Re: [ccp4bb] self rotation education
I absolutely agree with Clemens; self rotation functions can mislead in some cases, and confuse in many more.. A peak in a self rotation does NOT mean you have a dimer or a trimer - just that one molecule in the asu can be related to another by the given operator. So for any peak ther are nsym*2 possible positions.. However old fashioned programs like polarrfn, almn, and amore list all symmetry equivalents of each peak which often illuminate things, and you often notice that the expected 3-fold generates 2 folds when combined with symmetry operators. You dont give the angles of your 3 fold, but if phi=45, omega = 36, the combination with crystallography 2 folds generates non-crystallographic two-folds in the a-b plane.. Eleanor Clemens Vonrhein wrote: Hi Francis, On Thu, Mar 18, 2010 at 09:03:13AM -0600, Francis E Reyes wrote: Hi all I have a solved structure that crystallizes as a trimer I guess you mean that you have 3 mol/asu? And not just a trimer in solution that then forms crystals, right? to a reasonable R/Rfree, but I'm trying to rationalize the peaks in my self rotation. That has very often fooled me: selfrotation functions can be very misleading - at least in my hands (even using different programs, resoluton limits, E vs F etc etc). Often peaks that should be there aren't and vice versa. The space group is P212121, calculating my self rotations from 50-3A, integration radius of 22 (the radius of my molecule is about 44). I can see the three fold NCS from my structure on the 120 slice Which one is it: the one at (90,90) or the one at (45,45)? Or both? but I'm trying to rationalize apparent two folds in my kappa=180. A picture of both slices is enclosed. The non crystallographic peaks for kappa=180, P222 begin to appear at kappa=150 and are strongest on the 180 slice. If you had a D_3 multimer (3-fold with three 2-folds perpendicular to it) I could interpret those as (a) 3-fold at (90,90) == 2-fold at ( 90,0) [direction cosines = 1.0 0.0 0.0] 2-fold at (210,0) [direction cosines = -0.5 -0.0 -0.86603] 2-fold at (330,0) [direction cosines = -0.5 -0.0 0.86603] (b) 3-fold at (45,45) == 2-fold at ( 90,315) [direction cosines = 0.70711 -0.70711 0.0] 2-fold at ( 45,180) [direction cosines = -0.70711 0.0 0.70711] 2-fold at (135, 90) [direction cosines = 0.0 0.70711 -0.70711] All those 2-folds axes have a 120-degree angle between them (obviously). I might have the exact angles wrong (there could be slight offsets from thoise ideal values and the self-rotation plot just piles the peaks exactly onto crystallographic symmetry operators because of the multiplicity of those symmetry elements) ... or maybe even more? But for both 3-fold axes in the kappa=120 section I can convince myself that there are the corresponding 2-folds to make up a D_3 multimer. Since you probably only have space for 3 mol/asu, I would guess case (a) to be the correct 3-fold NCS with the 2-folds in (a) resulting from the 21 parallel to your 3-fold and the peaks in (b) resulting from the remaining symmetry. Does that fit? Cheers Clemens My molecule looks close to a bagel (44A wide and 28A tall). The three fold NCS is down the axis of looking down on the bagel hole. I'm trying to find the two fold. I imagine it could be slicing the bagel in half (like to eat it for yourself) or slicing it vertically (like to share amongst kids) but I'm not exactly sure what's the best way to visualize this. Is there something easier than correlation maps with getax (since I have the rotation (polarrfn) and translation?). If you have an eye for spotting symmetry, Ill send the pdb in confidence. Thanks! FR - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
Re: [ccp4bb] Why Do Phases Dominate?
