Re: [ccp4bb] [ccp4bb] Oxford University Press
Indeed! Scientists in the Soviet Bloc got paid for publishing their scientific papers (and maybe for citations as well - not sure about that one)! We need to change the current system! Although these changes could be accompanied by many other pleasant virtues of the Soviet regime. Petr > On Jun 29, 2018, at 8:11 AM, Hughes, Jon > wrote: > > whose paper? our universities pay subscriptions for these journals and we > even pay on top of that for the pages of our publications (even when they're > not actually printed!), whilst we review papers for free! sounds like a > well-validated way to use taxpayers' money to keep the expensive company cars > etc. nice and shiny. why don't universities just require reimbursement for > the time we invest to insure that the merchandise is up to standard? €100 per > hour would be cheap. seems to me as though some capitalists need to add a few > lines to their balance sheets > best, jon > > -Ursprüngliche Nachricht- > Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Robbie > Joosten > Gesendet: Freitag, 29. Juni 2018 13:42 > An: CCP4BB@JISCMAIL.AC.UK > Betreff: Re: [ccp4bb] Oxford University Press > > Yes, but think of all the money they miss due to your pirating of their paper > ;) It's the typical discussion about whether piracy of copyrighted material > leads to loss or gain of revenue. There are a lot of models here, but not > necessarily well-validated. > > Anyway, if people want to read your papers and cannot get them from > ResearchGate, I'm sure they can find them on another online collection, a hub > of some sort ;) > > Cheers, > Robbie > >> -Original Message- >> From: Bernhard Rupp [mailto:hofkristall...@gmail.com] >> Sent: Friday, June 29, 2018 13:23 >> To: 'Robbie Joosten'; CCP4BB@JISCMAIL.AC.UK >> Subject: RE: [ccp4bb] Oxford University Press >> >> Agreed, but for 10 years old papers this seems a bit of overkill >> >> >> >> From: CCP4 bulletin board On Behalf Of Robbie >> Joosten >> Sent: Friday, June 29, 2018 12:11 >> To: CCP4BB@JISCMAIL.AC.UK >> Subject: Re: [ccp4bb] Oxford University Press >> >> >> >> Were they open access papers? If they were, than OUP is being too >> aggressive (IMO), but otherwise it makes sense. I also find the >> ResearchGate is rather aggressive in bugging you to upload papers that >> are readily available from the publisher. The whole business bit in >> scientific publishing is a necessary (?) evil, but I guess if given >> the choice one should publish somewhere where you as an author retain >> copyright. >> >> >> >> Cheers, >> >> Robbie >> >> >> >> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of >> Bernhard Rupp >> Sent: Friday, June 29, 2018 11:42 >> To: CCP4BB@JISCMAIL.AC.UK >> Subject: [ccp4bb] Oxford University Press >> >> >> >> Hi Fellows, >> >> >> >> just an advisory that Oxford University Press is pretty aggressive in >> >> enforcing copyright - I had to remove 2 Bioinformatics papers >> >> from ResearchGate. >> >> >> >> Fortunately, authors have choices, too >> >> >> >> Cheers, BR >> >> -- >> >> Bernhard Rupp >> >> http://www.hofkristallamt.org/ >> >> b...@hofkristallamt.org >> >> +1 925 209 7429 >> >> +43 676 571 0536 >> >> -- >> >> Many plausible ideas vanish >> >> at the presence of thought >> >> -- >> >> >> >> >> >> >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 >> >> >> >> >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Crystal structure of an unknown protein
To keep this thread on topic - there is no Blue Stone on the Galveston island. Lots of white sand beaches, lots of black birds, lots of new BMW cars in the port (they unload the ship here), a few oil rigs, an occasional cruise ship, but no Blue Stone… Petr Petr Leiman University of Texas Medical Branch Department of BMB Basic Sciences Building 6.600D 301 University Blvd Galveston, TX 77555-0647 Cell: 832 908 6635 Office: 409 747 2078 https://scsb.utmb.edu/faculty/Leiman.asp > On Dec 16, 2017, at 4:42 PM, Anastassis Perrakis <a.perra...@nki.nl> wrote: > > > I wonder why you assume know there are "about 20 point mutation sites” if > "this protein is an unknown protein”. > It looks like you are comparing the sequence of a protein you do not know > what it is to the sequence of a protein you dont really know what it is (1). > > I would consider it more likely, it is the E. coli protein and the electron > density is ambigious so some side chains might have been erronously assigned > to a false identity. > > A. > > (1) > Percy: You know, they do say that the Infanta's eyes are more beautiful than > the famous Stone of Galveston. > Edmund: Mm! ... What? > Percy: The famous Stone of Galveston, My Lord. > Edmund: And what's that, exactly? > Percy: Well, it's a famous blue stone, and it comes ... from Galveston. > Edmund: I see. And what about it? > Percy: Well, My Lord, the Infanta's eyes are bluer than it, for a start. > Edmund: I see. And have you ever seen this stone? > Percy: (nods) No, not as such, My Lord, but I know a couple of people who > have, and they say it's very very blue indeed. > Edmund: And have these people seen the Infanta's eyes? > Percy: No, I shouldn't think so, My Lord. > Edmund: And neither have you, presumably. > Percy: No, My Lord. > Edmund: So, what you're telling me, Percy, is that something you have never > seen is slightly less blue than something else you have never seen. > > >>> Dear CCP4bb, >>> In 2014, I collected a high quality data set from a crystal. But I could >>> not solve the structure of that crystal because this protein is a >>> contaminate. >>> Recently, I used StruBE's Contaminer and fortunately got the solution. >>> Thanks ContaMiner!!! This protein is a contaminate protein. >>> However, I found this protein is an unknown protein (about 180 residues) >>> whose amino acid sequence is not totally same as E.coli. There are about 20 >>> point mutation sites comparing to the E.coli protein. This means this >>> protein may be from an unknown bacteria. >>> The space group of this crystal is new. There is also a new ligand in this >>> protein. >>> My question is how could I found the primary structure of this protein and >>> how to deposit this protein in PDB. >>> Best regards, >>> Jiyong >> >> >
Re: [ccp4bb] Using Coot and CCP4 program for cryoEM data
If your signal goes all the way to the half Nyquist frequency, oversample your map to have the pixel size equal to 1/3rd of the highest resolution. Your map will look much better in coot. Real space fitting will work much better as well. Best, Petr > On May 17, 2017, at 11:24 AM, MyeongSeon Lee > <0e01bd27cd0f-dmarc-requ...@jiscmail.ac.uk> wrote: > > Hi, all. > > I have collected cryoEM data and want to use Coot and CCP4 program to build > model and to refine it. > > 1. What is the steps to do this? > 2. How do I convert cryoEM map file to MTZ file? > 3. Can I also use Phenix for this purpose? > > Thanks to all for your help in advance.
Re: [ccp4bb] on final R value
A small erratum is needed unfortunately. The sequence identity of 4UHV to 2P5Z is 19% (but not the exceptional 15% as I wrote originally). Nevertheless, Phaser successfully finding a solution for a 19% SI model is no small feat. > On Mar 16, 2016, at 09:48, Petr Leiman <petr.lei...@epfl.ch> wrote: > > Dear Prof. Bricogne, > > As your statements carry a huge weight in this community, I have to mention > that exceptions to the rule you formulated exist. > >> On Mar 15, 2016, at 17:21, Gerard Bricogne <g...@globalphasing.com> wrote: >> >> Dear Smith, >> >>The only way to achieve such a low R-value at low resolution is >> to inject extra geometric restraints based on the knowledge of a very >> similar structure already refined against high-resolution data, e.g. >> the structure that was used to get an MR solution. > > Here is one example (3.3 A resolution and R-free of 19.5%): > http://www.rcsb.org/pdb/explore.do?structureId=4MTK > There is a caveat of course. High resolution here is mimicked by a very high > solvent content - 82% or 86%. > > Before anyone starts to suspect that this structure is based on a higher > resolution structure (PDB code 4UHV), I urge the unbelievers to inspect the > deposition and release dates on the two entries. Our structure was released > 1.5 years before the higher resolution structure was deposited… Also, please > check the refinement quality parameters of the two entries. > > Other notes: we solved our structure by MR using a homologous structure of a > fragment as a search model (PDB 2P5Z). The model represented 56% of the unit > cell content and had only 15% sequence identity. And amazingly Phaser worked > (thanks Randy Read!). The second remarkable thing was Resolve pulling density > out of ‘thin air’ using 6-fold averaging (thanks Tom Terwiligger!). In this > figure, panel A is the MR density and panel B is the 6-fold NCS-averaged map: > https://www.dropbox.com/s/kbf3b3c1lkdj3ph/Figure-S2.jpg?dl=0 > > We never published this because the focus of the paper has been changed > several times since the structure was solved. But the draft is 98% ready now, > so it will be published soon. > > Sincerely, > > Petr > > P.S. I can share the raw data if anyone is interested in examining this > dataset in detail. > > -- > Petr Leiman > EPFL > BSP 415 > CH-1015 Lausanne > Switzerland > Office: +41 21 69 30 441 > Mobile: +41 79 538 7647 > Fax: +41 21 69 30 422 > http://lbbs.epfl.ch > > >> We have called this >> "targeting" - for a method of doing this, see >> >> Smart et al. (2008). Abstr. Annu. Meet. Am. Crystallogr. Assoc., >> Abstract TP139, p. 117. >> >> subsequently described in more detail in >> >> http://journals.iucr.org/d/issues/2012/04/00/ba5178/stdsup.html >> >> and the implementation of similar ideas in REFMAC using ProSmart (not >> the same Smart :-) ) . >> >>These "external restraints" try to preserve the local geometry of >> the target structure by keeping short internal interatomic distances >> in the structure being refined against low-resolution data as close as >> possible to what they are in the target structure. Phenix uses a >> similar idea, but based on imposing a similarity of torsion angles: >> >> http://journals.iucr.org/d/issues/2014/05/00/rr5054/stdsup.html >> >>An early and rather extreme way of doing this was to use the MR >> model in a rigid body refinement and be lucky enough that this MR >> model was spot on. >> >>Keeping track of the fact that such a targetting has been applied >> in a refinement, and how, (i.e. Dale's question about how such a model >> was created) is an obvious challenge in relation to deposition: if the >> use of this procedure is not recorded nor documented, you will get >> outliers with respect to the usual trends in R-values vs. resolution, >> just like the one you have spotted, and all the data mining of these >> trends will be messed up. >> >> >>With best wishes, >> >> Gerard >> >> -- >> On Tue, Mar 15, 2016 at 08:34:31AM -0700, Dale Tronrud wrote: >>> Without knowing the structure it is hard to make any comment. >>> Usually the only way to get an R value this low at 3.9 A resolution is >>> to start with a high resolution model and MR it into the low resolution >>> map. >>> >>> It is a good sign for the future of methods development that a good >>> model will fit a low resolution data set but we don't know h
Re: [ccp4bb] CCP4 PATH variable
Dear All, I have to apologize for my somewhat insinuating message about CCP4 behavior. In order to retain command line functionality of CCP4 programs, I always sourced CCP4 setup script in my bashrc file, and this is what caused a significant amount of grief for me later. However, sourcing CCP4 setup is unnecessary for the ccp4i interface, which is self-consistent and fully contained in terms of environmental variables, and this is how we are supposed to use CCP4 today anyway. Sincerely, Petr P.S. Many thanks to Ed Pozharski for giving me pointers to figure out this problem. On 03/12/2015 08:49 PM, Petr Leiman wrote: Dear Community, What is the reason of placing the CCP4 PATH and other path-related variables in front of existing variables? This forces a linux system to use CCP4-distributed wish in all applications by default. Note that the ccp4i script calls CCP4 distributed wish explicitly with its full path. This might be trivial, and the fix is also trivial, but trivial things like that cause a lot of lost time and head scratching when tcl/tk programs compile without errors and perform some operations correctly but segfault on others - all due to a mixup of libraries and wish executables caused by CCP4 wish. Would it be possible to append CCP4 path variables by default instead of rather rudely jumping in front of the queue? Thank you, Petr -- Petr Leiman EPFL BSP 415 CH-1015 Lausanne Switzerland Office: +41 21 69 30 441 Mobile: +41 79 538 7647 Fax: +41 21 69 30 422 http://lbbs.epfl.ch
[ccp4bb] CCP4 PATH variable
