number of mouse clicks in Coot or PyMol or ccp4mg that feed the information to Raster3D for rendering. But nothing is currently in place that would allow a label "no actual brains were consumed in producing this figure". Ethan -- Ethan A Merritt Biomolecular Structure Center University of Washington, Seattle 98195-7742
Re: [ccp4bb] Computer hardware and OS "survey"
.. but OSX gives you Unix AND you can run Word /Powerpoint without rebooting. And you get a user-friendly ergonomic windowing system that kicks the out of XP/Vista/KDE/Gnome... best wishes Pete On 2 May 2009, at 11:32, Nicholas M Glykos wrote: Dear All, We confuse scientific computing with the individual scientists' computing needs: just because a scientist has to write a grant application using word, does not make windows a platform suitable for scientific computing (or anything else for that matter). Using computing machines for doing science boils down to actually using computing machines to compute things, and for that you need a proper open-source, production-oriented, stable programming environment, ie. GNU/Linux. What individual scientists prefer for satisfying their desktop needs is interesting, but, at least to my mind, largely irrelevant. My twopence, Nicholas -- Dr Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620, Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/
Re: [ccp4bb] coupling between occupancy and b-values in refinement
Dear Patrick Long ago we (Cheetham et a (1992) J Molec Biol 224:613-628) did some refinements on hen lysozyme + substrate complexes at 1.75A and 2A resolution and showed that B and occupancy are negatively correlated, especially at 2.0A. In simplistic terms this is because at medium resolution low density at the atomic position could be the result of either low occupancy or high B factor. We ran parallel refinements using assumed occupancies at 0.1 intervals. We looked at R factors but they werent much help - this was pre-Rfree so the latter might be a valuable criterion now. I think a good strategy is to refine your substrate complex at intervals of o=0.1, 0.2 ... (with a non-complex model at 1-o, ass positions of side chains and waters may well be different) and look at the B factors. At the correct(ish) occupancy substrate Bs will be expected to be similar to those of the ligating residues from the protein. But it does get to be quite subjective until you have higher resolution. best wishes Pete On 31 May 2009, at 16:58, Patrick Loll wrote: Hi all, I'm looking for a reference to bolster my response to a referee, in which I defend my decision not to refine the occupancy of a ligand in structure refined at around 2 A resolution (note the ligand binding slte lies on a two-fold crystallographic axis, so the maximum occupancy is 0.5) I recall reading a paper a LONG time ago (decades) in which someone described some careful refinement experiments, and concluded that the correlation between occupancy and B-value is so strong that it simply makes no sense to "independently" refine both parameters (at least for light atoms, and in the absence of super high resolution data). Alas, all that I recall is this take-home message. I have no idea of where the paper appeared, or the names of the authors (or indeed, if I'm even remembering the paper's message correctly). I've tried trolling through Acta, without success. Does anyone have a better idea of where I might find this paper, or one espousing a similar message? Thanks, Pat - Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.l...@drexel.edu