It is quite instructibe to draw the 2-d vector representing the amplitude and then the error vector when you assume certain things... Change the magnitude by 50% and see the error vector, then change the phase by a random shift - say 90 degrees and draw the error vector. In general it is much more severe for case 2 than case 1.. eleanor Edward A. Berry wrote: This bias is exacerbated by the convention that phases go from 0 to 360* while amplitudes go from zero to Plus. Thus the phase decides where to put it, and whether to add or take away, while the amplitude only decides how much. If phase was 0 to 180* and amplitude was Minus to Plus, then amplitude would decide whether to add or take away as well as how much. Lijun Liu wrote: Does anybody have a good way to understand this? = There are a lot of good ways to understand this. The amplitudes determines how much to put, while the phases tell you where to/how to correctly put. For example, treating San Francisco as a cell, the heights of buildings and lines of streets determine the landscape. Moving all buildings along some streets separately will change more the landscape than just changing some buildings' height along the street. Another example, taken at different lighting/darkness conditions, the photos from the same face could be easily recognized and compared. However, with the same light condition, when the position of nose, eyes, mouth, etc., are dislocated from their original positions, the face will be very different. One possible answer is it is the nature of the Fourier Synthesis to emphasize phases. (Which is a pretty unsatisfying answer). But, could there be an alternative summation which emphasizes amplitudes? If so, that might be handy in our field, where we measure amplitudes... == It does have. For example, Patterson function. Lijun Regards, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu mailto:j-kell...@northwestern.edu *** Lijun Liu Cardiovascular Research Institute University of California, San Francisco 1700 4th Street, Box 2532 San Francisco, CA 94158 Phone: (415)514-2836
Re: [ccp4bb] self rotation education
I have to agree with Clemens and Eleanor. After I had come to the wrong conclusion about NCS and the number of molecules in the asymmetric unit several times I gave up using the self-rotation function. Nevertheless, I have been shown examples (especially NCS with Cn symmetry and unsual n) where the self-rotation function was spectacular. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Mon, 22 Mar 2010, Eleanor Dodson wrote: I absolutely agree with Clemens; self rotation functions can mislead in some cases, and confuse in many more.. A peak in a self rotation does NOT mean you have a dimer or a trimer - just that one molecule in the asu can be related to another by the given operator. So for any peak ther are nsym*2 possible positions.. However old fashioned programs like polarrfn, almn, and amore list all symmetry equivalents of each peak which often illuminate things, and you often notice that the expected 3-fold generates 2 folds when combined with symmetry operators. You dont give the angles of your 3 fold, but if phi=45, omega = 36, the combination with crystallography 2 folds generates non-crystallographic two-folds in the a-b plane.. Eleanor Clemens Vonrhein wrote: Hi Francis, On Thu, Mar 18, 2010 at 09:03:13AM -0600, Francis E Reyes wrote: Hi all I have a solved structure that crystallizes as a trimer I guess you mean that you have 3 mol/asu? And not just a trimer in solution that then forms crystals, right? to a reasonable R/Rfree, but I'm trying to rationalize the peaks in my self rotation. That has very often fooled me: selfrotation functions can be very misleading - at least in my hands (even using different programs, resoluton limits, E vs F etc etc). Often peaks that should be there aren't and vice versa. The space group is P212121, calculating my self rotations from 50-3A, integration radius of 22 (the radius of my molecule is about 44). I can see the three fold NCS from my structure on the 120 slice Which one is it: the one at (90,90) or the one at (45,45)? Or both? but I'm trying to rationalize apparent two folds in my kappa=180. A picture of both slices is enclosed. The non crystallographic peaks for kappa=180, P222 begin to appear at kappa=150 and are strongest on the 180 slice. If you had a D_3 multimer (3-fold with three 2-folds perpendicular to it) I could interpret those as (a) 3-fold at (90,90) == 2-fold at ( 90,0) [direction cosines = 1.0 0.0 0.0] 2-fold at (210,0) [direction cosines = -0.5 -0.0 -0.86603] 2-fold at (330,0) [direction cosines = -0.5 -0.0 0.86603] (b) 3-fold at (45,45) == 2-fold at ( 90,315) [direction cosines = 0.70711 -0.70711 0.0] 2-fold at ( 45,180) [direction cosines = -0.70711 0.0 0.70711] 2-fold at (135, 90) [direction cosines = 0.0 0.70711 -0.70711] All those 2-folds axes have a 120-degree angle between them (obviously). I might have the exact angles wrong (there could be slight offsets from thoise ideal values and the self-rotation plot just piles the peaks exactly onto crystallographic symmetry operators because of the multiplicity of those