Re: [ccp4bb] problem in transformation of pqe 30 clone
Hi, I only read the topic this morning - In some cases, I have to wait 30+ hours to see colonies when I transform BL21 DE3 Star while normally they should appear after 14 hours. Dianfan ar...@xtals.org wrote: Hello In order to know *exactly* what the reason for poor transformation outcome was one has to do all sorts of experiments. This is not likely to be your goal, right? Leaky expression, overload of DNA, somehow compromised cells, or even plain old user error - and numerous other reasons can be proposed (including some esoteric ones like incompatibility of your gene product with a specific strain, for reasons going beyond protocol errors and simple considerations). This can take a couple of years to sort out. If you're talking about using M15[pREP4] cells then the reason why you failed earlier is likely to be toxicity - pREP4 plasmid supplies lacI in-trans, which represses 'stray' transcription reasonably well. The cells that you used before and did not succeed with must have had low intrinsic levels of lacI and thus permitted leakage. To test this theory you could streak a couple of colonies of the M15[pREP4] cells on a plate that has a small amount of IPTG in the agar (say 0.1 mM) - if the colonies don't grow at all, or appear to be very tiny then you know it's your protein toxicity that's the issue here. Keep in mind that bacteria are extremely survival-oriented and therefore you will eventually generate 'safe' mutants and recombinants that will be able to grow even on IPTG. Likely those mutants will be useless to you from practical standpoint. Once you induce the M15[pREP4] cells - the toxicity will manifest itself again. You will likely observe total cessation of growth (for a long period of time) and possibly even lysis of the culture. Therefore you may have to adjust your fermentation protocol to take this into account. One of the common adjustments is deliberate induction at higher OD, another is to include 0.8% glucose in the growth medium; there are other options available to you. Hopefully once you induce transcription, the gene products do not shut down protein synthesis - which would be a disaster since it would likely shut down its own synthesis as well. Since I don't know what you're growing, this is just one of the possibilities :) Artem now i have transformed pqe 30 clone into the m15 host successfully, can someone let me know exactly what was reason behind the problem into transformation??is it leaky expression into the other host that is toxic for the cells,if it so then will i would be able to get good expression into this host??? atul -Original Message- From: CCP4 bulletin board on behalf of ar...@xtals.org Sent: Tue 5/5/2009 6:24 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] problem in transformation of pqe 30 clone To clarify: I am not implying that I've worked with many proteins that express better in XL1-blue cells than they would express in BL21(DE3) or such if cloned into a pET vector or similar. In fact I can probably recall only one or two that expressed *better* in XL1 cells. However in the good old days pQE series of vectors was quite commonly used and I had things in that were inherited from others - these 'things' were fairly simple to express in XL1-blue whereas they gave me loads of trouble in other strains and I was too busy/lazy to re-clone them. Artem Hello Artem, We express almost all our proteins in BL21 derivatives. It sounds like you've worked with many proteins that express/behave better in XL1-Blue? ho UC Berkeley - XL1-Blue is a strain of E. coli. Whether it is or isn't an expression host depends on the definition, and I am not going to argue semantics. The T5 promoter works with regular garden variety RNApol of E. coli. Therefore ANY E. coli strain is an 'expression host' for vectors that contain this promoter. I've expressed many proteins in XL1-Blue and I see no reason why you can't express yours, either. Artem
Re: [ccp4bb] heavy atom derivative choice
David Briggs schrieb: Bart Hazes used to have an excellent set of notes online about heavy atom derivatisation - I can't seem to find the URL right now... I believe the CCP4 wiki has the information that you're looking for (at http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Soaking_with_heavy_atoms ) Now if people would add their notes to the wiki that would actually become an even better ressource ... Unfortunately it seems that Bart Hazes' webpage cannot currently be accessed, and the cache results do no longer seem to appear in my Google searches! best, Kay -- Kay Diederichshttp://strucbio.biologie.uni-konstanz.de email: kay.diederi...@uni-konstanz.deTel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature smime.p7s. smime.p7s Description: S/MIME Cryptographic Signature