Dear Community, What is the reason of placing the CCP4 PATH and other path-related variables in front of existing variables? This forces a linux system to use CCP4-distributed wish in all applications by default. Note that the ccp4i script calls CCP4 distributed wish explicitly with its full path. This might be trivial, and the fix is also trivial, but trivial things like that cause a lot of lost time and head scratching when tcl/tk programs compile without errors and perform some operations correctly but segfault on others - all due to a mixup of libraries and wish executables caused by CCP4 wish. Would it be possible to append CCP4 path variables by default instead of rather rudely jumping in front of the queue? Thank you, Petr -- Petr Leiman EPFL BSP 415 CH-1015 Lausanne Switzerland Office: +41 21 69 30 441 Mobile: +41 79 538 7647 Fax: +41 21 69 30 422 http://lbbs.epfl.ch
[ccp4bb] Meeting announcement: Phage/Virus Assembly (PVA) conference
Dear All, I would like to bring to your attention the XXIV Phage/Virus Assembly (PVA) meeting: http://lbbs.epfl.ch/XXIV-PVA-conference which will take place in Les Diablerets, Switzerland on June 7-12, 2015. This conference is an exceptional opportunity to learn all about new discoveries in the fields of phage/virus structure, morphogenesis (particle assembly and genome packaging), and molecular details of the infection process. The conference is highly multidisciplinary with contributions from virologists, geneticists, biochemists, structural biologists and biophysicists (both, experiment and theory). The spirit of the meeting is that most people’s requests to speak are tried to be accommodated, but all talks are very short (each slot is only 15 min long). There are no invited speakers. The program will be organized similar to the program of the previous meeting: http://pva.scripps.edu/program.html The all-inclusive registration fee is rather modest considering that the site is a 4-star resort hotel and all talks will take place in a large congress hall. Hope to see you in Les Diablerets! Sincerely, Petr Leiman -- Petr Leiman Laboratory of Structural Biology and Biophysics http://lbbs.epfl.ch EPFL BSP-415 CH-1015 Lausanne Phone: +41 21 69 30441 Mobile: +41 79 538 7647
Re: [ccp4bb] Systematically shifted peak in 2Fo-Fc and BDF maps
Thanks to all who replied to my message. The most logical explanation to the observed phenomenon is likely the following. During crystallization, Sr ions from the crystallization solution kick out a fraction of the Mg(OH)6 ions from the binding site in question. The cavity of the binding site is big and the Sr ion binds at a slightly different position compared to the Mg(OH)6 ion. The BDF map shows the shifted position of the Sr ion, whereas the 2Fo-Fc map shows the position of the Mg(OH)6 ion. This is possible because the occupancy of the Sr ion at that site is low - the height of the Sr peak in the BDF map is less than 15% of the maximal peak height - and the contribution of the Sr ion to the 2Fo-Fc map is negligibly small. The “normal” (2Fo-Fc) scattering of the Sr ion is essentially completely masked by the Mg(OH)6 ion scattering because the two overlap (they are 0.47 A apart) and the latter has a 5-6 times higher occupancy. Eleanor’s and Phoebe Rice’s comments were extremely useful in solving this puzzle (at least for me - we will see if the referees agree that this is a solution). This particular comment by Phoebe was really insightful considering she did not see the actual data but only read my somewhat incomplete description: “Could it be a mix of species - partly Sr and partly some non-anomalous-scattering entity that sits in a slightly shifted position?” CCP4BB is an incredible resource full of really clever people! Thanks to all again! Petr On Apr 24, 2014, at 11:39, Petr Leiman petr.lei...@epfl.chmailto:petr.lei...@epfl.ch wrote: Dear All, We are looking for an explanation for a very strange observation. Problem: We have two fully independent data sets (two different crystals), in which the Bijvoet Difference Fourier map peak of one particular metal site is shifted by 0.47 A from its position in the 2Fo-Fc map. Relevant information: The resolution of both data sets is 1.5-1.6 A. The 2Fo-Fc and BDP maps are calculated using the same phases. The metal ion is water hydrated and all the details are crystal clear in both 2Fo-Fc maps. The crystals are grown in the presence of Sr and the data sets are collected at the Sr K-edge. There are many other Sr sites and all strong peaks in the BDF map overlap with 2Fo-Fc map peaks perfectly. The Sr site in question is not the strongest, but it is well above the noise level of the BDF map. Additional information: The weird site is actually fully buried inside an internal cavity (it is surrounded by protein atoms from all sides), but a Sr atom is able to diffuse into this cavity somehow. All other Sr sites are on the surface of the protein. Any thoughts about why a non-noise BDF map peak would not overlap with a 2Fo-Fc map peak are welcome! Thank you very much, Petr -- Petr Leiman EPFL BSP 415 CH-1015 Lausanne Switzerland Office: +41 21 69 30 441 Mobile: +41 79 538 7647 Fax: +41 21 69 30 422
[ccp4bb] Systematically shifted peak in 2Fo-Fc and BDF maps
Dear All, We are looking for an explanation for a very strange observation. Problem: We have two fully independent data sets (two different crystals), in which the Bijvoet Difference Fourier map peak of one particular metal site is shifted by 0.47 A from its position in the 2Fo-Fc map. Relevant information: The resolution of both data sets is 1.5-1.6 A. The 2Fo-Fc and BDP maps are calculated using the same phases. The metal ion is water hydrated and all the details are crystal clear in both 2Fo-Fc maps. The crystals are grown in the presence of Sr and the data sets are collected at the Sr K-edge. There are many other Sr sites and all strong peaks in the BDF map overlap with 2Fo-Fc map peaks perfectly. The Sr site in question is not the strongest, but it is well above the noise level of the BDF map. Additional information: The weird site is actually fully buried inside an internal cavity (it is surrounded by protein atoms from all sides), but a Sr atom is able to diffuse into this cavity somehow. All other Sr sites are on the surface of the protein. Any thoughts about why a non-noise BDF map peak would not overlap with a 2Fo-Fc map peak are welcome! Thank you very much, Petr -- Petr Leiman EPFL BSP 415 CH-1015 Lausanne Switzerland Office: +41 21 69 30 441 Mobile: +41 79 538 7647 Fax: +41 21 69 30 422
Re: [ccp4bb] Structure factor equation
The actual wave term A/(R-r) * exp(i 2Pi (kR - vt)) - where R is a vector from the origin of a chosen coordinate system to the detector, r is a vector from from the origin to the electron, k is a wave vector of the scattered wave, and A is a vector proportional to the E vector of the incident wave - is not even mentioned in the expression you are referring to. Note that the scattered wave is spherical but not planar. However, compared to the phase shift term exp(i 2Pi rS), the 1/(R-r) and A terms can be considered constant over the diameter of the atom, the unit cell, and even the complete crystal (the Fraunhofer diffraction regime), and 1/(R-r) = 1/R. A wave scattered by a crystal in the direction of vector k is: A/R * exp(i 2Pi (kR - vt)) * FT[rho(r)] where rho(r) is the complete electron density of the crystal. In principle, if we call this expression a structure factor, it is a vector because a wave is a vector field. The Fourier transform term FT[rho(r)] of a scalar field-type function rho(r) (r^3 |- rho) is a scalar field-type function of complex numbers F (S^3 |- F), and calling this part of the scattered wave a structure factor makes it a non-vector. This semantics should not distract us from the original question about the missing wave term on page 121 in Blundell and Johnson. I agree with BR that scattering is a single-photon process (flame suit on) and the temporal term does not matter in how diffraction is recorded by the detectors we use today and we can simply ignore it. Petr Petr Leiman EPFL Switzerland On 04/02/2014 04:39 AM, Edward A. Berry wrote: Encouraged by recent help from the BB in filling in gaps in my understanding, maybe I can get help with another question: At the top of page 121 in Blundell and Johnson, it is written: The total wave scattered by a small unit of volume dv at a position r relative to the wave scattered from the origin will therefore have an amplitude proportional to Rho(r)dv and phase 2Pi i(r.S)dv (OK so far) i.e. wave scattered = Rho(r)exp(2Pi i r.S)dv How is that a wave? r and S are constant vectors. My best explanation so far is to say this is a complex coefficient that will adjust the weight and phase of the wave scattered by this point. Say the wave scattered from one electron at the origin will result in a temporal cosine wave at the surface of the detector: E = exp(2Pi i wt) = cos(2Pi wt) (not sure if 2Pi is needed when w is radians/sec) Then the wave at the same point, scattered by dv at r, would be the same multiplied by the quantity in question: E = rho(r)exp(2Pi i r.s)dv * exp(2pi i wt) = rho(r)exp(2pi i (wt - r.S)) i.e. phase-shifted by 2Pi (r.S), and multiplied by Rho(r)dv Is that more or less it? (since these quantities add up to the Structure Factor F(s), I guess I'm really asking what a structure factor is. Rupp says a structure fator is a vector representing the diffracted X-rays, which i take to be consistent with this if vector is in the complex plane)
Re: [ccp4bb] AW: [ccp4bb] Dependency of theta on n/d in Bragg's law
. This might be why Bragg decided to put an n in there. But it seems that fairly rapidly after people starting diffracting x-rays off of crystals, the Miller Index became generalized to h,k,l as integers, and we never looked back. It is a mistake, however, to think that there are contributions from different structure factors in a given spot. That does not happen. The harmonics you are thinking of are actually part of the Fourier transform. Once you do the FFT, each h,k,l has a unique F and the intensity of a spot is proportional to just one F. The only way you CAN get multiple Fs in the same spot is in Laue diffraction. Note that the n is next to lambda, not d. And yes, in Laue you do get single spots with multiple hkl indices (and therefore multiple structure factors) coming off the crystal in exactly the same direction. Despite being at different wavelengths they land in exactly the same place on the detector. This is one of the more annoying things you have to deal with in Laue. A common example of this is the harmonic contamination problem in beamline x-ray beams. Most beamlines use the h,k,l = 1,1,1 reflection from a large single crystal of silicon as a diffraction grating to select the wavelength for the experiment. This crystal is exposed to white beam, so in every monochromator you are actually doing a Laue diffraction experiment on a small molecule crystal. One good reason for using Si(111) is because Si(222) is a systematic absence, so you don't have to worry about the lambda/2 x-rays going down the pipe at the same angle as the lambda you selected. However, Si(333) is not absent, and unfortunately also corresponds to the 3rd peak in the emission spectrum of an undulator set to have the fundamental coincide with the Si(111)-reflected wavelength. This is probably why the third harmonic is often the term used to describe the reflection from Si(333), even for beamlines that don't have an undulator. But, technically, Si(333) is n ot a har monic of Si(111). They are different reciprocal lattice points and each has its own structure factor. It is only the undulator that has harmonics. However, after the monochromator you generally don't worry too much about the n=2 situation for: n*lambda = 2*d*sin(theta) because there just aren't any photons at that wavelength. Hope that makes sense. -James Holton MAD Scientist On 8/20/2013 7:36 AM, Pietro Roversi wrote: Dear all, I am shocked by my own ignorance, and you feel free to do the same, but do you agree with me that according to Bragg's Law a diffraction maximum at an angle theta has contributions to its intensity from planes at a spacing d for order 1, planes of spacing 2*d for order n=2, etc. etc.? In other words as the diffraction angle is a function of n/d: theta=arcsin(lambda/2 * n/d) several indices are associated with diffraction at the same angle? (I guess one could also prove the same result by a number of Ewald constructions using Ewald spheres of radius (1/n*lambda with n=1,2,3 ...) All textbooks I know on the argument neglect to mention this and in fact only n=1 is ever considered. Does anybody know a book where this trivial issue is discussed? Thanks! Ciao Pietro Sent from my Desktop Dr. Pietro Roversi Oxford University Biochemistry Department - Glycobiology Division South Parks Road Oxford OX1 3QU England - UK Tel. 0044 1865 275339 -- Petr Leiman EPFL BSP 415 CH-1015 Lausanne Switzerand Office: +41 21 69 30 441 Mobile: +41 79 538 7647 Fax: +41 21 69 30 422
