Re: [ccp4bb] Survey for the CCP4 community study
Dear Eleanor, you are certainly The Queen of the CCP4BB!! Thanks for
infinite patience!
Bob
On Mon, 17 Dec 2018, Eleanor Dodson wrote:
I am an old hand at the BB - I guess I am both a methodoligist (Sp?) and
formerly a software developer.
You can only develop useful software if you continuously liase with users -
it is all too easy to produce a beautiful artefact that no-one either wants
or can use easily. And all too easy to fail to spot the bugs in your
code..The BB has been one of the valuable links between users and
developers, and gives us all a quick and straightforward way to communicate
.
I am proud of the way developers are now putting real effort in to
reporting results, and providing a meaningful analysis of potential
problems. But this sort of online guideance needs user response too - is it
comprehenible? Is it accurate? etc etc.
It will be interesting if you can stimulate debate about these issues.
Thank you
Eleanor Dodson
On Mon, 17 Dec 2018 at 19:01, Robbie Joosten
wrote:
Hi Marie-Hélène,
Thanks for having such a wide 5-20 years category. Keeps me from feeling
really old ;)
I can honestly say that I've learned a lot on the BB and that some of the
discussions have really broadened my knowledge beyond the standard books. I
try to pay it forward whenever I can.
It is wonderful that we have a community where the oldest members are four
times as old as the youngest ones and many people contribute not just
knowledge and insight, but also historical perspective on our long-standing
field.
Cheers,
Robbie
Cheers,
Robbie
On 17 Dec 2018 19:19, LE DU Marie-Hélène <
marie-helene.l...@i2bc.paris-saclay.fr> wrote:
Dear CCP4 users ,
Not only is CCP4 a historical project born to promote the collaborative
development of software dedicated to crystallography, but it has played a
key role in building the biological crystallography community and remains
an international reference and a keystone.
CCP4 also represents a very valuable teaching community through
interactions between newcomers and experts.
Following the French MOOC " Voyage au coeur du vivant avec les rayons X :
la cristallographie." "("A journey I the heart of life with X-ray:
crystallography"), I have initiated an analysis of CCP4 as a teaching
community.
In order to complete this analysis, your contribution would be very
useful. Thank you in advance for completing the following short survey
(5-10 min):
https://docs.google.com/forms/d/1JMP9HISMefYOYDm077VgALrVJWo7vqRuUvhW1wqbk8s/edit
Best regards
*Marie-Hélène Le Du*
*Attention, nouvelles coordonnées :*
CEA/DRF/JOLIOT/I2BC, UMR 9198
Bâtiment 21, Avenue de la Terrasse
91190 Gif-sur-Yvette
France
E-mail : *marie-helene.l...@i2bc.paris-saclay.fr
*
Tel : (33) (0)1 69 82 46 73
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=
Robert M. Sweet E-Dress: sw...@bnl.gov
Deputy Director, LSBR: The Life Science and ^ (that's L
Biomedical Technology Research Center at NSLS-II not 1)
Photon Sciences and Biology Dept
Office and mail, Bldg 745, a.k.a. LOB-5
Brookhaven Nat'l Lab. Phones:
Upton, NY 11973 631 344 3401 (Office)
U.S.A.631 338 7302 (Mobile)
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Re: [ccp4bb] AW: Re: [ccp4bb] Basic Crystallography/Imaging Conundrum
This has been a fascinating thread. Thanks. I will dip my oar in the water. Here are a couple of snippets. Jacob: It was good of proto-crystallographers to invent diffraction as a way to apply Fourier Series. and Ethan: So here's the brain-teaser: Why does Nature use Fourier transforms rather than Wavelet transforms? Or does she? Probably Jacob was joking, but I believe we should say that physicists (and Ms. Nature) employ the Fourier transform/synthesis because this models pretty precisely the way that we believe light rays/waves of all energies interfere with one another. Warm regards, Bob On Fri, 10 Nov 2017, Keller, Jacob wrote: My understanding is that EM people will routinely switch to diffraction mode when they want accurate measurements. You lose the phase information but, since EM lenses tend to have imperfections, you get better measurements of the intensities. Only to my knowledge in the case of crystalline samples like 2D crystals. Of course the loss of phases is a serious problem when you don't have a model of the object as precise as our atomic models. From where does this precision arise, I wonder? I guess priors for atom-based models are pretty invariant. On the other hand, who says that such priors, albeit of many more varieties, don't exist for larger biological samples, such as zebrafish brains and drosophila embryos/larvae? Anyway, right now, the state of the art of modelling in these fluorescence data sets is hand-drawing circles around things that look interesting, hoping the sample does not shift too much, or perhaps using some tracking. But it could be so much better! JPK