[ccp4bb] NCCR Symposium on New Trends in Structural Biology / NCCR Practical Course on Biomolecular Modelling
Dear colleagues, we have two announcements to make: _ 7th International NCCR Symposium on New Trends in Structural Biology 7 + 8 September 2009, ETH Zürich, Lecture Hall HG E7, Zürich, Switzerland www.structuralbiology.uzh.ch/symposium2009 The lecture program is available online at: http://www.structuralbiology.uzh.ch/symposium2009/program.asp Plenary lecturers: Frédéric Allain, Pietro de Camilli, Raimund Dutzler, Arthur L. Horwich, Brian Kobilka, Harry Noller, Anna Marie Pyle, Ben Schuler, David Wemmer, Masasuke Yoshida Online registration to this event is still possible through the symposium homepage or directly at: http://www.structuralbiology.uzh.ch/symposium2009/registration09.asp _ 8th NCCR Practical Course and 2nd Winter School Biomolecular Modelling The 8th NCCR Practical Course will cover key topics in the area of computational structural biology. The course format includes morning lectures by experts in the field that alternate with later afternoon to evening tutorials and discussions. The course will be organized as a winter retreat in the Swiss alps offering participants the opportunity to learn in a stimulating atmosphere, enjoy winter activities in the swiss alps during course breaks, and network and exchange ideas on an informal basis with fellow participants, tutors, and lecturers. More information at http://www.structuralbiology.uzh.ch/course2010.asp Online Application will be possible as of July 31, 2009 _ Please do not hesitate to contact me anytime if you need further information (stic...@bioc.uzh.ch). With best regards, Patrick Sticher The NCCR Structural Biology is a research initiative of the Swiss Science Foundation. Its research encompasses the fields of recombinant protein technologies, macromolecular structure determination and computational biomolecular sciences with a special focus on membrane proteins and supramolecular assemblies/interactions. 13 research groups from Swiss Universities and Research Institutions participate in this network. www.structuralbiology.uzh.ch/ -- _ Visit the NCCR on the Internet www.structuralbiology.uzh.ch Dr. Patrick Sticher Moser NCCR Scientific Officer Institute of Biochemistry University of Zürich Winterthurerstrasse 190 CH - 8057 Zürich Phone +41 / (0)44 / 635 54 84 Fax +41 / (0)44 / 635 59 08 Mailstic...@bioc.uzh.ch
[ccp4bb] Postdoc Position at EMBL Grenoble
The Schaffitzel laboratory at the European Molecular Biology Laboratory (EMBL) Grenoble, France seeks to recruit an outstanding postdoctoral scientist in structural biology with a research focus directed towards the structure of macromolecular assemblies. The major theme within the group is structure and function of ribosomal complexes, co-translational targeting and translocation (Schaffitzel et al., Nature 2006; Mitra, Schaffitzel et al., Nature 2005; Kohler et al., Mol.Cell 2009). More information: http://www.embl.fr/research/unit/schaffitzel/index.html This position requires a Ph.D. in biochemistry or a related field, with a strong background in protein biochemistry. Applicant should have experience in guiding structure determination projects from start to finish, experience in expressing and purifying membrane proteins and/or electron microscopy would be advantageous. The candidate should be a highly motivated individual who enjoys working as part of a collaborative and multidisciplinary team. The laboratory is well-situated in a structural biology environment at the Polygone Scientifique in Grenoble. End of 2009, we will be equipped with a state-of-the-art electron microscope (Polara, FEI). Access to modern biophysical instrumentation (analytical ultracentrifugation, surface Plasmon resonance, dynamic light scattering, isothermal calorimetry, CD spectrometer) is provided. The position is available from January 2010 and funded for 2 years. It may be extended dependent on performance. To apply please send your CV, a statement of research interests, and names (including email address) of at least two referees by email to Dr. Christiane Schaffitzel (schaffit...@embl.fr mailto:schaffit...@embl.fr). Applications will be accepted until the position is filled.