Re: [ccp4bb] phaser 2.5.2 in ccp4 6.3.0 does not output Hendrickson Lattman coefficients
Dear Randy, Thank you for your quick response. Obviously, you have given this a lot of thought. I would like to have the HL coefficients in the phaser output file for downstream compatibility with density modification programs such as resolve. Thank you, Petr On 07/03/2013 10:46 AM, Randy Read wrote: Dear Petr, Presumably you're just talking about Phaser for molecular replacement, because Phaser still produces HL coefficients for SAD phasing. There were two major reasons we made this change. First, the presence of HL coefficients can fool some programs into thinking that you have experimental phase information that is independent of your model, which is not true for phases from molecular replacement. Second, for unimodal sources of phase information like model phases, the HL coefficients are redundant and can be generated from the phase and FOM, e.g. by using the HLCONV command in sftools. We could easily put this option back in, controlled for instance by setting the VERBOSE flag, if there were a compelling reason. No-one else has complained since we made this change a year ago, but maybe they have been suffering in silence! Could you let us know why you find this feature extremely useful? Best wishes, Randy Read On 2 Jul 2013, at 18:41, Petr Leiman petr.lei...@epfl.ch wrote: I have just found out that phaser v. 2.5.2 in ccp4 6.3.0-021 does not output columns with HL coefficients. I cannot find a combination of buttons in CCP4i GUI to enable this extremely useful feature. This is the first time I tried phaser in the latest CCP4 release and I am shocked this problem has not been discovered and fixed already. If there is a reason to this new output column behavior, it would be very useful to hear this reason. Sincerely, Petr -- Petr Leiman EPFL BSP 415 CH-1015 Lausanne Switzerand Office: +41 21 69 30 441 Mobile: +41 79 538 7647 Fax: +41 21 69 30 422 -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
[ccp4bb] phaser 2.5.2 in ccp4 6.3.0 does not output Hendrickson Lattman coefficients
I have just found out that phaser v. 2.5.2 in ccp4 6.3.0-021 does not output columns with HL coefficients. I cannot find a combination of buttons in CCP4i GUI to enable this extremely useful feature. This is the first time I tried phaser in the latest CCP4 release and I am shocked this problem has not been discovered and fixed already. If there is a reason to this new output column behavior, it would be very useful to hear this reason. Sincerely, Petr -- Petr Leiman EPFL BSP 415 CH-1015 Lausanne Switzerand Office: +41 21 69 30 441 Mobile: +41 79 538 7647 Fax: +41 21 69 30 422
Re: [ccp4bb] Strand distorsion and residue disconnectivity in pymol
On May 30, 2013, at 5:31 PM, Phoebe A. Rice pr...@uchicago.edumailto:pr...@uchicago.edu wrote: In the olden days, when dinosaurs did roam, Ribbons had a nice fix-up feature that would gently move the alpha carbon end of the stick so that it met the ribbon. Looked MUCH better than the current wavy ribbon one gets with side chain helper, and I haven't been able to find a trick like that in pymol. So pymol developers, please consider yourselves wheedled ... Well, there is another program, which is probably (no flames please!) more powerful, feature-rich than pymol and at the same time much easier to use called… drumroll… UCSF Chimera. One can display wavy and smooth secondary structure cartoons with it. The Chimera engine takes care of connecting side chains to the secondary structure cartoons in both representations. The command to control the cartoon representation is in the Ribbon Style Editor menu: https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html The name of the command (can be run from the command line prompt in Chimera or chosen from the above menu) is ribspline: https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribspline.html Best wishes, Petr -- Petr Leiman EPFL BSP 415 CH-1015 Lausanne Switzerland Office: +41 21 69 30 441 Mobile: +41 79 538 7647 Fax: +41 21 69 30 422 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK] on behalf of Jason Vertrees [jason.vertr...@schrodinger.commailto:jason.vertr...@schrodinger.com] Sent: Thursday, May 30, 2013 10:17 AM To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Strand distorsion and residue disconnectivity in pymol Hi Jacob, Sure, but I believe Donghui wanted to only show sidechains, not any backbone atoms, as sticks. Doing this will leave fragments floating in space as the original email noted. Cheers, -- Jason On Thu, May 30, 2013 at 10:13 AM, Jacob Keller j-kell...@fsm.northwestern.edumailto:j-kell...@fsm.northwestern.edu wrote: Can't you just show both cartoon (smoothed) and sticks (not smoothed) for the given area? JPK On Thu, May 30, 2013 at 11:06 AM, Jason Vertrees jason.vertr...@schrodinger.commailto:jason.vertr...@schrodinger.com wrote: Hi Donghui, Bernhard is correct: PyMOL flattens out secondary structure to produce more aesthetically appealing images. You can disable this for beta sheets and loops by typing: # disable smoothing of sheets set cartoon_flat_sheets, 0 # disable smoothing of loops set cartoon_smooth_loops, 0 The cartoon_sidechain_helper setting automatically modulates these settings. If for some reason you need to disable cartoon_sidechain_helper you can imitate the look with: hide show cartoon show sticks, not (n. C+CA+O+N) extend 1 set cartoon_smooth_loops, 0 set cartoon_flat_sheets, 0 Again as Bernhard noted, smoothing representations adjusts the representations' positions in space; therefore, you have the option of being positionally correct or aesthetically more pleasing. Cheers, -- Jason On Wed, May 29, 2013 at 10:29 PM, wu donghui wdh0...@gmail.commailto:wdh0...@gmail.com wrote: Dear all, I found a problem when I use pymol to prepare structure interface. Strand is distorted when residue from the strand is connected to the strand by turning on side_chain_helper on. However when side_chain_helper is off, the strand turns to normal shape but the residue from it is disconnected to the strand. I attached the picture for your help. I know there must be some tricks for this. Welcome for any input. Thanks a lot. Best, Donghui -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.commailto:jason.vertr...@schrodinger.com (o) +1 (603) 374-7120tel:%2B1%20%28603%29%20374-7120 -- *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.orgmailto:kell...@janelia.hhmi.org *** -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) jason.vertr...@schrodinger.commailto:jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
[ccp4bb] Postdoctoral position in Switzerland
A postdoctoral position is available at the Laboratory of Structural Biology and Biophysics at the Swiss Federal Institute of Technology in Lausanne (Ecole Polytechnique Fédérale de Lausanne, EPFL). Research topic: Structure and function of large, multicomponent biological macromolecular complexes such as the bacterial type VI secretion system (T6SS), R-type pyocins, and selected tailed bacterial viruses (bacteriophages). Research methods: A hybrid approach involving a combination of X-ray crystallography, electron microscopy, bioinformatics, and microbiology/molecular biology. Location and work environment: http://maps.google.ch/maps?q=bsp+415 and http://information.epfl.ch/page-16430-en.html Salary: Very high. Required skills: Experience in all aspects of X-ray crystallography, strong publication record, some teaching experience. Teaching duties: About 2 academic hours per week during autumn and spring semesters. Highly desired skills: Driving license, background in physics (to participate in physics teaching curriculum), some knowledge of French. Starting date: As soon as possible. Duration: The contract is renewable every year for up to 5 years. For application and additional information please contact Prof. Petr Leiman (petr.lei...@epfl.chmailto:petr.lei...@epfl.ch) --- Petr Leiman EPFL BSP 415 CH-1015 Lausanne Switzerland Office: +41 21 69 30 441 Mobile: +41 79 538 7647 Fax: +41 21 69 30 422
Re: [ccp4bb] refinement protein structure
Dear Tom, As far as I know you are the first person who sent his/her data that are supposed to be _private_ to 1000+ CCP4BB subscribers. The person who suggested you send this type of message to CCP4BB board played a very cruel practical joke on you. To CCP4BB support staff: Is it possible to block emails with 1+MB attachments? Thank you, Petr Prof. Petr Leiman EPFL BSP-415 CH-1015 Lausanne Switzerland On Mar 27, 2013, at 5:22 PM, Tom Van den Bergh wrote: Dear members of ccp4bb, I need some help with the refinement of my structure of a variant of mRFP (monomer red fluorescent protein, sequence in attachment). I have done molecular replacement with phaser with model 2VAD of protein database. Then i have done some model building phenix.autobuild. (2 pdb's (overall...), freeR flags and log file attached) When i refine with phenix.refine my structure i get a R-value of 0,42 which is still way too high. (redfluorescent protein.pdb, .mtz and logfile attached) When i look at the structure in coot i find many unmodelled blobs and many outliers in density analysis and rotamer analysis. The problem is that there are so many problems with my structure, that i dont know where to begin. Could you try some refinement for me, because this is first structure that i need to solve as a student and i dont have too many experience with it. Greetings, Tom overall_best.pdbexptl_fobs_phases_freeR_flags.mtzoverall_best_placed.pdbredfluorescentprotein_refine_10.pdbredfluorescentprotein_refine_10.mtzmRFPsequentiezondertag.fastaredfluorescentprotein_refine_10.logAutoBuild_run_6_1.log
Re: [ccp4bb] refinement protein structure
Since this is now public domain knowledge and if this gets ever published, Phil has my vote to be the first author! Petr On Mar 27, 2013, at 6:09 PM, Phil Jeffrey wrote: That's quite brave - shipping your entire structure to people that could be actual competitors. But it was fun to play at 1.4 Angstrom over lunch. Practical points: * not everyone loves 12Mb of attachments in one email in their inbox, so if you do this again please put the files on a webserver and point us there Structural points: * the map looks pretty good, but I think the sequence is misassigned in some regions (e.g. A118-A122 etc). Automation is a good tool but a poor master, and extreme caution is required before taking the results too literally. Usually you'd expect a 1.4 Angstrom to be easy to autobuild but I recently had a sequence misassignment at just that resolution. That map was trivial to interpret with the correct sequence however - one of the joys of working with Arp/wArp at 1.4 Angstrom. * the large number of positive difference density blobs and water molecules clustered in what otherwise would be the solvent void strongly suggest that there's a second molecule present. If I take redfluorescentprotein_refine_10.pdb (waters removed) and exptl_fobs_phases_freeR_flags.mtz and ask Phaser to look for two molecules, it finds them quite successfully. (for the record an LLG of 15111 using nominal sequence identity of 90%). I will send this to you off-list. Please note that Phaser is using a different origin for this molecular replacement solution so the coordinates and your previous map do not overlap. This rather nicely explains why your structure had an R-factor in the 40's despite being a half-way decent model. The new MR solution has an R-free in the 30's in the phenix.refine job I'm running right now. Going forward I suggest you utilize the Arp/wArp program to autobuild your structure for you, starting from the molecular replacement solution (or, perhaps with it stripped to ALA). While you could use Autobuild, this is the CCP4 list and so you should use CCP4 programs. Phil Jeffrey Princeton On 3/27/13 12:22 PM, Tom Van den Bergh wrote: Dear members of ccp4bb, I need some help with the refinement of my structure of a variant of mRFP (monomer red fluorescent protein, sequence in attachment). I have done molecular replacement with phaser with model 2VAD of protein database. Then i have done some model building phenix.autobuild. (2 pdb's (overall...), freeR flags and log file attached) When i refine with phenix.refine my structure i get a R-value of 0,42 which is still way too high. (redfluorescent protein.pdb, .mtz and logfile attached) When i look at the structure in coot i find many unmodelled blobs and many outliers in density analysis and rotamer analysis. The problem is that there are so many problems with my structure, that i dont know where to begin. Could you try some refinement for me, because this is first structure that i need to solve as a student and i dont have too many experience with it. Greetings, Tom
Re: [ccp4bb] Hgen ccp4i gui is broken
I have to follow up on my own thread because Hgen GUI does not start on my Mac
(10.6.8) either. The same error message, which tells me that the tcl/tk code is
broken. CCP4 is up-to-date.