[ccp4bb] Please attend a workshop on Measurement and Interpretation of Diffuse Scattering in X-Ray Diffraction for Macromolecular Crystallography
Driven by recent advances in this field we will hold a workshop to discuss it. The workshop will be on Monday, May 15, 2017 at Brookhaven Nat'l Laboratory, and will be affiliated with the 2017 Users' Meeting for NSLS-II and the Center for Functional Nanomaterials. The current draft agenda is on-line here: http://usersmeeting.ps.bnl.gov/workshops/workshop.aspx?year=2017=136 Registration for the Workshop and Users' Meeting is here: http://usersmeeting.ps.bnl.gov/registration/?year=2017 A description of the workshop is below. The Organizers: Robert Sweet (NSLS-II, BNL), Michael Wall (LANL), Nozomi Ando (Princeton University), James S. Fraser (University of California, San Francisco), George N. Phillips, Jr. (Rice University) For answers to questions, please contact Wall: mew...@lanl.gov or Sweet: sw...@bnl.gov Description: X-ray diffraction from macromolecular crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering reflects the mean electron density in the unit cells of the crystal. The diffuse scattering arises from correlations in the variations of electron density that may occur from one unit cell to another, and therefore contains information about collective motions in proteins. A major focus of the workshop will be to provide a roadmap to the acquisition of reliable data by surveying measurement methods and discussing the increase in measurement accuracy enabled by improved detectors, experimental methods, and data integration. Missing from recent results is real information about the behavior of the molecules being studied that would guide the thinking of biochemists and biologists. To discuss these and their relative merits will be a second major focus of the workshop. The charge to this workshop will be to provide a roadmap to efforts that will provide the biological understanding we believe is hidden in the data. = Robert M. Sweet E-Dress: sw...@bnl.gov Deputy Director, LSBR: The Life Science and ^ (that's L Biomedical Technology Research Center at NSLS-II not 1) Photon Sciences and Biology Dept Office and mail, Bldg 745, a.k.a. LOB-5 Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A.631 344 2741 (Facsimile) =
Re: [ccp4bb] Alexander Rich passed away Monday April 27, 2015
I am really sorry to hear this. May his soul rest in peace. With great respect and affection for Alex, I doubt seriously if he will rest in peace. My memory of him as a beamline user was that he was demanding and difficult to satisfy, but in the end grateful for the effort we exerted, and he always had interesting things to study. I suspect that wherever his soul is now he's found something to complain about, and is trying to find someone to improve it. Bob Ranti Dev Shukla, Doctoral fellow, Structural Biology laboratory, Chonnam National University, Gwangju, South Korea. On Wed, Apr 29, 2015 at 7:32 AM, Ho,Shing shing...@colostate.edu wrote: It is with great sadness to announce that Dr. Alexander Rich, Sedgwick Professor of Biophysics at MIT, passed away on Monday April 27, 2015 at Massachusetts General Hospital – he was 90. Alex, a member of the RNA tie club, contributed significantly to our understanding of RNA and DNA structure and function. Scientifically, he was innovative and often controversial. The list of crystallographers and structural biologist who trained in Alex’s lab is long, and of those who’s scientific lives he touched even longer. An obituary for Alex has been posted on the MIT web site ( http://newsoffice.mit.edu/2015/obituary-alexander-rich-dies-90-0428). P. Shing Ho, Ph.D. Professor Chair Biochemistry Molecular Biology 1870 Campus Delivery Colorado State University Fort Collins, CO 80523-1870 970-491-0569 (phone) = Robert M. Sweet E-Dress: sw...@bnl.gov Principal Investigator, LSBR: The Life Science ^ (that's L and Structural Biology Resource at NSLS-II not 1) Photon Sciences and Biosciences Dept Office and mail, Bldg 745, a.k.a. LOB-5 Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A.631 344 2741 (Facsimile) =