[ccp4bb] Keystroke changes on Coot
I obtained Coot using Fink, and I'm on a MacBook Pro running OS 10.5.7. I've found that in Coot, but in no other programs, my keystrokes are altered. Space bar unzooms, 2 reads r, and delete returns a ,. Downloading from William Scott's webpage didn't help. Any suggestions? -Sarah _ Windows Live™ SkyDrive™: Get 25 GB of free online storage. http://windowslive.com/online/skydrive?ocid=TXT_TAGLM_WL_SD_25GB_062009
Re: [ccp4bb] Keystroke changes on Coot
I had this problem earlier in the week. Apparently it's recently become an issue. I found the answer here http://www.techsupportforum.com/alternative-computing/mac-support/389812-x1 1-keyboard-map-messed-up.html Briefly, there seems to be a problem with they keyboard mapping in X11. You probably see the same thing in other X11 programs like CCP4. If you delete /usr/X11/share/X11/xkb the problem should go away. Good luck, Mike Michael S. Murray, Ph.D. National Institute of Environmental Health Sciences MD E3-01 P.O. Box 12233 Research Triangle Park, NC 27709 Phone: (919) 541-0268 On 7/17/09 11:06 AM, sharotka godzina sgodz...@hotmail.com wrote: I obtained Coot using Fink, and I'm on a MacBook Pro running OS 10.5.7. I've found that in Coot, but in no other programs, my keystrokes are altered. Space bar unzooms, 2 reads r, and delete returns a ,. Downloading from William Scott's webpage didn't help. Any suggestions? -Sarah Windows Live SkyDrive: Get 25 GB of free online storage. Get it on your BlackBerry or iPhone. http://windowslive.com/online/skydrive?ocid=TXT_TAGLM_WL_SD_25GB_062009
Re: [ccp4bb] OpenGL Stereo 3D on 120 Hz LCDs, at last!
Warren, Do you have a link to the beta drivers? On Fri, Jul 17, 2009 at 1:20 AM, Warren DeLano war...@delsci.com wrote: FYI, for folks not subscribed to pymol-users: nVidia today released beta drivers which at last enable OpenGL-based stereo 3D visualization on 120 Hz LCDs using Quadro graphics cards. So long as you are willing to put up with Windows, you can finally abandon those old CRTs without spending a fortune and without sacrificing quality of the stereo 3D effect. Details posted at http://www.pymol.org Cheers, Warren -- Jim Fairman Graduate Research Assistant Department of Biochemistry, Cellular, and Molecular Biology (BCMB) University of Tennessee -- Knoxville 216-368-3337 jfair...@utk.edu james.fair...@case.edu
[ccp4bb] Scalepack error model?
Does anyone know of a detailed rigorous discussion of how the scalepack error model/Bayesian reasoning works? The scalepack manual has no equations for this. Richard Gillilan MacCHESS
[ccp4bb] What is a Macromolecular Complex? Amsterdam, 1-2 October 2009
Dear all, The EU FP7 programs SPINE-2-Complexes, 3d-Repertoire and TEACH-SH are organizing a joined workshop about: What is a Macromolecular Complex? As the subtitle implies, we want to look at the Shades of Meaning across Cellular, Systems and Structural Biology. We have what we believe that is an excellent collection of speakers, Philippe Bastiaens (Dortmund), Gianni Cesareni (Rome) Elena Conti (Martinsried), Stephen Cusack (Grenoble), Jan Ellenberg (Heidelberg),Toby Gibson (Heidelberg), Christina Kiel (Barcelona),Andreas Ladurner (Heidelberg), Ohad Medalia (Beer-Sheva), Dino Moras (Illkirch) Andrea Musacchio (Milano), Laurence Pearl (London), Bertrand Seraphin (Gif-sur-Yvette) Holger Stark (Gottingen), Ulrich Stelzl (Berlin), Dave Stuart (Oxford), Peter Tompa (Budapest), The exact talks will travel across many scientific subjects covering cell, molecular, structural, computation and systems biology, and we hope to put together a lively and useful two-day workshop, that will help to shape interests, interactions, and approaches for the future. The workshop will take two days, 1-2 October, will take place in Amsterdam with all its cultural amenities, and is free for everybody to attend, following registration. Any such workshop would be nothing without keen and lively participants, so we invite you to have a look at http://xtal.nki.nl/Oct2009 for details on the program, dates, etc and - we hope - to register soon! Last but not least, our Dutch readers, should check the note about the Protein Facility opening event in the morning of the 1st of October. best regards, Stephen Cusack Andrea Musacchio Carlo Petosa Anastassis Perrakis
[ccp4bb] EPMR statistics
Dear ALL: We are trying to do a molecular replacement using EPMR. IT is weird that we got high CC(0.56) but with high R factor about 0.89 as well. How can we optimize our EPMR trials to get a definitive correct solutions? Thanks a lot for the help. Have a nice weekend! Jerry McCully _ Lauren found her dream laptop. Find the PC that’s right for you. http://www.microsoft.com/windows/choosepc/?ocid=ftp_val_wl_290
Re: [ccp4bb] Scalepack error model?