symmetry elements) ... or maybe even more? But for both 3-fold axes in the kappa=120 section I can convince myself that there are the corresponding 2-folds to make up a D_3 multimer. Since you probably only have space for 3 mol/asu, I would guess case (a) to be the correct 3-fold NCS with the 2-folds in (a) resulting from the 21 parallel to your 3-fold and the peaks in (b) resulting from the remaining symmetry. Does that fit? Cheers Clemens My molecule looks close to a bagel (44A wide and 28A tall). The three fold NCS is down the axis of looking down on the bagel hole. I'm trying to find the two fold. I imagine it could be slicing the bagel in half (like to eat it for yourself) or slicing it vertically (like to share amongst kids) but I'm not exactly sure what's the best way to visualize this. Is there something easier than correlation maps with getax (since I have the rotation (polarrfn) and translation?). If you have an eye for spotting symmetry, Ill send the pdb in confidence. Thanks! FR - Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
[ccp4bb] movies
Dear all, My group will be representing the MX users of Diamond at the Royal Society's 350th Anniversary Summer Science Exhibition http://royalsociety.org/Summer-Science-Exhibition-2010/ and for this we will be producing a short (15 minute) video to show the kind of work that we do at Diamond and its relevance to science and the wider population. The discussion a few weeks back on videos of teaching materials flagged up a lot of interesting movies and animations that would be the kind of thing that we think this video should show. Rather than reinvent the wheel, it would be great if we could include some of these in our presentation, this would obviously reflect positively on the MX and CCP4 community and all samples that we use would be duly acknowledged. If anyone would like to contribute a movie or has particular favourites in the public domain then please get in touch. Cheers, Rick -- R. J. Lewis Professor of Structural Biology Institute for Cell and Molecular Biosciences Faculty of Medical Sciences Tel: +44 (0)191 222 5482 University of Newcastle Fax: +44 (0)191 222 7424 Newcastle upon Tyne, NE2 4HH, UKEmail: r.le...@ncl.ac.uk
[ccp4bb] Question about mathematical modeling of membranes, pores and transporters
Hello, From experimental crystallography kinetics background, I have arrived at a situation where I need to model certain membrane related phenomena and correlate it to experimental (metabolonomic) data. In particular, I am looking for mathematical expressions and derivations for: a) Change of properties of the lipid membrane upon chemical reactions, such as oxidation b) ATP-ion co transporters c) Voltage gated pores. Could someone suggest me any source for such information? Regards, Partha
Re: [ccp4bb] self rotation education
Dear Elanor et al, On Mon, Mar 22, 2010 at 09:30:31AM +, Eleanor Dodson wrote: A peak in a self rotation does NOT mean you have a dimer or a trimer - just that one molecule in the asu can be related to another by the given operator. Exactly - and sometimes even the notion of 'molecule' breaks down: the self-rotation function couldn't care less about what we call 'molecule'. You can get peaks in the self-rotation function even if only single molecule is present: * one helix matches any other helix pretty well * you can place a rough 2-fold axis into a beta-sheet * two domains with a similar fold, TIM barrels ... etc I guess that's why choosing the radii can be quite important. Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
[ccp4bb] Buried surface area (BSA) vs. oligomeric interface
Dear All, We found that our structure is having a large buried surface in its dimer interface (~18% as calculated by AREAIMOL). This dimer has not been observed in earlier studies and right now we have less data to support this strong interface formation. I am looking for some literature which provide guidelines to understand the relation of BSA or crystal contacts with oligomeric interfaces. Any suggestion is highly appreciated Thanks in advance Yogi
Re: [ccp4bb] inexpensive source of DDM
Hi Tony I use the US company Anatrace for bDDM it has various grades form around $640 to crystallisation grade at $785 for 25g. If you are interested in the Euro conversion this is ~460-580 Euro. Miroslav Tony Wu wrote: Hello, I am looking for an inexpensive US source for large quantities of dodecylmaltoside. Can anyone help me? Thank you!
[ccp4bb] Buried surface area (BSA) vs. oligomeric interface
Dear All, We found that our structure is having a large buried surface in its dimer interface (~18% as calculated by AREAIMOL). This dimer has not been observed in earlier studies and right now we have less data to support this strong interface formation. I am looking for some literature which provide guidelines to understand the relation of BSA or crystal contacts with oligomeric interfaces. Any suggestion is highly appreciated Thanks in advance Yogi
[ccp4bb] Butandiol as cryopotectant
Hi everybody, has anyone experience with Butandiol and its different isoforms as cryoprotectant ? Thanks, Ulrike
Re: [ccp4bb] Why Do Phases Dominate?