It would be great if at least one person tries pressing the Hgen button in
ccp4i and gives a feedback to me or CCP4BB.
Thank you,
Petr
On Nov 22, 2012, at 3:04 PM, Petr Leiman wrote:
Dear all,
Hgen GUI does not start (the error message is below). The CCP4 version is
6.3.0-009 (64 bit). The system is 2.6.35-32-generic #67-Ubuntu SMP x86_64
GNU/Linux. Is this unique to our system configuration?
Thank you.
Petr
The error message is:
can't use non-numeric string as operand of !
can't use non-numeric string as operand of !
while executing
if { ![$task_setup typedef $arrayname] } {
PleaseWait
return
}
(procedure RunTask line 96)
invoked from within
RunTask hgen
invoked from within
.module.menu.action.canvas.frame.t.f_47 invoke
(uplevel body line 1)
invoked from within
uplevel #0 [list $w invoke]
(procedure tk::ButtonUp line 22)
invoked from within
tk::ButtonUp .module.menu.action.canvas.frame.t.f_47
(command bound to event)
[ccp4bb] Hgen ccp4i gui is broken
Dear all,
Hgen GUI does not start (the error message is below). The CCP4 version is
6.3.0-009 (64 bit). The system is 2.6.35-32-generic #67-Ubuntu SMP x86_64
GNU/Linux. Is this unique to our system configuration?
Thank you.
Petr
The error message is:
can't use non-numeric string as operand of !
can't use non-numeric string as operand of !
while executing
if { ![$task_setup typedef $arrayname] } {
PleaseWait
return
}
(procedure RunTask line 96)
invoked from within
RunTask hgen
invoked from within
.module.menu.action.canvas.frame.t.f_47 invoke
(uplevel body line 1)
invoked from within
uplevel #0 [list $w invoke]
(procedure tk::ButtonUp line 22)
invoked from within
tk::ButtonUp .module.menu.action.canvas.frame.t.f_47
(command bound to event)
[ccp4bb] coot, shelx res files and R32 (H32)
Dear Developers of Coot, I believe that coot has never been able to display the crystallographic symmetry of a R32:H shelxl .res file. As a result, water picking does not work properly for such a file. Everything else seems to work fine. This is not a huge problem, but it would be nice to be able to see symmetry atoms without loading the corresponding shelxl .pdb (which accidentally lacks the space group information anyway, so it has to be edited prior to loading). Again, not a big problem but I believe it is an easy fix in the code, so hopefully this will be done at some point in the future. Thank you, Petr Petr Leiman EPFL BSP-415 CH-1015 Lausanne Switzerland
Re: [ccp4bb] coot, shelx res files and R32 (H32)
Dear George, Thank you very much for your continuing development of the shelx suite. A lot of users (yours truly included) are happy to continue using .res files in coot. It's just the stupid R32/H32 spacegroup that causes coot to misbehave a little. And I am simply very surprised of why this bug has survived so many revisions of coot. Thank you, Petr On Nov 19, 2012, at 2:33 PM, George Sheldrick wrote: shelxl-2012 does include the space group in a way that Coot understands when it writes a .pdb file. This version is in the final beta-testing stage with a lot of new features (mainly for small molecules) and no known bugs, so I hope to release it soon. If anyone would like to try it now please send me an email. George On 11/19/2012 02:13 PM, Petr Leiman wrote: Dear Developers of Coot, I believe that coot has never been able to display the crystallographic symmetry of a R32:H shelxl .res file. As a result, water picking does not work properly for such a file. Everything else seems to work fine. This is not a huge problem, but it would be nice to be able to see symmetry atoms without loading the corresponding shelxl .pdb (which accidentally lacks the space group information anyway, so it has to be edited prior to loading). Again, not a big problem but I believe it is an easy fix in the code, so hopefully this will be done at some point in the future. Thank you, Petr Petr Leiman EPFL BSP-415 CH-1015 Lausanne Switzerland -- 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
Re: [ccp4bb] Tool for calculating RMSD
Would anyone be kind enough to explain what kind of information does the RMSD for two not-yet-superimposed structures transmit? If two structures are indeed identical but are apart spatially, then it is more appropriate to calculate the COM and the inertia tensor for both structures and report the displacement and the rotation (moleman or moleman2 do just that, right?). Reporting RMSD in this case does not seem to make sense because the same RMSD describes an infinite number of spatial configurations of the two structures. If two structures are not identical, one HAS to superimpose them, i.e. to move all (or selected) atoms to be as close in space as possible and only then calculate the RMSD for the superimposed or all atoms. Thank you in advance, Petr Petr Leiman EPFL BPS-415 CH-1015 Lausanne Suisse On Jun 19, 2012, at 5:04 PM, Claudia Millán Nebot wrote: Hello everyone :) I would like to know if it exist some tool that allows to calculate RMSD between 2 pdbs that are identic, but just displaced in space. It should not make a superposition, beause if this is the case it will just say that RMSD is 0 . I know is not such a difficult problem in terms of scripting, but i was wondering if there are tools already. Claudia Millán (cmn...@ibmb.csic.esmailto:cmn...@ibmb.csic.es) Institut de Biologia Molecular de Barcelona (IBMB-CSIC) Barcelona, Spain
Re: [ccp4bb] Tool for calculating RMSD
I am not sure I understood what you are asking. But let me explain my question a little further. If two structures are not identical, then the RMSD is a good enough parameter to describe the superposition: this many atoms were used in the superposition and they can be moved in such a way that this rmsd is achieved. The final result is just one global minimum or a finite number of local minima that all have the same RMSD. If two structures are identical and the RMSD is calculated without moving either of them, the number of configurations that have the same RMSD is infinite. Petr On Jun 20, 2012, at 12:38 AM, Jacob Keller wrote: Is part of your question based there being many ways to superimpose structures, which there are? JPK On Tue, Jun 19, 2012 at 5:34 PM, Petr Leiman petr.lei...@epfl.ch wrote: Would anyone be kind enough to explain what kind of information does the RMSD for two not-yet-superimposed structures transmit? If two structures are indeed identical but are apart spatially, then it is more appropriate to calculate the COM and the inertia tensor for both structures and report the displacement and the rotation (moleman or moleman2 do just that, right?). Reporting RMSD in this case does not seem to make sense because the same RMSD describes an infinite number of spatial configurations of the two structures. If two structures are not identical, one HAS to superimpose them, i.e. to move all (or selected) atoms to be as close in space as possible and only then calculate the RMSD for the superimposed or all atoms. Thank you in advance, Petr Petr Leiman EPFL BPS-415 CH-1015 Lausanne Suisse On Jun 19, 2012, at 5:04 PM, Claudia Millán Nebot wrote: Hello everyone :) I would like to know if it exist some tool that allows to calculate RMSD between 2 pdbs that are identic, but just displaced in space. It should not make a superposition, beause if this is the case it will just say that RMSD is 0 . I know is not such a difficult problem in terms of scripting, but i was wondering if there are tools already. Claudia Millán (cmn...@ibmb.csic.es) Institut de Biologia Molecular de Barcelona (IBMB-CSIC) Barcelona, Spain -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Postdoc postion at SLS
Jacob, do not worry. Data collection for a typical crystal takes only 0.75 seconds. Petr On May 9, 2012, at 5:18 PM, Jacob Keller wrote: I saw something online about the EIGER 16M: 201 GB of data per second! Is that number correct? JPK On Wed, May 9, 2012 at 9:58 AM, Meitian Wang meitian.w...@psi.chmailto:meitian.w...@psi.ch wrote: Postdoctoral Fello Next Generation Detector for Protein Crystallography Your tasks Built on the success of PILATUS detector technology, PSI and Dectris Ltd. are developing the next generation single-photon counting detector (EIGER) featuring smaller pixel size, higher frame rate and dynamic range. The proposed project is to exploit PILATUS and EIGER detectors in protein crystallography applications: * Systematic data acquisition and processing optimization using PILATUS 2M/6M detectors * Development of fast data acquisition and processing methods with EIGER 1M detector in protein micro-crystallography * Commissioning of the EIGER 16M detector at a protein crystallography beamline Your profile You hold a PhD degree in (bio-)chemistry or physics, and have several years of experience in protein crystallography. Working knowledge for data processing programs, and various phasing and refinement software is a must. Experience in computer programming would be a significant advantage. If you are a good team player with fine communication skills and sense of responsibility, this position will offer a great opportunity for you to develop your research career in an exciting and highly multidisciplinary environement. For further information please contact Dr Meitian Wang, phone +41 56 310 41 75tel:%2B41%2056%20310%2041%2075, or Dr. Clemens Schulze-Briese, clemens.schulzebri...@dectris.commailto:clemens.schulzebri...@dectris.com Please submit your application online (including list of publications and addresses of referees) for the position as Postdoctoral Fellow (index no. 6112-00). Paul Scherrer Institut, Human Resources, Elke Baumann, 5232 Villigen PSI, Switzerland http://www.psi.ch/pa/offenestellen/0329-2 __ Meitian Wang Swiss Light Source at Paul Scherrer Institut CH-5232 Villigen PSI - http://www.psi.ch/sls/ Phone: +41 56 310 4175tel:%2B41%2056%20310%204175 Fax: +41 56 310 5292tel:%2B41%2056%20310%205292 -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edumailto:j-kell...@northwestern.edu ***
Re: [ccp4bb] Envelope Phasing.