Described in: Borek, D., Minor, W. Otwinowski, Z. (2003) Measurement errors and their consequences in protein crystallography. Acta Cryst. D59: 2031-2038. http://scripts.iucr.org/cgi-bin/paper?ba5035 (open access) or http://bones.swmed.edu/pdf/7_Borek_et_al_ActaCrystD_2003_D59_2031-2038%5B1%5D.pdf Dominika Does anyone know of a detailed rigorous discussion of how the scalepack error model/Bayesian reasoning works? The scalepack manual has no equations for this. -- Dominika Borek UT Southwestern Medical Center 5323 Harry Hines Boulevard Room ND10.214 Dallas, Texas 75390-8816 phone: +1 214-645-6378 fax: +1 214-645-6353 domin...@work.swmed.edu
Re: [ccp4bb] Scalepack error model?
Dear Richard, I *think* it works like this, don't know if it's detailed or rigourous enough for you! If I(l,h,i) is the intensity of the ith observation of reflection h on frame l, with error sig(l,h,i), and S(l) is the (inverse) scale factor to be applied to frame l, then the error in the scaled intensity I(l,h,l)/S(l) is parameterised in terms of the error scale factor (E1) and estimated error (E2) as sqrt( (E1*sig(l,h,i))**2 + (E2*I(h)*S(l))**2 ) where I(h) is the weighted mean of the scaled intensity values for index h (i.e. the merged, scaled intensity). The reasoning behind this that the errors in the intensities of strong and weak reflections generally arise from different sources. Weak data are noisy, whilst very strong data can often be systematically badly measured, especially in DENZO, which assumes that all your spots are the same size and shape, or overloaded. E1 and E2 thus tend to dominate the error model at high and low resolutions, respectively. Hope that helps, Joe Does anyone know of a detailed rigorous discussion of how the scalepack error model/Bayesian reasoning works? The scalepack manual has no equations for this. Richard Gillilan MacCHESS
Re: [ccp4bb] Scalepack error model?
Dear Richard, I *think* it works like this, don't know if it's detailed or rigourous enough for you! If I(l,h,i) is the intensity of the ith observation of reflection h on frame l, with error sig(l,h,i), and S(l) is the (inverse) scale factor to be applied to frame l, then the error in the scaled intensity I(l,h,l)/S(l) is parameterised in terms of the error scale factor (E1) and estimated error (E2) as sqrt( (E1*sig(l,h,i))**2 + (E2*I(h)*S(l))**2 ) where I(h) is the weighted mean of the scaled intensity values for index h (i.e. the merged, scaled intensity). The reasoning behind this that the errors in the intensities of strong and weak reflections generally arise from different sources. Weak data are noisy, whilst very strong data can often be systematically badly measured (especially in DENZO, which assumes that all your spots are the same size and shape) or overloaded. E1 and E2 thus tend to dominate the error model at high and low resolutions, respectively. Hope that helps, Joe Does anyone know of a detailed rigorous discussion of how the scalepack error model/Bayesian reasoning works? The scalepack manual has no equations for this. Richard Gillilan MacCHESS
Re: [ccp4bb] MAD wavelength
Use the scan. And yes, don't fry your crystal doing it. The best way to do this is put the fluorescence detector as close to the sample as you can and then optimize the count rate by attenuating the beam. However, some beamlines are set up to hit your crystal with full beam and then back off the fluorescence detector to the other side of the room where it can bask in the warm sunny glow of your precious crystal. On beamlines like this, you must use a sacrificial crystal to do your absorption scan. Obviously, I am not a fan of the latter method, but it really does depend on what beamline you are going to use. Ask your beamline scientist about this! Note: technically, a MAD scan is not a fluorescence scan, it is an absorption scan. You are measuring absorption and using fluorescence as a tally. A fluorescence scan would have the fluorescent photon energy on the x-axis. Unfortunately, methods of doing absorption scans are not the only thing that differs from beamline to beamline and wavelength calibration is notoriously difficult to do with an accuracy of five decimal places (1 eV in 12 keV). Personally, I calibrate on copper metal, since it is very stable and well understood, and the absolute Bragg angle I see from silicon powder gives me a consistent wavelength. Some beamlines calibrate on SeMet, but the problem with SeMet is that the actual energy of the edge is NOT the canonical Se edge found in the literature (it is about 1 eV higher). SeMet is also relatively toxic, expensive and tends to oxidize, shifting the peak. Probably the best example of the shifting