- Original Message - From: Gerard Bricogne g...@globalphasing.com To: CCP4BB@JISCMAIL.AC.UK Sent: Friday, March 19, 2010 2:32 PM Subject: Re: [ccp4bb] Why Do Phases Dominate? Dear Marius, Thank you for pointing this out - I was about to argue in the same direction, i.e. that the Fourier transform is at the heart of diffraction and is not just a convenient, but perhaps renegotiable, procedure for analysing diffraction data. I wonder how one can establish that a certain mathematical function is at the heart of a phenomenon? Does mathematics cause phenomena, or consitute the essence of a phenomenon? Many believe that it does, and I am not saying that I do not feel this way about some relationships between mathematics and phenomena--but there seems to be a gradation. On one side, the trajectory of the stream of water from a garden hose is all-too-obviously essentially a parabola, and on the other side, laws like Moore's law seem completely descriptive and not at all causal or essential. A gray-area case for me is whether the manifest world is fundamentally Euclidean, or other such questions. (It certainly *feels* Euclidean, but...) But what I am unsure about is what standard we use to decide whether a given phenomenon is *inherently* tied to a given mathematical function. A troubling thought is that there are many historical examples of phenomena being *fundamentally* one way mathematically--and unthinkably otherwise--and later we have revised our certainty. One thinks of the example Ian Tickle cited of negative numbers being meaningless, or also of the Earth's being the center of the universe and orbits being perfectly circular. A medieval philosopher wanted once to emphasize the certainty of his conclusions, and he wrote that they were as clear and certain as the Earth's being the center of the universe! (Ergo: how certain can we be, then, about *his* conclusions...?). Anyway, one could speculate that there be an alternative model to diffraction which does not involve the Fourier synthesis, it seems. But would that be just a model, and the Fourier-based one the reality? Another instance of such natural hardwiring of the Fourier transform into a physical phenomenon is Free Induction Decay in NMR. There, however, one can measure the phases, as it is the Larmor precession of the population of spins that is measured along two orthogonal directions and gives the real and imaginary parts of the FID signal. Equal opportunity for real and imaginary part: doesn't that make a crystallographer dream ... ? With best wishes, Gerard. -- On Fri, Mar 19, 2010 at 08:15:05PM +0100, Marius Schmidt wrote: The great thing with diffraction, from crystals and from objects in microscopy is THAT this is A NATURALLY OCCURRING FORM of Fourier transform once one accepts that light is a wave (could be something else). If Fourier transform would not have been invented with another problem from engineering, then it would have emerged NATURALLY from diffraction. Diffraction is an analog (not a digital) Fourier transform. A crystal is a low-noise, analog, natural Fourier amplifier!!! If you want to build the fastest Fourier transform of the world, you could represent your function, which you want to Fourier transform, as density fluctuation and scatter from it, or, you could amplify scattering into certain direction by putting this, your, function in a unit cell of a 1-D, 2-D or even 3-D lattice. The Patterson function is also a special Fourier-transform, the convolution of one Fourier with itself. Yes there are other functions that are also conceivable. They also map real space (E-density) to reciprocal space (structure factor). For example, manifold embedding techniques might never ever even refer to a Fourier transform and other highly flexible functions are used for this mapping. But the physics behind it is scattering of waves (as long as you believe that there are waves, of course). Marius Perhaps this was really my question: Do phases *necessarily* dominate a reconstruction of an entity from phases and amplitudes, or are we stuck in a Fourier-based world-view? (Lijun pointed out that the Patterson function is an example of a reconstruction which ignores phases, although obviously it has its problems for reconstructing the electron density when one has too many atoms.) But perhaps there are other phase-ignoring functions besides the Patterson that could be used, instead of the Fourier synthesis? Simply: are phases *inherently* more important than amplitudes, or is this merely a Fourier-thinking bias? Also, Are diffraction phenomena inherently or essentially Fourier-related, just as, e.g., projectile trajectories are inherently and essentially parabola-related? Is the Fourier synthesis really the mathematical essence of the phenomenon, or is it just a nice tool? In far-field diffraction from a periodic object, yes,
Re: [ccp4bb] Question about mathematical modeling of membranes, pores and transporters