Using an envelope or a mask to start phasing even with high NCS is still worse than using a low res model from cryoEM that is characterized by an (almost) proper density distribution. One has to measure the intensities of the very low res reflections (0 0 1 and the likes) precisely. The presence of high NCS does not guarantee a success even if your initial model is good as described in Section 9 here: http://www.ncbi.nlm.nih.gov/pubmed/11526317 Petr -- Petr Leiman EPFL IPSB-LBBS BSP-415 CH-1015 Lausanne Suisse
Re: [ccp4bb] MAD
It would be so much more convenient to call these techniques (MAD, SAD, etc.) by their inventor's name. This would simplify things immensely simultaneously eliminating CCP4BB MADisagreements. Although in our days of copyrights wars, the journals and perhaps conferences where these methods were presented for the first time would insist on using their names as part of the method's name... Petr On Jan 19, 2012, at 7:42 PM, Ethan Merritt wrote: On Thursday, 19 January 2012, Ian Tickle wrote: So what does this have to do with the MAD acronym? I think it stemmed from a visit by Wayne Hendrickson to Birkbeck in London some time around 1990: he was invited by Tom Blundell to give a lecture on his MAD experiments. At that time Wayne called it multi-wavelength anomalous dispersion. Tom pointed out that this was really a misnomer for the reasons I've elucidated above. Wayne liked the MAD acronym and wanted to keep it so he needed a replacement term starting with D and diffraction was the obvious choice, and if you look at the literature from then on Wayne at least consistently called it multi-wavelength anomalous diffraction. Ian: The change-over from dispersion to diffraction in MAD protein crystallography happened a couple of years earlier, at least with regard to work being done at SSRL. I think the last paper using the term dispersion was the 1988 Lamprey hemoglobin paper. The next two papers, one a collaboration with Wayne's group and the other a collaboration with Hans Freeman's group, used the term diffraction. WA Hendrickson, JL Smith, RP Phizackerley, EA Merritt. Crystallographic structure-analysis of lamprey hemoglobin from anomalous dispersion of synchrotron radiation. PROTEINS-STRUCTURE FUNCTION AND GENETICS, 4(2):77–88, 1988. JM Guss, EA Merritt, RP Phizackerley, B Hedman, M Murata, KO Hodgson, HC Freeman. Phase determination by multiple-wavelength X-ray-diffraction - crystal-structure of a basic blue copper protein from cucumbers. SCIENCE, 241(4867):806–811, AUG 12 1988. WA Hendrickson, A Pahler, JL Smith, Y Satow, EA Merritt, RP Phizackerley. Crystal structure of core streptavidin determined from multiwavelength anomalous diffraction of synchrotron radiation. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 86(7):2190–2194, APR 1989. On the other hand, David and Lilo Templeton continued to use the term anomalous dispersion for at least another decade, describing their diffraction experiments exploring polarization effects and other characteristics of near-edge X-ray scattering by elements all over the periodic table. Ethan Cheers -- Ian On 18 January 2012 18:23, Phil Jeffrey pjeff...@princeton.edu wrote: Can I be dogmatic about this ? Multiwavelength anomalous diffraction from Hendrickson (1991) Science Vol. 254 no. 5028 pp. 51-58 Multiwavelength anomalous diffraction (MAD) from the CCP4 proceedings http://www.ccp4.ac.uk/courses/proceedings/1997/j_smith/main.html Multi-wavelength anomalous-diffraction (MAD) from Terwilliger Acta Cryst. (1994). D50, 11-16 etc. I don't see where the problem lies: a SAD experiment is a single wavelength experiment where you are using the anomalous/dispersive signals for phasing a MAD experiment is a multiple wavelength version of SAD. Hopefully one picks an appropriate range of wavelengths for whatever complex case one has. One can have SAD and MAD datasets that exploit anomalous/dispersive signals from multiple difference sources. This after all is one of the things that SHARP is particularly good at accommodating. If you're not using the anomalous/dispersive signals for phasing, you're collecting native data. After all C,N,O,S etc all have a small anomalous signal at all wavelengths, and metalloproteins usually have even larger signals so the mere presence of a theoretical d difference does not make it a SAD dataset. ALL datasets contain some anomalous/dispersive signals, most of the time way down in the noise. Phil Jeffrey Princeton On 1/18/12 12:48 PM, Francis E Reyes wrote: Using the terms 'MAD' and 'SAD' have always been confusing to me when considering more complex phasing cases. What happens if you have intrinsic Zn's, collect a 3wvl experiment and then derivatize it with SeMet or a heavy atom? Or the MAD+native scenario (SHARP) ? Instead of using MAD/SAD nomenclature I favor explicitly stating whether dispersive/anomalous/isomorphous differences (and what heavy atoms for each ) were used in phasing. Aren't analyzing the differences (independent of source) the important bit anyway? F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder
Re: [ccp4bb] MAD
On Jan 19, 2012, at 10:05 PM, Dale Tronrud wrote: ... If someone wrote in their paper the Rossmann method was used to solve this structure what method would come to mind? The American method of course! Place the crystal in the beam, allow the autoindexing routine to find the crystal orientation (here the American method stops however), then continue to process the data. Then take a sphere, do MR, and phase extend using NCS and solvent flattening. My previous message, as well as this one, was intended to be a joke (kind of). Sincerely, Petr P.S. Dale, I am sorry you are likely to receive this message twice... Dale Tronrud On 1/19/2012 12:51 PM, Petr Leiman wrote: It would be so much more convenient to call these techniques (MAD, SAD, etc.) by their inventor's name. This would simplify things immensely simultaneously eliminating CCP4BB MADisagreements. Although in our days of copyrights wars, the journals and perhaps conferences where these methods were presented for the first time would insist on using their names as part of the method's name... Petr On Jan 19, 2012, at 7:42 PM, Ethan Merritt wrote: On Thursday, 19 January 2012, Ian Tickle wrote: So what does this have to do with the MAD acronym? I think it stemmed from a visit by Wayne Hendrickson to Birkbeck in London some time around 1990: he was invited by Tom Blundell to give a lecture on his MAD experiments. At that time Wayne called it multi-wavelength anomalous dispersion. Tom pointed out that this was really a misnomer for the reasons I've elucidated above. Wayne liked the MAD acronym and wanted to keep it so he needed a replacement term starting with D and diffraction was the obvious choice, and if you look at the literature from then on Wayne at least consistently called it multi-wavelength anomalous diffraction. Ian: The change-over from dispersion to diffraction in MAD protein crystallography happened a couple of years earlier, at least with regard to work being done at SSRL. I think the last paper using the term dispersion was the 1988 Lamprey hemoglobin paper. The next two papers, one a collaboration with Wayne's group and the other a collaboration with Hans Freeman's group, used the term diffraction. WA Hendrickson, JL Smith, RP Phizackerley, EA Merritt. Crystallographic structure-analysis of lamprey hemoglobin from anomalous dispersion of synchrotron radiation. PROTEINS-STRUCTURE FUNCTION AND GENETICS, 4(2):77–88, 1988. JM Guss, EA Merritt, RP Phizackerley, B Hedman, M Murata, KO Hodgson, HC Freeman. Phase determination by multiple-wavelength X-ray-diffraction - crystal-structure of a basic blue copper protein from cucumbers. SCIENCE, 241(4867):806–811, AUG 12 1988. WA Hendrickson, A Pahler, JL Smith, Y Satow, EA Merritt, RP Phizackerley. Crystal structure of core streptavidin determined from multiwavelength anomalous diffraction of synchrotron radiation. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 86(7):2190–2194, APR 1989. On the other hand, David and Lilo Templeton continued to use the term anomalous dispersion for at least another decade, describing their diffraction experiments exploring polarization effects and other characteristics of near-edge X-ray scattering by elements all over the periodic table. Ethan Cheers -- Ian On 18 January 2012 18:23, Phil Jeffreypjeff...@princeton.edu wrote: Can I be dogmatic about this ? Multiwavelength anomalous diffraction from Hendrickson (1991) Science Vol. 254 no. 5028 pp. 51-58 Multiwavelength anomalous diffraction (MAD) from the CCP4 proceedings http://www.ccp4.ac.uk/courses/proceedings/1997/j_smith/main.html Multi-wavelength anomalous-diffraction (MAD) from Terwilliger Acta Cryst. (1994). D50, 11-16 etc. I don't see where the problem lies: a SAD experiment is a single wavelength experiment where you are using the anomalous/dispersive signals for phasing a MAD experiment is a multiple wavelength version of SAD. Hopefully one picks an appropriate range of wavelengths for whatever complex case one has. One can have SAD and MAD datasets that exploit anomalous/dispersive signals from multiple difference sources. This after all is one of the things that SHARP is particularly good at accommodating. If you're not using the anomalous/dispersive signals for phasing, you're collecting native data. After all C,N,O,S etc all have a small anomalous signal at all wavelengths, and metalloproteins usually have even larger signals so the mere presence of a theoretical d difference does not make it a SAD dataset. ALL datasets contain some anomalous/dispersive signals, most of the time way down in the noise. Phil Jeffrey Princeton On 1/18/12 12:48 PM, Francis E Reyes wrote: Using the terms 'MAD' and 'SAD' have always been confusing to me when considering more complex phasing cases
Re: [ccp4bb] Efficient way of showing residue conservation
Dear Bostjan, There is Chimera for almost anything you can think of. Search for Structure-Based Sequence Alignment on this page: http://www.cgl.ucsf.edu/chimera/features.html Petr On Dec 8, 2011, at 6:39 AM, Bostjan Kobe wrote: Consurf will do this for you. Bostjan --- Bostjan Kobe NHMRC Research Fellow Professor of Structural Biology School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience (Division of Chemistry and Structural Biology) and Centre for Infectious Disease Research Cooper Road University of Queensland Brisbane, Queensland 4072 Australia Phone: +61 7 3365 2132 Fax: +61 7 3365 4699 E-mail: b.k...@uq.edu.au URL: http://www.scmb.uq.edu.au/staff/bostjan-kobe Office: Building 76 Room 329 Notice: If you receive this e-mail by mistake, please notify me, and do not make any use of its contents. I do not waive any privilege, confidentiality or copyright associated with it. Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland. On 8/12/11 3:26 PM, Yuri Pompeu yuri.pom...@ufl.edu wrote: I once saw a figure showing the protein as surface, but instead of having it coloured by atom type or potential, it was shown by percent conservation in the family. Something like red highly conserved, all the way to white, not conserved at all... Now, I assume the figure was done by uploading aligned sequnces of several members of a family, and the colouring the generated surface accordingly. Does anyone know a way to do this more elegantly than what I tried doing? ps. I quit colouring them manually after I remebered my protein was 407 aa long...
Re: [ccp4bb] Efficient way of showing residue conservation
Do I feel stupid! My previous message about Chimera should have been addresses to Yuri Pompeu, but not to Bostjan Kobe. Sincerely, Petr On Dec 8, 2011, at 6:26 AM, Yuri Pompeu wrote: I once saw a figure showing the protein as surface, but instead of having it coloured by atom type or potential, it was shown by percent conservation in the family. Something like red highly conserved, all the way to white, not conserved at all... Now, I assume the figure was done by uploading aligned sequnces of several members of a family, and the colouring the generated surface accordingly. Does anyone know a way to do this more elegantly than what I tried doing? ps. I quit colouring them manually after I remebered my protein was 407 aa long...