edge of Se I know of is figure 1 in Sarret et. al. (2005) Applied and Environmental Microbiology, 71(5), 2331–2337. This paper contains spectra for nine Se-containing reference compound, a substantial fraction of the total that are known. Because of all this, I have been pushing the use of dandruff shampoo as an internationally recognized, inexpensive and particularly rad-hard selenium reference. Selsun Blue(R) (and the extra strength variety of Head Shoulders(R)) is 1% selenium sulfide, and gives a nice clear spectrum with a sharp white line. What remains is to calibrate this stuff against some NIST-traceable Standard Reference Material. So, my advice is to ask your beamline scientist, and don't forget to pack shampoo. -James Holton MAD Scientist Jerry McCully wrote: Dear All: Next week we are going to try some seleno-Met labeled crystals. We checked the literature to try to find out the peak wavelength that has been used for SAD or MAD data collection. But they are slightly different ( may be 50 ev) in different papers. I guess this is due to the discrepancy between the fluorescence scanning and the theoretical vaules of f' and f''. When we collect the data, which wavelength should we use? Should we trust the scanning results? Thanks a lot for your comments. All the best, Jerry McCully Insert movie times and more without leaving Hotmail®. See how. http://windowslive.com/Tutorial/Hotmail/QuickAdd?ocid=TXT_TAGLM_WL_HM_Tutorial_QuickAdd_062009
[ccp4bb] FPLC price
Hi everyone, I forgot to mention the price in the advertisement for the FPLC. We are asking $11,000 CAD for the system. Thanks, Natalie Roy
[ccp4bb] FW: EPMR statistics
Dear ALL: We are trying to do a molecular replacement using EPMR. IT is weird that we got high CC(0.58) but with high R factor about 0.89 as well. The second tier of solutions have cc about 0.54 and R factor about 0.95. How can we optimize our EPMR trials to get a definitive correct solutions? Thanks a lot for the help. Have a nice weekend! Jerry McCully Lauren found her dream laptop. Find the PC that’s right for you. _ Lauren found her dream laptop. Find the PC that’s right for you. http://www.microsoft.com/windows/choosepc/?ocid=ftp_val_wl_290
Re: [ccp4bb] Scalepack error model?
Thanks Joe and others. Bits and pieces of this story appear in 11.4.8 of International Tables volume F, Borek et. al. Acta Cryst D59 (2003) and the Scalepack manual, but none are complete or have enough detail to follow easily. None of them give the expression for Chi-square for this problem. I found a presentation by Jay Ponder online (for his Bio5325 course) that gives: chi-2 = 1/N sum (I_avg - I_meas)^2/(sigma_avg^2 + sigma_meas^2) where the sum probably runs over all reflections and the I_avg is the average of the appropriate group of symmetry-related reflections. Sigma_avg^2 should be the sigma computed from the error model below (not given in the presentation) I think and sigma_meas is the sigma^2 from the actual symmetry-related reflections. One would then adjust the error parameters below to give chi-square approx unity and this leads to the proper scaling factors for intensities and sigmas. One confusing hitch seems to be that (according to the International Tables F Eqs.(11.4.8.5) and (11.4.8.6)), the error model is also implicitly defined and must be solved iteratively ... though it's hard to see that from the text. Does this sound right? Richard On Jul 17, 2009, at 4:12 PM, cockb...@pasteur.fr wrote: Dear Richard, I *think* it works like this, don't know if it's detailed or rigourous enough for you! If I(l,h,i) is the intensity of the ith observation of reflection h on frame l, with error sig(l,h,i), and S(l) is the (inverse) scale factor to be applied to frame l, then the error in the scaled intensity I(l,h,l)/S(l) is parameterised in terms of the error scale factor (E1) and estimated error (E2) as sqrt( (E1*sig(l,h,i))**2 + (E2*I(h)*S(l))**2 ) where I(h) is the weighted mean of the scaled intensity values for index h (i.e. the merged, scaled intensity). The reasoning behind this that the errors in the intensities of strong and weak reflections generally arise from different sources. Weak data are noisy, whilst very strong data can often be systematically badly measured, especially in DENZO, which assumes that all your spots are the same size and shape, or overloaded. E1 and E2 thus tend to dominate the error model at high and low resolutions, respectively. Hope that helps, Joe Does anyone know of a detailed rigorous discussion of how the scalepack error model/Bayesian reasoning works? The scalepack manual has no equations for this. Richard Gillilan MacCHESS
Re: [ccp4bb] Scalepack error model?