dear Partha, You could try looking up the biomodels database ( http://www.ebi.ac.uk/biomodels-main/). There must be several mathematical models in there that may be of use to you. regards Ganesh ** Blow, blow, thou winter wind Thou art not so unkind As man's ingratitude; Thy tooth is not so keen, Because thou art not seen, Although thy breath be rude. -William Shakespeare ** On Mon, 22 Mar 2010 17:50:57 +0530, Partha Chakrabarti ppc...@gmail.com wrote: Hello, From experimental crystallography kinetics background, I have arrived at a situation where I need to model certain membrane related phenomena and correlate it to experimental (metabolonomic) data. In particular, I am looking for mathematical expressions and derivations for: a) Change of properties of the lipid membrane upon chemical reactions, such as oxidation b) ATP-ion co transporters c) Voltage gated pores. Could someone suggest me any source for such information? Regards, Partha --
Re: [ccp4bb] Buried surface area (BSA) vs. oligomeric interface
Hi, just a place I would perhaps start looking: http://www.ebi.ac.uk/msd-srv/prot_int/picite.html ~L~ __ Lari Lehtiö Pharmaceutical Sciences, Department of Biosciences Åbo Akademi University, BioCity, FIN-20520 Turku Finland +358 2 215 4270 http://www.users.abo.fi/llehtio/ __ Quoting Sollepura Yogesha yoge...@scripps.edu: Dear All, We found that our structure is having a large buried surface in its dimer interface (~18% as calculated by AREAIMOL). This dimer has not been observed in earlier studies and right now we have less data to support this strong interface formation. I am looking for some literature which provide guidelines to understand the relation of BSA or crystal contacts with oligomeric interfaces. Any suggestion is highly appreciated Thanks in advance Yogi
Re: [ccp4bb] self rotation education
I'll happily add my name to the consensus! However it's interesting to consider why some rotation functions are frankly uninterpretable and some, as George says, are spectacular. In fact the major cause of failure of MR has been known for a long time; in a word: incompleteness. The reason is obvious: the effect of omitting a reflection from the Patterson function is the same as adding to the true Patterson the Fourier term corresponding to the negative intensity of the omitted reflection, and of course if that intensity happens to be large then it's hardly surprising that it has a deleterious effect. Of course you won't know whether or not it's large - because obviously it's not there in processed dataset! There's a golden rule of experimental data collection: never throw away data - if you do it's likely to come back to bite you! Usually the problem is having a few strong low resolution reflections missing due to detector overloads or backstop occlusion, though this situation is improving as the dynamic range of modern detectors gets bigger. I don't think backstops have improved much though - in the old days to avoid getting a backstop shadow we used to make one by gluing a piece of lead (obviously as small as possible while still blocking the beam) to a strip of sticky tape. I guess you're probably not allowed to do that any more! Having a whole shell of reflections missing can be equally problematic, which is why it's probably a good idea to use all available data in a self-rotation function; for a cross-rotation function of course there are other issues to consider such as the expected similarity of the model and target structures. Something I've always thought would be useful is for the image integration programs to set an error status instead of rejecting an overloaded/overlapped/occluded reflection, since obviously for MR any estimate of an intensity which is less than the true intensity is better than no estimate (ice spots, zingers etc could be a problem though). Then the user has the option to include the reflection in MR: obviously for refinements and difference maps where what matters is essentially the difference between the observed calculated amplitudes you would want to omit reflections flagged with an error status. I suspect that the problem of getting agreement on the form of the error status between the various programmers means this idea will never get off the ground! One explanation of why using Es sometimes helps is that the missing overloads will mostly be at low resolution and Es of course down-weight the low-res data (including the missing ones!). There's an article I wrote for the CCP4 newsletter many years ago where we showed that the rotation function is very sensitive to a very small number of missing large reflections (maybe only 1 or 2% of the total), but that this sensitivity is reduced if Es are used. Cheers -- Ian On Mon, Mar 22, 2010 at 11:37 AM, George M. Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote: I have to agree with Clemens and Eleanor. After I had come to the wrong conclusion about NCS and the number of molecules in the asymmetric unit several times I gave up using the self-rotation function. Nevertheless, I have been shown examples (especially NCS with Cn symmetry and unsual n) where the self-rotation function was spectacular. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Mon, 22 Mar 2010, Eleanor Dodson wrote: I absolutely agree with Clemens; self rotation functions can mislead in some cases, and confuse in many more.. A peak in a self rotation does NOT mean you have a dimer or a trimer - just that one molecule in the asu can be related to another by the given operator. So for any peak ther are nsym*2 possible positions.. However old fashioned programs like polarrfn, almn, and amore list all symmetry equivalents of each peak which often illuminate things, and you often notice that the expected 3-fold generates 2 folds when combined with symmetry operators. You dont give the angles of your 3 fold, but if phi=45, omega = 36, the combination with crystallography 2 folds generates non-crystallographic two-folds in the a-b plane.. Eleanor Clemens Vonrhein wrote: Hi Francis, On Thu, Mar 18, 2010 at 09:03:13AM -0600, Francis E Reyes wrote: Hi all I have a solved structure that crystallizes as a trimer I guess you mean that you have 3 mol/asu? And not just a trimer in solution that then forms crystals, right? to a reasonable R/Rfree, but I'm trying to rationalize the peaks in my self rotation. That has very often fooled me: selfrotation functions can be very misleading - at least in my hands (even using different programs, resoluton limits, E vs F etc etc). Often peaks that should be there aren't and vice versa. The space group is