Re: [ccp4bb] better way to post your density snapshots
herman.schreu...@sanofi.com wrote: I am not sure that sending links is the way to go. Our company blocks many websites that it considers not of professionel interest and were employees may spend too much time. What a brilliant idea! If only this could be implemented in academia. Our Ph.D. students would stop asking stupid questions on this BB but instead read books and journal articles. Yes, everything except PDB, sciencedirect, webofscience, pubmed and arxiv (this one is for real science geeks) must be blocked! Petr -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Mark J van Raaij Sent: Thursday, December 08, 2011 4:50 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] better way to post your density snapshots posting these attachments as links rather than attachments in CCP4bb messages is the way to go I think. many institutions offer this service (ours does), and there are also free and for-pay online ways to do this (for example www.yousendit.com, but there are many others). Then it is also not a problem to send (sorry, link) even large files. The only disadvantage I can think of is that they expire after some time. Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/content/research/macromolecular/mvraaij On 8 Dec 2011, at 16:39, Ed Pozharski wrote: Colleagues, One recurring question on this bb is I got this blob of density - is it my ligand or what in the name of pink unicorns this is? Often, a screen snapshot is posted, which is very helpful. But it may be better if those helping out could rotate density around in 3D. Understandably, posting the full model/map is not the way to go. However, I'd see no harm in posting just a small cutout of the map in the region of interest. It's not a difficult task (fft/mapmask or perhaps some usf magic), but is there some user-friendly approach to cutting out a small map volume? One can use coot to mask the map and then export it, but this seems to generate the ccp4-formatted map that covers more than just the masked region, thus the files are fairly large. Does anyone know of a simple solution other than placing dummy atoms in the region of interest and running fft/mapmask combination? (Is there phenix.cut_the_map_around_this_weird_blob ? :) Cheers, Ed. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] better way to post your density snapshots
For the second time today I have to apologize. In no way I wanted to discourage anyone and especially people new to crystallography from posting questions to this BB. Especially good thoughtful questions. Sincerely, Petr On Dec 8, 2011, at 5:24 PM, Petr Leiman wrote: herman.schreu...@sanofi.com wrote: I am not sure that sending links is the way to go. Our company blocks many websites that it considers not of professionel interest and were employees may spend too much time. What a brilliant idea! If only this could be implemented in academia. Our Ph.D. students would stop asking stupid questions on this BB but instead read books and journal articles. Yes, everything except PDB, sciencedirect, webofscience, pubmed and arxiv (this one is for real science geeks) must be blocked! Petr -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Mark J van Raaij Sent: Thursday, December 08, 2011 4:50 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] better way to post your density snapshots posting these attachments as links rather than attachments in CCP4bb messages is the way to go I think. many institutions offer this service (ours does), and there are also free and for-pay online ways to do this (for example www.yousendit.com, but there are many others). Then it is also not a problem to send (sorry, link) even large files. The only disadvantage I can think of is that they expire after some time. Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/content/research/macromolecular/mvraaij On 8 Dec 2011, at 16:39, Ed Pozharski wrote: Colleagues, One recurring question on this bb is I got this blob of density - is it my ligand or what in the name of pink unicorns this is? Often, a screen snapshot is posted, which is very helpful. But it may be better if those helping out could rotate density around in 3D. Understandably, posting the full model/map is not the way to go. However, I'd see no harm in posting just a small cutout of the map in the region of interest. It's not a difficult task (fft/mapmask or perhaps some usf magic), but is there some user-friendly approach to cutting out a small map volume? One can use coot to mask the map and then export it, but this seems to generate the ccp4-formatted map that covers more than just the masked region, thus the files are fairly large. Does anyone know of a simple solution other than placing dummy atoms in the region of interest and running fft/mapmask combination? (Is there phenix.cut_the_map_around_this_weird_blob ? :) Cheers, Ed. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] PHENIX vs REFMAC refinement had me fooled
Dear Tim, I agree with you completely. The question then becomes why does the automatic weighting scheme in refmac allow R and R-free to run away from each other by 8% in a 1.1 A resolution structure? Petr On Dec 8, 2011, at 6:50 PM, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Christopher, if your R/Rfree from Refmac5 really are 10% vs. 18%, you might simply be looking at an electron density map with strong model bias, i.e. the map shows the features of the model and not of the data. Although at 1.1A resolution this seems quite unlikely, but that's what might explain this great gap between R and Rfree. Tim On 12/08/2011 06:36 PM, Christopher Browning wrote: Dear All, Question: Has anybody ever refined the same structure using PHENIX and then tried REFMAC to see what happens? I did and I stumbled on something funny. I'm refining a structure at 1.1A resolution which was solved with Iodine phasing using PHENIX AutoSolve. Got a great map and the structure was built almost completely. I had to build a few residues myself, and using the published sequence, I started filling in the residues, but as I came nearer the N-terminus, it looked like the density did not match residues from the sequence. I kept the residues as in the sequence, but as you can see from the PHENIX refined picture (below is the link) it still looks like the amino acid sequence in the crystal does not match the published protein sequence. Out of interest I refined the same file in REFMAC, and now the electron density is correct, and the sequence of the amino acids in the crystal matches the published sequence (see link for picture below). Not only that. my R/Rfree improved (16.5/19 for PHENIX, 10/18 for REFMAC). I've also refined the occupancies of the iodide, however the the output FO-FC map from PHENIX complains and the REFMAC map is fine. How can this be and what causes this? Link for the pictures: Both maps are at identical Sigma levels in both pictures. PHENIX: http://dl.dropbox.com/u/51868657/PHENIX_refined.png REFMAC: http://dl.dropbox.com/u/51868657/REFMAC_refined.png Cheers, Chris Browning - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFO4PjgUxlJ7aRr7hoRAszXAKCNmTZvCVaDUm6v3lQjp051H+ilDgCgxd1l as9CcWEseq9uEV8qMZsOfsg= =KKUr -END PGP SIGNATURE-
Re: [ccp4bb] off-topic: Topology diagram
That lmgtfy.com is as almost as cool as HHpred. Thanks for a very useful piece of information! Petr On Nov 3, 2011, at 2:06 PM, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Zhang Qi, I like this url: http://www.lmgtfy.com/?q=topology+diagram+protein which quickly takes you to e.g. pdbsum. Tim On 11/03/2011 01:48 PM, lysudiezhang1985 wrote: Dear all Does anyone know what tools can get a topology diagram ? Thanks! Zhang Qi lysudiezhang1985 via foxmail - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFOspHrUxlJ7aRr7hoRAl96AJ96OykVMr0a68Xm5HtvJ4ifvkUbPgCcDqP2 ru9oCeO1ZG0u++KJMCnrivs= =trrx -END PGP SIGNATURE-
[ccp4bb] phaser 2.3.0 floating point exception
Dear Randy and the Phaser team, Phaser 2.3.0 brought us several enhancement, but similar to Alexander Schiffer's experience, Phaser has failed several times now with a floating point exception error at different stages of automated MR: it has stopped in the beginning of RF and then in a new run it stopped in the middle of TF. The remedy is to explicitly lower the resolution of the input data (that was a 1.2 A resolution data with a smallish unit cell). I can provide the log files and the mtz file if necessary. Sincerely, Petr --- Petr Leiman EPFL IPSB-LBBS BSP-415 CH-1015 Lausanne, Suisse http://lbbs.epfl.ch
[ccp4bb] Denzo/HKL2000 for Pilatus 6M detector
Dear all, What is the status of Denzo/HKL2000 availability/support for the Pilatus 6M detector? Thank you, Petr
Re: [ccp4bb] generate large symmetry model
Apologies for suggesting a non-CCP4 solution, but UCSF Chimera can do that and more (interactively!): Tools - Higher Order Structure - Unit cell Petr On Jun 30, 2011, at 2:52 PM, Hargreaves, David wrote: Does anyone have a rigorous method (or script) for generating an extended lattice e.g 3x3x3 unit cells from any pdb file? Any help gratefully received, Dave David Hargreaves Associate Principal Scientist _ AstraZeneca DECS, CPSS Mereside, 50F49, Alderley Park, Cheshire, SK10 4TF Tel +44 (0)01625 518521 Fax +44 (0) 1625 232693 David.Hargreaves @astrazeneca.com Please consider the environment before printing this e-mail AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking compliance with our Code of Conduct and policies.
Re: [ccp4bb] Nanodrop versus Nanophotomter Pearl versus good old Bradford.
Totally support the statements below. We have had several proteins with A280 absorbance of 0.1 or less (at 1 mg/ml). You _have_ to use Bradford in the Nanodrop or whatnot to measure the concentration. Before purchasing the Nanodrop we used a Hellma TrayCell and a normal UV/Vis instrument. Similar to the Nanodrop, the sample volume in TrayCell is 2-3 ul. Traycell works well at a fraction of the Nanodrop cost, but Nanodrop is a lot more convenient to use for high concentration quick measurements (especially if you need to measure several things in succession), so you get what you pay for. Petr P.S. Expasy's Protparam tool has been around for ages (10-12+ years?). That plus the Nanodrop are two essential and synergetic tools of a protein chemist/crystallographer. On Jun 16, 2011, at 10:31 PM, Edward A. Berry wrote: Bradford is an assay, Nanodrop is a spectrophotometer. Both the A280 and Bradford methods are strongly dependent on amino acid composition, so unless you correct A280 for that as mentioned by Filip, either one is semiquantitative. Occasionally you come across a protein with no tryptophan which will have a much lower extinction coefficient. Try making a 1 g/l solution of gelatin (collagen?) and see what its A280 is! I noticed recently the protparam tool at http://ca.expasy.org/cgi-bin/protparam estimates the extinction coefficient given a sequence. David Briggs wrote: ~~~ I wouldn't touch Bradford with a barge-pole. I've found it to be wildly inaccurate for certain proteins I've handled, where as the OD280 measurements have been fine. One wonders what does fine mean, like same as with Biuret or Kjeldahl nitrogen, or solution made up by weight?
Re: [ccp4bb] Femtosecond Electron Beam
Jacob We should not be comparing the Xray and electron beam fluxes in terms of particle density as the scattering cross sections are very different. I have to admit I did not see the number you are quoting, which is very low. One needs 20-30 electrons per A^2 to acheive 3A resolution. Presumably the beam can be focused to this density at the specimen plane, but I do not know for sure. Fabrizio Carbone has just sent me his latest estimates for the numbers we are discussing. But let's do as Colin suggested and discuss this further off the board and post a summary later. Cheers, Petr Sent from my iPhone On 15 Apr 2011, at 03:40, Jacob Keller j- kell...@fsm.northwestern.edu wrote: One of the figures they cite is 2.5 electrons per um^2, which I think means once the whole bunch has gone through. That struck me as being pretty far from where one needs to be to get structures. Do you know off hand a comparable figure for the FEL experiment? I assume it would be many orders of magnitude greater. For example, how many total photons were in each bunch with the FEL? JPK On Thu, Apr 14, 2011 at 5:24 PM, Colin Nave colin.n...@diamond.ac.uk wrote: Petr Well, not sure - are we doing imaging or diffraction/scattering? What energy are the electrons in these sources? The idea of pulsed sources is to put more electrons/A^2 and still beat radiation damage. Can one do this when there are only around 10^6 electrons in perhaps a rather divergent beam? Shall we discuss off line (with Jacob) and present our conclusions when/if we get agreement? Regards Colin -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Petr Leiman Sent: 14 April 2011 22:59 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Femtosecond Electron Beam Colin, We know that with a dose of 20-30 electrons per A^2, a lot of image processing, and insane amount of luck, one can reconstruct cryoEM images to 3 A resolution or better. A typical protein molecule is say 100 A in diameter, which is ~8000 A^2 in projection. So, in an ideal case one needs only 240,000 electrons to record an image of a protein molecule with a signal extending to 3A resolution. Jacob, Yes, you are correct. Jom et al. manipulate electron bunches of 1+ Mln electrons, which should be enough to record an image of a protein molecule. Best, Petr On Apr 14, 2011, at 11:13 PM, Colin Nave wrote: Petr Yes, I saw the figure. Similar ones appear in the Hastings et. al. paper (the SLAC one I referenced). They use a much higher energy beam to get the short pulse length. I still believe the issues are 1. For diffraction, can you get a low enough electron beam divergence to resolve larger unit cells? The peaks appear rather broad in the foil experiments. Luiten et. al. believe they can extend the technique to resolve cells of a few tens of nm which would be fine. Their ideas for doing this appear to be quite novel. I don't know if they have demonstrated this though. 2. Given the above, will there be enough electrons in one of the short pulses to get enough statistics for a biological molecule or protein nano-crystal? I have not seen calculations for this for electron beams (as has been done for the FEL x-ray beams). Actually it should be quite easy to do as the cross sections are all available. 3. For imaging (i.e. using an objective lens) is the blurring I mention going to be a fundamental limitation and what will this limitation be? These instruments would be useful for material science applications and fast chemistry investigations where some of the above issues would not be relevant. Not sure for imaging biological molecules. We will see. Finally saying Phys Rev Let is not a high impact journal would probably upset my physicist colleagues - that's fine though! Regards Colin -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Petr Leiman Sent: 14 April 2011 21:07 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Femtosecond Electron Beam Dear Colin and all interested in the FEL development. Please look at the figures in the first link I mentioned. Jom Luiten et al. are able to record a 1.25 A resolution diffraction pattern of a gold foil using a pulse compressed to 50 fs. Ahmed Zewail is a pioneer of the technique but as far as I know his instrumentation is nowhere near Jom's amazing machine. Why Jom's paper was not published in one of the high profile journals, ahem, magazines, is a mystery to me. Petr On Apr 14, 2011, at 9:11 PM, Colin Nave wrote: Petr has provided the Eindhoven links. For more details on fast electron imaging (as opposed to diffraction) see https://e-reports-ext.llnl.gov/pdf/343044.pdf Apparently stochastic scattering of the electrons at the high current densities necessary for short pulsed sources result
Re: [ccp4bb] Femtosecond Electron Beam