The scalepack log file gives the formula: Summary of reflections intensities and R-factors by intensity bins R linear = SUM ( ABS(I - I)) / SUM (I) R square = SUM ( (I - I) ** 2) / SUM (I ** 2) Chi**2 = SUM ( (I - I) ** 2) / (Error ** 2 * N / (N-1) ) ) which equivalent to the Jay Ponder's formula, with the important addition, that sigma_avg and Iavg represent the average of all _other_ measurements with the same reduced hkl index. All sigmas are calculated from the error model described in the publications. Some of the error model parameters are defined at the moment by user, they can be refined iteratively by experimenter by adjusting parameters in subsequent runs of scalepack, but most of the time it is not required. New version will adjust all these parameters automatically. Zbyszek Otwinowski Richard Gillilan wrote: Thanks Joe and others. Bits and pieces of this story appear in 11.4.8 of International Tables volume F, Borek et. al. Acta Cryst D59 (2003) and the Scalepack manual, but none are complete or have enough detail to follow easily. None of them give the expression for Chi-square for this problem. I found a presentation by Jay Ponder online (for his Bio5325 course) that gives: chi-2 = 1/N sum (I_avg - I_meas)^2/(sigma_avg^2 + sigma_meas^2) where the sum probably runs over all reflections and the I_avg is the average of the appropriate group of symmetry-related reflections. Sigma_avg^2 should be the sigma computed from the error model below (not given in the presentation) I think and sigma_meas is the sigma^2 from the actual symmetry-related reflections. One would then adjust the error parameters below to give chi-square approx unity and this leads to the proper scaling factors for intensities and sigmas. One confusing hitch seems to be that (according to the International Tables F Eqs.(11.4.8.5) and (11.4.8.6)), the error model is also implicitly defined and must be solved iteratively ... though it's hard to see that from the text. Does this sound right? Richard -- Zbyszek Otwinowski UT Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, TX 75390-8816 (214) 645 6385 (phone) (214) 645 6353 (fax) zbys...@work.swmed.edu
Re: [ccp4bb] EPMR statistics
Here are the solutions from 100 runs(sorry for the long list). Would you please help to have a look? Thanks a million.---Jerry Soln 1 Rot= 162.63 98.47 303.11 Trn= 26.48 73.35 105.32 CC= 0.452 R= 0.996 Soln 1 Rot= 111.26 104.75 41.63 Trn= 31.00 24.66 69.53 CC= 0.528 R= 0.961 Soln 2 Rot= 157.54 79.66 260.98 Trn= -14.86 57.85 124.36 CC= 0.513 R= 0.971 Soln 3 Rot= 113.99 91.61 264.87 Trn= 8.06 72.05 53.61 CC= 0.521 R= 0.946 Soln 4 Rot= 337.86 88.06 347.72 Trn= 4.17 75.16 127.45 CC= 0.520 R= 0.952 Soln 5 Rot= 146.81 78.67 75.86 Trn= 56.22 44.05 11.76 CC= 0.546 R= 0.941 Soln 