[ccp4bb] 2010 NIGMS Enabling Technologies Workshop: Abstract Deadline Extended to COB March 26, 2010
Dear Colleagues, We are very keen to have the widest possible participation in the upcoming NIGMS Enabling Technologies in Structure and Function Workshop to be held in the Natcher Conference Center on the NIH campus on April 19-21, 2010. To encourage this we have extended the deadline for the submission of poster abstracts to be considered for selection to the oral program to COB March 26, 2010. If you have not already done so please send your one page abstract to Ms. Soncerray Bolling at nigms2010works...@blseamon.commailto:nigms2010works...@blseamon.com. Please include in the abstract text an indication of the topical session to which your submission relates as described at http://meetings.nigms.nih.gov/index.cfm?event=extraID=8126tabID=8500. Abstracts for inclusion in the poster program only should be provided and meeting registration completed at http://meetings.nigms.nih.gov/index.cfm?event=registrationID=8126 no later than COB April 9. If you have already submitted an abstract but have not nominated it for a topical session please indicate your preference by email to Ms. Soncerray Bolling, sboll...@blseamon.commailto:sboll...@blseamon.com. Please forward this message to members of your organization. If you have any questions or we can be of any other assistance please do not hesitate to contact either me or my colleague, Ms. Krystal T. Kelly, (301) 594-4646, kk3...@nih.govmailto:kk3...@nih.gov. We look forward to seeing you here in April. cge --- Charles G. Edmonds, Ph.D. Program Director Cell Biology and Biophysics Division National Institute of General Medical Sciences Building 45, Room 2As-13K Bethesda, MD 20892-6200 (301) 594-4428 (voice) (301) 480-2004 (FAX) edmon...@nigms.nih.govmailto:edmon...@nigms.nih.gov
Re: [ccp4bb] Buried surface area (BSA) vs. oligomeric interface
Hi, have a look at this paper. I believe it's exactly what you're looking for. Protein-protein interaction and quaternary structure. http://www.ncbi.nlm.nih.gov/pubmed/18812015 Janin J, Bahadur RP, Chakrabarti P. Q Rev Biophys. 2008 May;41(2):133-80. Review.PMID: 18812015 http://www.ncbi.nlm.nih.gov/pubmed/18812015 best vincent Sollepura Yogesha wrote: Dear All, We found that our structure is having a large buried surface in its dimer interface (~18% as calculated by AREAIMOL). This dimer has not been observed in earlier studies and right now we have less data to support this strong interface formation. I am looking for some literature which provide guidelines to understand the relation of BSA or crystal contacts with oligomeric interfaces. Any suggestion is highly appreciated Thanks in advance Yogi -- Vincent Chaptal Dept. of Physiology at UCLA http://www.physiology.ucla.edu/Labs/Abramson/index.html http://www.physiology.ucla.edu/Labs/Abramson/index.html/ Phone: 1-310-206-1399 IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.
[ccp4bb] Postdoctoral Position in Structural Biology of Nuclear-Cytoplasmic Transport at UT Southwestern
Postdoctoral Position in Structural Biology of Nuclear-Cytoplasmic Transport at UT Southwestern Applications are invited for a postdoctoral position in the Chook Lab, Department of Pharmacology, UT Southwestern, Dallas, TX, USA, to work on the structure determination, biochemistry and biophysics of nuclear-cytoplasmic transport mediated by the Karyropherin family of proteins. We seek a highly motivated recent Ph.D. with extensive experience in biochemical studies and protein structure determination by X-ray crystallography. Experience with protein purification, crystallization, X-ray data collection, structure determination and interpretation are essential. Applicants must have a Ph.D. and fewer than 2 years of postdoctoral experience. Applicants should send their CV, and the names and contact information of three referees to: Yuh Min Chook, Ph.D. e-mail: yuhmin.ch...@utsouthwestern.edu Associate Professor and Eugene McDermott Scholar in Biomedical Research Department of Pharmacology University of Texas Southwestern Medical Center 6001 Forest Park, ND8.120c Dallas, TX 75390-9041 (214) 645-6167 (Office) (214) 645-6168 (Laboratory) (214) 645-6166 (Fax) e-mail: yuhmin.ch...@utsouthwestern.edu http://www4.utsouthwestern.edu/chooklab/
Re: [ccp4bb] Butandiol as cryopotectant
Hello Ulrike, in our lab 2,3-Butanediol has had a good reputation. Tim On Mon, Mar 22, 2010 at 01:32:33PM +, Ulrike Demmer wrote: Hi everybody, has anyone experience with Butandiol and its different isoforms as cryoprotectant ? Thanks, Ulrike -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
Re: [ccp4bb] Why Do Phases Dominate?