People are looking into how to fit the old retired MeV microscopes with pulsed electron guns (problem is there are very few of those beasts left). If this works, such a machine will produce equivalent results to FEL but at a fraction of the cost. The group at Eindhoven, which Colin had mentioned, has already made a significant progress in achieving both time and spatial coherence. They are able to manipulate electrons in ultrashort electron bunches akin to spins in an NMR machine: http://prl.aps.org/abstract/PRL/v105/i26/e264801 http://jap.aip.org/resource/1/japiau/v109/i3/p033302_s1 And this is due to the fact that electrons can be focused with lenses. Amazing stuff. We will hear more about this for sure. Sincerely, Petr From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Colin Nave [colin.n...@diamond.ac.uk] Sent: Thursday, April 14, 2011 16:50 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Femtosecond Electron Beam Jacob Very good question. People are considering this sort of thing. See for example http://www-spires.slac.stanford.edu/cgi-wrap/getdoc/slac-pub-12162.pdf Due to coulomb explosion one normally needs MeV beams to get the short bunch length. MeV beams also give a more reasonable penetration depth (not relevant for single molecules). I think the problem is that the divergence is too high to resolve diffraction spots from protein crystals (or in other words insufficient coherence). Probably fine for many small molecule crystals though. You mentioned single molecules, presumably protein molecules and I think the same would apply if trying to observe the scattering. One could try imaging (i.e. with an electron lens) rather than do diffraction. I presume this is what you mean by focussed to solve the phase problem. However, I understand that there are problems with this as well for MeV beams but I can't remember the exact details. Can look it up if you are interested. There could of course be technical advances which would make some of these ideas possible. I think a group at Eindhoven have plans to get round some of the problems. Again I would have to look up the details. Regards Colin -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob Keller Sent: 14 April 2011 14:39 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Femtosecond Electron Beam Dear Crystallographers, is there any reason why we are not considering using super-intense femtosecond electron bursts, instead of photons? Since the scattering of electrons is much more efficient, and because they can be focussed to solve the phase problem, it seems that it might be worthwhile to explore that route of single-molecule structure solution by using electrospray techniques similar to the recently-reported results using the FEL. Is there some technical limitation which would hinder this possibility? JPK -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Femtosecond Electron Beam
Dear Colin and all interested in the FEL development. Please look at the figures in the first link I mentioned. Jom Luiten et al. are able to record a 1.25 A resolution diffraction pattern of a gold foil using a pulse compressed to 50 fs. Ahmed Zewail is a pioneer of the technique but as far as I know his instrumentation is nowhere near Jom's amazing machine. Why Jom's paper was not published in one of the high profile journals, ahem, magazines, is a mystery to me. Petr On Apr 14, 2011, at 9:11 PM, Colin Nave wrote: Petr has provided the Eindhoven links. For more details on fast electron imaging (as opposed to diffraction) see https://e-reports-ext.llnl.gov/pdf/343044.pdf Apparently stochastic scattering of the electrons at the high current densities necessary for short pulsed sources result in blurring in the image. The paper says that 10nm spatial and 10ps temporal resolution could be achieved with 5MeV electrons and annular dark field imaging. Of course more recent developments at Eindhoven and elsewhere might get round some of the limitations. Colin -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Petr Leiman Sent: 14 April 2011 16:23 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Femtosecond Electron Beam People are looking into how to fit the old retired MeV microscopes with pulsed electron guns (problem is there are very few of those beasts left). If this works, such a machine will produce equivalent results to FEL but at a fraction of the cost. The group at Eindhoven, which Colin had mentioned, has already made a significant progress in achieving both time and spatial coherence. They are able to manipulate electrons in ultrashort electron bunches akin to spins in an NMR machine: http://prl.aps.org/abstract/PRL/v105/i26/e264801 http://jap.aip.org/resource/1/japiau/v109/i3/p033302_s1 And this is due to the fact that electrons can be focused with lenses. Amazing stuff. We will hear more about this for sure. Sincerely, Petr From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Colin Nave [colin.n...@diamond.ac.uk] Sent: Thursday, April 14, 2011 16:50 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Femtosecond Electron Beam Jacob Very good question. People are considering this sort of thing. See for example http://www-spires.slac.stanford.edu/cgi-wrap/getdoc/slac-pub-12162.pdf Due to coulomb explosion one normally needs MeV beams to get the short bunch length. MeV beams also give a more reasonable penetration depth (not relevant for single molecules). I think the problem is that the divergence is too high to resolve diffraction spots from protein crystals (or in other words insufficient coherence). Probably fine for many small molecule crystals though. You mentioned single molecules, presumably protein molecules and I think the same would apply if trying to observe the scattering. One could try imaging (i.e. with an electron lens) rather than do diffraction. I presume this is what you mean by focussed to solve the phase problem. However, I understand that there are problems with this as well for MeV beams but I can't remember the exact details. Can look it up if you are interested. There could of course be technical advances which would make some of these ideas possible. I think a group at Eindhoven have plans to get round some of the problems. Again I would have to look up the details. Regards Colin -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob Keller Sent: 14 April 2011 14:39 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Femtosecond Electron Beam Dear Crystallographers, is there any reason why we are not considering using super-intense femtosecond electron bursts, instead of photons? Since the scattering of electrons is much more efficient, and because they can be focussed to solve the phase problem, it seems that it might be worthwhile to explore that route of single-molecule structure solution by using electrospray techniques similar to the recently-reported results using the FEL. Is there some technical limitation which would hinder this possibility? JPK -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Femtosecond Electron Beam
Colin, We know that with a dose of 20-30 electrons per A^2, a lot of image processing, and insane amount of luck, one can reconstruct cryoEM images to 3 A resolution or better. A typical protein molecule is say 100 A in diameter, which is ~8000 A^2 in projection. So, in an ideal case one needs only 240,000 electrons to record an image of a protein molecule with a signal extending to 3A resolution. Jacob, Yes, you are correct. Jom et al. manipulate electron bunches of 1+ Mln electrons, which should be enough to record an image of a protein molecule. Best, Petr On Apr 14, 2011, at 11:13 PM, Colin Nave wrote: Petr Yes, I saw the figure. Similar ones appear in the Hastings et. al. paper (the SLAC one I referenced). They use a much higher energy beam to get the short pulse length. I still believe the issues are 1. For diffraction, can you get a low enough electron beam divergence to resolve larger unit cells? The peaks appear rather broad in the foil experiments. Luiten et. al. believe they can extend the technique to resolve cells of a few tens of nm which would be fine. Their ideas for doing this appear to be quite novel. I don't know if they have demonstrated this though. 2. Given the above, will there be enough electrons in one of the short pulses to get enough statistics for a biological molecule or protein nano-crystal? I have not seen calculations for this for electron beams (as has been done for the FEL x-ray beams). Actually it should be quite easy to do as the cross sections are all available. 3. For imaging (i.e. using an objective lens) is the blurring I mention going to be a fundamental limitation and what will this limitation be? These instruments would be useful for material science applications and fast chemistry investigations where some of the above issues would not be relevant. Not sure for imaging biological molecules. We will see. Finally saying Phys Rev Let is not a high impact journal would probably upset my physicist colleagues - that's fine though! Regards Colin -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Petr Leiman Sent: 14 April 2011 21:07 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Femtosecond Electron Beam Dear Colin and all interested in the FEL development. Please look at the figures in the first link I mentioned. Jom Luiten et al. are able to record a 1.25 A resolution diffraction pattern of a gold foil using a pulse compressed to 50 fs. Ahmed Zewail is a pioneer of the technique but as far as I know his instrumentation is nowhere near Jom's amazing machine. Why Jom's paper was not published in one of the high profile journals, ahem, magazines, is a mystery to me. Petr On Apr 14, 2011, at 9:11 PM, Colin Nave wrote: Petr has provided the Eindhoven links. For more details on fast electron imaging (as opposed to diffraction) see https://e-reports-ext.llnl.gov/pdf/343044.pdf Apparently stochastic scattering of the electrons at the high current densities necessary for short pulsed sources result in blurring in the image. The paper says that 10nm spatial and 10ps temporal resolution could be achieved with 5MeV electrons and annular dark field imaging. Of course more recent developments at Eindhoven and elsewhere might get round some of the limitations. Colin -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Petr Leiman Sent: 14 April 2011 16:23 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Femtosecond Electron Beam People are looking into how to fit the old retired MeV microscopes with pulsed electron guns (problem is there are very few of those beasts left). If this works, such a machine will produce equivalent results to FEL but at a fraction of the cost. The group at Eindhoven, which Colin had mentioned, has already made a significant progress in achieving both time and spatial coherence. They are able to manipulate electrons in ultrashort electron bunches akin to spins in an NMR machine: http://prl.aps.org/abstract/PRL/v105/i26/e264801 http://jap.aip.org/resource/1/japiau/v109/i3/p033302_s1 And this is due to the fact that electrons can be focused with lenses. Amazing stuff. We will hear more about this for sure. Sincerely, Petr From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Colin Nave [colin.n...@diamond.ac.uk] Sent: Thursday, April 14, 2011 16:50 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Femtosecond Electron Beam Jacob Very good question. People are considering this sort of thing. See for example http://www-spires.slac.stanford.edu/cgi-wrap/getdoc/slac-pub- 12162.pdf Due to coulomb explosion one normally needs MeV beams to get the short bunch length. MeV beams also give a more reasonable penetration depth (not relevant for single
Re: [ccp4bb] Question about movie making
Hi Mark, What about UCSF Chimera? Very easy to use. http://www.cgl.ucsf.edu/chimera/tutorials/movies08/moviemaking.html More on the topic: http://www.cgl.ucsf.edu/chimera/animations/animations.html Check out the Nuclear pores movie. Amazing stuff. A few years back one had to pay huge $$$ for Maya to make something like that. And the script to make that movie is only 6-7 lines (they removed it from the webpage for some reason). Chimera comes packaged with ffmpeg, which is an alternative to mencoder, and, by default, you won't even see the frames before they become the final product - your movie in the format and quality of your choice. Petr From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of mjvdwo...@netscape.net [mjvdwo...@netscape.net] Sent: Monday, March 07, 2011 22:21 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Question about movie making All, Pardon the slightly off-topic question. We would like to use Pymol and generate movies with it on a WINDOWS computer. We are very familiar with Pymol and how to make the correct views etc. We write the individual frames out into PNG files. So what is left to do, is to stitch together the PNG images to an MPEG file. On Linux you could do this with mencoder. But we would like to do this on Windows and installing mencoder on windows is possible but not easy. We have found videomach, which costs a very small amount of money to obtain. Similarly, Adobe Premiere is affordable for an educational institution. We don't mind paying, but before we go there, does anyone have experience with making MPEG movies from PNG files on windows? What is your experience with quality of product and especially with user friendliness? If you have any insight, we would appreciate your comments. Thanks! Mark van der Woerd Colorado State University
Re: [ccp4bb] linux flavors
Another vote for Ubuntu. I have to say that a Live CD version is not a good test of this excellent Linux distro. We have 3 identical PCs. On two of these the latest version of 10.10 64bit live cd loads to a blank (completely black) screen. Google: blank screen ubuntu live cd - thankfully there is a remedy that works. A few month old 10.10 64bit live cd works fine on all of three machines (?!) But once the system is installed it runs fine (automatic updates, etc). The documentation is good and there is something useful written on any problem I've seen so far. The native ubuntu nvidia/nouveau driver problem (what a stupid headache!) is solved in 10.10 (the current version) and one can enjoy fully automated kernel upgrades, which include building a new nvidia kernel module automatically. Cheers, Petr Sent from my iPhone On 22 Feb 2011, at 16:29, Roger Rowlett rrowl...@colgate.edumailto:rrowl...@colgate.edu wrote: I switched from FC8 to Ubuntu 9.04 a few years ago. Ubuntu worked with all of my hardware and peripherals out of the box, even newish motherboards, and I had fewer issues with WINE compatibility for CrysalisPro a WIndows-based X-ray data processing program for our Oxford Diffraction instrument. Ubuntu 10.04 LTS is even better, and I'm scheduling an upgrade of my workstations this summer. Ubuntu will install NVidia drivers for you through a GUI setting with automatic updates, or you can do it manually, too. Each distro has its own specific headaches. For FC, it was SELinux and a few other random driver and package issues, for Ubuntu it's other things, but I'm finding Ubuntu less problematic at the moment for the stuff I want to run. Cheers. On 2/22/2011 10:16 AM, David Roberts wrote: Hello all, Quick question on linux varieties. For years (and years) I have used fedora (after Ultrix of course). In fact, most of my computers are running FC7 (that long ago), it's very stable and works fine. However, since it is no longer supported, I'm toying with upgrading. I upgraded one machine to FC13. However, this nouveau driver thing is killing me, and getting my nvidia drivers installed is hopeless (I have followed every thread on this and I simply give up - it's not worth it). With a Zalman monitor it doesn't matter - nouveau works fine and my stereo is good - so I don't really care (or do I). The question is this - what flavors of linux out there are simplest to install - work instantly with various hardwares, and run stereo seamlessly (either Zalman stereo or hardware stereo with an emitter). For zalman anything works - which is why I'm going that way - but I still need hardware stereo on a few machines. So, for hardware, I need my nvidia drivers to install easily. I'm downloading ubuntu - is that a good choice? Can I run different flavors of linux with nfs and share drives in a local network (so one has fc7, one has fc13, and another has ubuntu)? Thanks Dave -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: mailto:rrowl...@colgate.edu rrowl...@colgate.edumailto:rrowl...@colgate.edu
[ccp4bb] Slightly off topic: Winter school announcement
Dear All, I hope that students and Postdocs reading this board will be interested in attending the doctoral school, which will take place in Crans-Montana on February 14-20, 2010. We were able to bring in great speakers from different 'domains' of structural biology and biophysics, which usually do not come to the same meetings. http://ipsb.epfl.ch/page82072.html There are two lectures in the morning, free afternoon, and discussion of the morning lectures in the evening: http://ipsb.epfl.ch/page82075.html The cost: A two person room costs 170-200 CHF per night. The food costs 50-65 CHF per day. The registration deadline: October 31, 2009 http://ipsb.epfl.ch/page82078.html Sincerely, Petr - Petr Leiman Head of the Laboratory of Structural Biology and Biophysics Institut de physique des systèmes biologiques École Polytechnique Fédérale de Lausanne (EPFL) Cubotron/BSP-415 CH-1015 Lausanne Switzerland Phone: +41 21 69 30441 Mobile: +41 79 538 7647 Fax:+41 21 69 30422
Re: [ccp4bb] temperature after 30 minutes using microscopes ?