6 Rot= 342.38 80.29 240.59 Trn= 73.71 6.92 85.48 CC= 0.582 R= 0.898 Soln 7 Rot= 321.28 101.88 329.83 Trn= 54.31 64.44 33.42 CC= 0.522 R= 0.967 Soln 8 Rot= 145.15 68.35 63.18 Trn= 73.90 11.90 91.09 CC= 0.545 R= 0.954 Soln 9 Rot= 162.94 101.78 301.17 Trn= -20.34 47.14 1.30 CC= 0.584 R= 0.892 Soln 10 Rot= 166.24 100.33 183.82 Trn= 5.93 64.49 55.04 CC= 0.537 R= 0.957 Soln 11 Rot= 333.36 94.38 303.46 Trn= 63.94 20.82 127.15 CC= 0.519 R= 0.953 Soln 12 Rot= 175.81 92.62 162.15 Trn= 48.20 37.76 12.37 CC= 0.514 R= 0.946 Soln 13 Rot= 359.03 57.14 234.96 Trn= -20.66 77.65 47.22 CC= 0.530 R= 0.949 Soln 14 Rot= 167.05 107.92 178.90 Trn= -32.85 65.33 96.19 CC= 0.545 R= 0.966 Soln 15 Rot= 350.98 29.83 44.82 Trn= -8.10 37.94 120.78 CC= 0.524 R= 0.957 Soln 16 Rot= 184.84 105.40 18.14 Trn= 67.66 39.49 14.13 CC= 0.509 R= 0.968 Soln 17 Rot= 304.53 52.96 238.53 Trn= 80.59 0.16 92.24 CC= 0.497 R= 0.967 Soln 18 Rot= 339.71 89.20 120.35 Trn= 64.77 13.44 83.29 CC= 0.514 R= 0.952 Soln 19 Rot= 166.17 97.98 319.60 Trn= -4.93 26.33 113.33 CC= 0.500 R= 0.972 Soln 20 Rot= 177.36 85.10 285.88 Trn= 56.63 20.33 12.66 CC= 0.520 R= 0.951 Soln 21 Rot= 336.13 92.27 305.89 Trn= 17.47 5.71 76.03 CC= 0.517 R= 0.951 Soln 22 Rot= 355.98 68.54 217.40 Trn= -23.88 47.54 120.73 CC= 0.529 R= 0.978 Soln 23 Rot= 291.68 75.51 137.91 Trn= 78.28 2.43 104.53 CC= 0.528 R= 0.960 Soln 24 Rot= 174.44 110.17 202.14 Trn= 52.50 3.31 9.91 CC= 0.534 R= 0.963 Soln 25 Rot= 162.68 100.62 59.90 Trn= 4.23 75.14 1.37 CC= 0.584 R= 0.894 Soln 26 Rot= 312.97 156.01 304.00 Trn= 7.59 32.89 124.82 CC= 0.498 R= 0.979 Soln 27 Rot= 337.74 94.26 42.32 Trn= 3.05 38.15 119.52 CC= 0.516 R= 0.960 Soln 28 Rot= 348.35 72.27 121.56 Trn= 55.07 8.17 77.60 CC= 0.542 R= 0.956 Soln 29 Rot= 343.30 78.23 358.20 Trn= 16.41 14.08 85.72 CC= 0.584 R= 0.890 Soln 30 Rot= 164.24 100.03 60.71 Trn= 51.06 48.06 88.46 CC= 0.581 R= 0.893 Soln 31 Rot= 313.33 42.12 123.12 Trn= 7.97 32.68 38.06 CC= 0.510 R= 0.974 Soln 32 Rot= 343.59 77.50 359.01 Trn= 16.54 68.19 42.23 CC= 0.584 R= 0.891 Soln 33 Rot= 342.42 80.30 240.46 Trn= 26.75 33.91 129.10 CC= 0.583 R= 0.895 Soln 34 Rot= 156.22 80.14 183.92 Trn= 54.43 41.33 11.32 CC= 0.536 R= 0.954 Soln 35 Rot= 159.62 137.49 132.22 Trn= 36.65 77.76 42.97 CC= 0.547 R= 0.946 Soln 36 Rot= 133.66 96.07 124.31 Trn= 32.78 23.18 11.54 CC= 0.521 R= 0.953 Soln 37 Rot= 300.33 86.94 286.01 Trn= 5.94 38.56 119.49 CC= 0.523 R= 0.950 Soln 38 Rot= 348.44 97.82 286.87 Trn= 65.97 43.64 1.05 CC= 0.524 R= 0.969 Soln 39 Rot= 137.08 80.87 328.12 Trn= 57.48 22.76 72.93 CC= 0.526 R= 0.947 Soln 40 Rot= 325.23 108.71 350.80 Trn= -9.07 27.08 45.15 CC= 0.534 R= 0.976 Soln 41 Rot= 164.88 113.78 48.57 Trn= 7.30 17.76 97.19 CC= 0.534 R= 0.954 Soln 42 Rot= 163.27 101.40 61.88 Trn= 4.00 21.22 44.79 CC= 0.584 R= 0.889 Soln 