Hi Jabob, Mathematics is abstract and does not cause anything (well maybe headaches). It describes behaviors of real-world phenomena and probably a lot of other things that have no tangible interpretation. What Gerard meant when he said that Fourier transform is at the heart of diffraction is not that it causes diffraction but that the properties of the Fourier transform form directly capture the properties of the physical phenomenon of diffraction. Unless our understanding of diffraction turns out to be wrong, like the early astronomers were wrong about the center of the universe, the Fourier transform will remain the natural mathematical model for this process. What does happen frequently is that a simpler mathematical model needs to be replaced by a more general model once more data becomes available. It is conceivable, at least to me, that some day we need a more generalized model for diffraction. For instance, our typical Fourier transforms assume that electron density can be treated as a real value, but heavy atoms also cause a phase shift of the diffracted wave and thus need to be modeled as an imaginary value. That doesn't mean that the initial model was wrong, just that it is only valid in a certain domain, and outside that domain we need to elaborate the model (which in this case is still a Fourier transform). In many (all?) cases the old model ends up being a special case of the more general variant, just like real numbers are just a special subset of the imaginary numbers. Bart Jacob Keller wrote: - Original Message - From: Gerard Bricogne g...@globalphasing.com To: CCP4BB@JISCMAIL.AC.UK Sent: Friday, March 19, 2010 2:32 PM Subject: Re: [ccp4bb] Why Do Phases Dominate? Dear Marius, Thank you for pointing this out - I was about to argue in the same direction, i.e. that the Fourier transform is at the heart of diffraction and is not just a convenient, but perhaps renegotiable, procedure for analysing diffraction data. I wonder how one can establish that a certain mathematical function is at the heart of a phenomenon? Does mathematics cause phenomena, or consitute the essence of a phenomenon? Many believe that it does, and I am not saying that I do not feel this way about some relationships between mathematics and phenomena--but there seems to be a gradation. On one side, the trajectory of the stream of water from a garden hose is all-too-obviously essentially a parabola, and on the other side, laws like Moore's law seem completely descriptive and not at all causal or essential. A gray-area case for me is whether the manifest world is fundamentally Euclidean, or other such questions. (It certainly *feels* Euclidean, but...) But what I am unsure about is what standard we use to decide whether a given phenomenon is *inherently* tied to a given mathematical function. A troubling thought is that there are many historical examples of phenomena being *fundamentally* one way mathematically--and unthinkably otherwise--and later we have revised our certainty. One thinks of the example Ian Tickle cited of negative numbers being meaningless, or also of the Earth's being the center of the universe and orbits being perfectly circular. A medieval philosopher wanted once to emphasize the certainty of his conclusions, and he wrote that they were as clear and certain as the Earth's being the center of the universe! (Ergo: how certain can we be, then, about *his* conclusions...?). Anyway, one could speculate that there be an alternative model to diffraction which does not involve the Fourier synthesis, it seems. But would that be just a model, and the Fourier-based one the reality? Another instance of such natural hardwiring of the Fourier transform into a physical phenomenon is Free Induction Decay in NMR. There, however, one can measure the phases, as it is the Larmor precession of the population of spins that is measured along two orthogonal directions and gives the real and imaginary parts of the FID signal. Equal opportunity for real and imaginary part: doesn't that make a crystallographer dream ... ? With best wishes, Gerard. -- On Fri, Mar 19, 2010 at 08:15:05PM +0100, Marius Schmidt wrote: The great thing with diffraction, from crystals and from objects in microscopy is THAT this is A NATURALLY OCCURRING FORM of Fourier transform once one accepts that light is a wave (could be something else). If Fourier transform would not have been invented with another problem from engineering, then it would have emerged NATURALLY from diffraction. Diffraction is an analog (not a digital) Fourier transform. A crystal is a low-noise, analog, natural Fourier amplifier!!! If you want to build the fastest Fourier transform of the world, you could represent your function, which you want to Fourier transform, as density fluctuation and scatter from it, or, you could amplify scattering into certain direction by putting
Re: [ccp4bb] Butandiol as cryopotectant
Hi Ulrike, 2,3-butanediol has worked very nicely as a cryoprotectant. In my hands it mostly seems to decrease mosaicity. I was able to switch from a three-step soaking protocol with glycerol and glucose to a quick (30 second to one minute) soak with 2,3-BD. It's a winner. Steve I Hello Ulrike, in our lab 2,3-Butanediol has had a good reputation. Tim On Mon, Mar 22, 2010 at 01:32:33PM +, Ulrike Demmer wrote: Hi everybody, has anyone experience with Butandiol and its different isoforms as cryoprotectant ? Thanks, Ulrike -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
Re: [ccp4bb] Why Do Phases Dominate?