Dear Jürgen, Unless you have to spend your money on a microscope immedeately, it is best to evaluate demo instruments from different vendors on site at the same time. All vendors will give you a demo instrument for a few hours to several days. The new Olympus LED instruments are excellent on paper, brighter than the halogen lamps, and produce virtually no heat detectable by hand. However, the new LED-containing base produces a diffuse light on the sample, compared to the focused beam of the old halogen lamp bases. In my opinion, the performance of the LED-containing base is the same or better of a halogen lamp-containing base in the highly oblique and dark field modes. In the bright field mode, the diffuse illumination of the LED base results in flattening of the object. Perhaps, our Olympus demo instrument (with a LED base) had flaws, but it performed worse than an older generation Nikon instrument (halogen lamp) with an objective of a smaller aperture. Petr - Petr Leiman École Polytechnique Fédérale de Lausanne (EPFL) Cubotron/BSP-415 CH-1015 Lausanne Switzerland - Original Message - From: Jürgen Bosch jubo...@jhsph.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, January 21, 2009 11:50 PM Subject: [ccp4bb] temperature after 30 minutes using microscopes ? Hi there, *warning, reading beyond this line might expose you to non CCP4 related topics* anybody out there who could do the following experiment: Turn on your microscope and measure the temperature after 30 minutes where you would place your precious crystal tray. In particular I'm interested in LED versus Halogen driven models. Is there anybody out there who would like to comment on LED driven microscopes for our purposes ? Thanks, Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Biochemistry and Molecular Biology, W8708 615 North Wolfe Street Baltimore, MD 21205 Phone: +1-410-614-4742 Fax: +1-410-955-3655
[ccp4bb] arp/warp 7.0.1 and ccp4i
Hello all, While testing a newly installed ARP/wARP interface (ver. 7.0.1) in ccp4i (ver. 6.1.0) on Ubuntu (8.10) I noticed that the Fobs and Sigma pull-down menus are missing from the ARP/wARP Quick Fold window. This is accompanied by the following error message, which is output in stderr by the ccp4i interface: ERROR CreateLabinLine: unrecognised argument -fileout To remedy this problem one has to edit the warp_albe.tcl file, which is located in $CCP4/ccp4i/tasks directory. Line 325 -fileout XYZOUT DIR_XYZOUT _helices_ has to be removed. All the best, Petr
[ccp4bb] Postdoctoral position in Michael Rossmann's laboratory
A post-doctoral position is available (in the department of Biological Sciences, Purdue University, Indiana 47907, USA) for structural studies of viruses and their interaction with host cells. Applicants should have experience in virus or protein crystallography and in molecular biology. Experience in electron microscopy would also be useful. Please send applications to Michael Rossmann ([EMAIL PROTECTED]).
[ccp4bb] Ph.D. student and Postdoctoral positions in Structural Biology/Biophysics at the Swiss Federal Institute of Technology in Lausanne (EPFL)
PH.D. STUDENT AND POSTDOCTORAL POSITIONS IN STRUCTURAL BIOLOGY/BIOPHYSICS AT THE SWISS FEDERAL INSTITUTE OF TECHNOLOGY IN LAUSANNE (EPFL) Ph.D. students and Postdocs are sought to study the structure and function of the bacterial type VI secretion machine, pyocins and encapsulated bacteria-specific bacteriophages using X-ray crystallography, electron microscopy and other biophysical techniques as well as utilizing basic microbiology. Due to the high interest of the field, the type VI secretion system and the pyocins projects are very competitive and require full dedication of the participants. In return, the candidates will be offered excellent salaries. The Swiss salary scale for graduate students and Postdocs surpasses that of any country in the world. PH.D. STUDENTS: M.S. or equivalent degree in physics, biophysics, chemistry or biological sciences is required. Depending on the background and the student's choice of Ph.D. program, the students will be affiliated with either the School of Basic Sciences (physics, chemistry or math) or the School of Life Sciences (biological sciences). Please, refer to the EPFL graduate school website (http://phd.epfl.ch/) for a complete list of Ph.D. program requirements. POSTDOCS: Ideally, a candidate should be capable of taking a gene and determining the structure of the corresponding gene product using either X-ray crystallography or electron microscopy, although individuals with training in any aspects of structural biology, biophysics or biochemistry are encouraged to apply. The positions are available starting October 1st, 2008. Applicants are invited to send a CV and a letter of motivation describing research experience, interests and key accomplishments, and contact information of two to four referees to Dr. Petr Leiman at 915 W. State St., Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA, or via email at [EMAIL PROTECTED]
[ccp4bb] Postdoctoral job in the laboratory of Michael Rossmann
On behalf of Michael Rossmann: A post-doctoral position is available in a virus structure laboratory. Applicants should have experience in computer program development or adaptation for crystallography or electron microscopy. Please e-mail applications to Michael Rossmann, [EMAIL PROTECTED] (Dept of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA).
Re: [ccp4bb] Fwd: [ccp4bb] crystallisation and mosaicity
yes you are right, but I assumed if people see a cloud of condensed fog over their LN2 bath they should remove that by a) filling up the bowl completely e.g. some LN2 drips out of the bowl b) blow the fog away before you dip I think the original poster meant the relatively low heat conduction of liquid N2, which causes boiling around the crystal immediately after plunging. The best way to freeze things is to put a small container of liquid ethane or propane into a liquid N2 bowl, and plunge into the ethane/propane (this methods was suggested earlier). Petr
Re: [ccp4bb] def file for restraining dna and long helices
Dear Raja, Do you seriously believe that you will find help on this board after making us all download your 2 * 4.1 MB of crap NOT RELATED TO CCP4??? Good luck in your future endeavors! Petr - Original Message - From: Raja Dey [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Sent: Thursday, April 10, 2008 4:12 PM Subject: [ccp4bb] def file for restraining dna and long helices Sorry for re-posting --this time with subject Hi All, I am sure there are some experienced persons who can help me to check what’s wrong is going with my def file I used in anneal.inp I attached the def and out file. I am trying to restrain the dna (4 chains K, L, D, E) via Watson-Crick base pair and two long helices(A and B) via H-bond in my structure. Any suggestion is well appreciated. Regrards... Raja Meet people who discuss and share your passions. Go to http://in.promos.yahoo.com/groups/bestofyahoo/
Re: [ccp4bb] The importance of USING our validation tools
- Original Message - From: Jenny Martin [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Sent: Thursday, August 23, 2007 5:46 PM Subject: Re: [ccp4bb] The importance of USING our validation tools My question is, how could crystals with 80% or more solvent diffract so well? The best of the three is 1.9A resolution with I/sigI 48 (top shell 2.5). My experience is that such crystals diffract very weakly. You must be thinking about Mark van Raaij's T4 short tail fibre structures. Yes, the disorder in those crystals is extreme. There are ~100-150 A thick disordered layers between the ~200 A thick layers of ordered structure. The diffraction pattern does not show any anomalies (as far as I can remember from 6 years ago). The spots are round, there are virtually no spots not covered by predictions, and the crystals diffract to 1.5A resolution. The disordered layers are perpendicular to the threefold axis of the crystal. The molecule is a trimer and sits on the threefold axis. It appears that the ordered layers somehow know how to position themselves across the disordered layers. I agree here with Michael Rossmann that in these crystals the ordered layers are held together by faith. Mark integrated the dataset in lower space groups, but the disordered stuff was not visible anyway. He will probably add more to the discussion. Petr Any thoughts? Cheers, Jenny
Re: [ccp4bb] Movie for Powerpoint in windows
I just found this old thread in my CCP4 folder. 1. mencoder can convert pymol's quicktime format movies into avi movies. 2. Powerpoint movie handling is beyond ancient and sometimes AVI movies can be played in MS mediaplayer but Powerpoint would not play them. The remedy is to use good-sized frames, i.e. the frame height and width should be divisible by 2, or, better, 4, or, even better, 8. 3. If your images produced using 24bit colors it is unwise to make movies via 8bit animated gifs, unless your images contain only a few basic colors. 4. Perhaps, the original poster can put up a few of his frames on a webserver for download and I (we) can take a look at what is wrong with them. Regards, Petr Quoting Ibrahim M. Moustafa [EMAIL PROTECTED]: Hi all, I'm trying to make a movie for a powerpoint presentation but going through some problems. I can make the frames in Pymol, so I have the series of .png files; no problem in that. The problem is to get a movie (.avi) so it can be inserted into the powerpoint. Googling showed a nice thread in ccp4bb and it is really helpful; but still can't make what I want exactly. I can make a movie.mov which can be played by Quicktime or realplayer; however, I don't like the way of playing the movie using other program during the presentation! I want the movie to play in the same slide, the case when you insert a movie, which can be played by the windows media player, into the powerpoint. Making the movie using the windows movie maker is not nice (slow, sluggish!may be there are ways to make it nicer! which I dunno!). Then I installed Mencoder and issued the command: mencoder mf://*.png type=png -o output.avi -ovc lavc -lavcopts vcodec=msmpeg4v2:vbitrate=9000 I tried various vcodec= values. I still unable to insert the .avi into the powerpoint. Windows media player cannot open the file either! I think there is something missing here!! I'd be appreciated if anyone can share his/her experience in making a movie that will play as part of the slide in the powerpoint on a PC laptop. P.S. I know that there might be other ways and a lot of options like CCP4mg..etc. But I don't want to spend time making the figures again. I already have the figures done in Pymol. thanks for your help in advance. thanks, Ibrhaim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., Uinversity Park Pennsylvania State University, PA16802 Tel. (814)863-8703 Fax. (814)865-7927 --