43 Rot= 292.62 133.66 249.87 Trn= -7.95 60.75 120.37 CC= 0.521 R= 0.940 Soln 44 Rot= 129.10 101.25 11.47 Trn= 19.75 46.82 0.67 CC= 0.529 R= 0.955 Soln 45 Rot= 333.46 97.93 119.71 Trn= 30.35 25.72 5.35 CC= 0.532 R= 0.938 Soln 46 Rot= 309.89 70.85 232.67 Trn= 15.98 34.33 69.16 CC= 0.500 R= 0.977 Soln 47 Rot= 347.87 92.61 39.46 Trn= -23.72 66.16 111.17 CC= 0.495 R= 0.990 Soln 48 Rot= 339.04 43.16 48.12 Trn= -10.05 57.51 43.93 CC= 0.547 R= 0.944 Soln 49 Rot= 333.86 146.88 262.49 Trn= 7.25 66.77 0.28 CC= 0.517 R= 0.942 Soln 50 Rot= 342.60 79.23 119.95 Trn= 50.97 60.27 85.66 CC= 0.584 R= 0.892 Soln 51 Rot= 149.45 80.28 75.52 Trn= 9.38 17.13 98.47 CC= 0.540 R= 0.945 Soln 52 Rot= 125.50 117.08 129.59 Trn= 7.97 27.45 48.21 CC= 0.509 R= 0.979 Soln 53 Rot= 162.42 72.13 6.02 Trn= -25.09 63.86 34.82 CC= 0.512 R= 0.957 Soln 54 Rot= 288.85 97.23 302.92 Trn= 32.91 21.23 19.83 CC= 0.527 R= 0.947 Soln 55 Rot= 300.72 87.57 167.67 Trn= 10.58 67.02 119.45 CC= 0.522 R= 0.954 Soln 56 Rot= 343.38 77.62 238.67 Trn= 73.47 7.48 85.75 CC= 0.584 R= 0.890 Soln 57 Rot= 345.98 65.40 118.41 Trn= -9.20 25.75 46.26 CC= 0.511 R= 0.960 Soln 58 Rot= 352.52 87.64 206.73 Trn= 65.26 37.12 127.62 CC= 0.505 R= 0.974 Soln 59 Rot= 295.75 81.01 144.81 Trn= 68.54 38.80 0.98 CC= 0.532 R= 0.954 Soln 60 Rot= 134.83 116.31 94.84 Trn= 66.49 36.90 124.94 CC=
[ccp4bb] Testers needed for RasMol 2.7.5
Testers would be appreciated for the release candidate binary kits for the RasMol 2.7.5 on sourceforge: http://downloads.sf.net/openrasmol/RasWin_2_7_5_Install_17Jul09.exe http://downloads.sf.net/openrasmol/RasMol_2_7_5_i686_Slackware_17Jul09.tar.gz http://downloads.sf.net/openrasmol/RasMol_2_7_5_i386_OSX_17Jul09.tar.gz The source tarball is http://downloads.sf.net/openrasmol/rasmol-2.7.5-17Jul09.tar.gz The manual is available at http://www.bernstein-plus-sons.com/software/RasMol_2.7.5/doc/rasmol.html Further documentation and web pages are in progress.l The MS Windows installer RasWin_2_7_5_Install_17Jul09.exe is run by double-clicking it after download. The Slackware and Intel Mac OSX installers are run by downloading, unpacking, entering the directory and executing rasmol_install.sh --compilefonts The major changes in this release are support for approximation to Lee-Richards surfaces by use of the commands map generate LRsurf mesh map generate LRsurf surface coloring of maps by map color atom and selection of atoms near a map contour by map select atom as well as preliminary support for the SBEVSL record movie making commands http://sbevsl.wiki.sourceforge.net/Movie+Making+Commands Bug reports, comments, correction and suggestions would be appreciated Please report problems to y...@bernstein-plus-sons.com = Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 y...@dowling.edu =