Dear Bart, Thank you for further analysing this idea of inherence, which is so striking in this case. I just wanted to point out that the most natural setting for Fourier transform theory is the space L2 of square-integrable functions (although L1 is the more natural one for convolution-related properties). Both of these are spaces of complex-valued functions from the start, so I am not aware of a restriction to real-valued functions anywhere in Fourier theory, and no initial framework thus needs to be broken to accommodate a complex-valued electron density. Real-valued functions in L1 or L2 are rather oddities, a little bit like centric reflections for us. Their Fourier transforms have the extra property of having Hermitian symmetry (the generic mathematical term for what we call Friedel symmetry). What happens when anomalous scattering gets us back to a general complex-valued electron density function is simply that we lose that extra property, not that the framework of Fourier theory has to be extended. This is a minor point, but worth bearing in mind. With best wishes, Gerard. -- On Mon, Mar 22, 2010 at 05:00:23PM -0600, Bart Hazes wrote: Hi Jabob, Mathematics is abstract and does not cause anything (well maybe headaches). It describes behaviors of real-world phenomena and probably a lot of other things that have no tangible interpretation. What Gerard meant when he said that Fourier transform is at the heart of diffraction is not that it causes diffraction but that the properties of the Fourier transform form directly capture the properties of the physical phenomenon of diffraction. Unless our understanding of diffraction turns out to be wrong, like the early astronomers were wrong about the center of the universe, the Fourier transform will remain the natural mathematical model for this process. What does happen frequently is that a simpler mathematical model needs to be replaced by a more general model once more data becomes available. It is conceivable, at least to me, that some day we need a more generalized model for diffraction. For instance, our typical Fourier transforms assume that electron density can be treated as a real value, but heavy atoms also cause a phase shift of the diffracted wave and thus need to be modeled as an imaginary value. That doesn't mean that the initial model was wrong, just that it is only valid in a certain domain, and outside that domain we need to elaborate the model (which in this case is still a Fourier transform). In many (all?) cases the old model ends up being a special case of the more general variant, just like real numbers are just a special subset of the imaginary numbers. Bart Jacob Keller wrote: - Original Message - From: Gerard Bricogne g...@globalphasing.com To: CCP4BB@JISCMAIL.AC.UK Sent: Friday, March 19, 2010 2:32 PM Subject: Re: [ccp4bb] Why Do Phases Dominate? Dear Marius, Thank you for pointing this out - I was about to argue in the same direction, i.e. that the Fourier transform is at the heart of diffraction and is not just a convenient, but perhaps renegotiable, procedure for analysing diffraction data. I wonder how one can establish that a certain mathematical function is at the heart of a phenomenon? Does mathematics cause phenomena, or consitute the essence of a phenomenon? Many believe that it does, and I am not saying that I do not feel this way about some relationships between mathematics and phenomena--but there seems to be a gradation. On one side, the trajectory of the stream of water from a garden hose is all-too-obviously essentially a parabola, and on the other side, laws like Moore's law seem completely descriptive and not at all causal or essential. A gray-area case for me is whether the manifest world is fundamentally Euclidean, or other such questions. (It certainly *feels* Euclidean, but...) But what I am unsure about is what standard we use to decide whether a given phenomenon is *inherently* tied to a given mathematical function. A troubling thought is that there are many historical examples of phenomena being *fundamentally* one way mathematically--and unthinkably otherwise--and later we have revised our certainty. One thinks of the example Ian Tickle cited of negative numbers being meaningless, or also of the Earth's being the center of the universe and orbits being perfectly circular. A medieval philosopher wanted once to emphasize the certainty of his conclusions, and he wrote that they were as clear and certain as the Earth's being the center of the universe! (Ergo: how certain can we be, then, about *his* conclusions...?). Anyway, one could speculate that there be an alternative model to diffraction which does not involve the Fourier synthesis, it seems. But would that be just a model, and the Fourier-based one the reality? Another instance