[ccp4bb] First-Science Discussions for Life-Science Beamlines at NSLS-II: April 21-22, 2015
We will hold a First Science at the ABBIX Beamlines meeting on Tuesday - Wednesday, April 21-22, 2015, pertaining to the National Institutes of Health (NIH)-sponsored Advanced Beamlines for Biological Investigations with X-rays (ABBIX) Project. These three state-of-the-art beamlines are now under construction at the National Synchrotron Light Source (NSLS)-II facility at Brookhaven National Laboratory (BNL). Two of the beamlines are for macromolecular crystallography (MX), and the third is for life sciences applications of x-ray scattering. Visit this web site for further information and registration materials: http://workshops.ps.bnl.gov/?w=ABBIXApr2015 Briefly, the MX beamline called FMX - Frontier MX - is optimized to address microbeam applications, and the other called AMX - Highly Automated MX - is optimized for highly automated throughput. The scattering beamline called LIX - High Brightness X-Ray Scattering for Life Sciences - will offer multiple modes of study. The MX beamlines view canted undulator sources, and the scattering beamline views a single undulator, providing world-leading brightness. Current plans are to conclude construction by the end of 2015 and start commissioning then. During the commissioning period, opportunities will arise to perform early experiments before the general user programs of the beamlines commence in 2016, and it is the upcoming meeting's purpose to explore and discuss scientific areas and opportunities on which early operation of the beamlines could capitalize. Note: Registration is required. There is no registration fee. Visit this site to register: http://workshops.ps.bnl.gov/?w=ABBIXApr2015 Those who registered for the original meeting planned for January must re-register for the new occurrence in April. Contributed presentations describing experiments that exploit the capabilities of the ABBIX beamlines will be selected from submitted abstracts. The meeting will consist of both plenary and parallel sessions. The plenary session will begin with presentations on science topics in research fields that the beamlines are designed to address, followed by facility presentations to update the community about the early scientific capabilities at the suite of ABBIX beamlines and, in addition, of the Life Science and Biomedical Technology Research Resource (LSBR), sponsored by the NIH and the Department of Energy Office of Biological and Environmental Research (DOE BER). Two parallel sessions on Tuesday afternoon will focus on MX and x-ray scattering, consisting mainly of presentations that will address specific opportunities in these areas. These will be followed by two more parallel sessions on Wednesday morning, also focusing on MX and x-ray scattering, which will include contributions. If you wish to give a contributed presentation during one of the parallel sessions, please submit an abstract here: http://workshops.ps.bnl.gov/abstracts/default.aspx?w=ABBIXApr2015 The parallel sessions are designed to provide forums to facilitate more detailed discussions about potential first experiments at specific beamlines and the formation of the experiment teams. Specifically, each parallel session group will be charged to accomplish these goals: 1. Identify key research projects and the associated first experiments that may be performed at the suite of ABBIX beamlines, emphasizing those projects that will take advantage of NSLS-II properties and ABBIX beamline capabilities. 2. Facilitate the formation of research teams to generate first experiment proposals for submission. 3. Identify key additional team members in such areas as theory and analysis, ancillary measurements, and specimen preparation, needed to achieve the research goals. Confirmed invited speakers: Karen Allen (Boston Univ), Martin Caffrey (Trinity College Dublin), Seth Darst (Rockefeller Univ), Richard Gillilan (Cornell Univ), Wayne Hendrickson (Columbia Univ), AndrHoelz (California Inst Tech), Huey Huang (Rice Univ), Shenping Liu (Pfizer), Lee Makowski (Northeastern Univ), David Ostrov (Univ of Florida), Rebecca Page (Brown Univ), Anna Marie Pyle (Yale Univ), Christian Riekel (ESRF), Thomas Schneider (EMBL-Hamburg), John Tainer (Scripps Research Inst). We would like two outcomes from this meeting: (a) a concise meeting report outlining how ABBIX beamlines will help to address outstanding problems in life sciences, and (b) a list of potential first experiments along with the corresponding research teams. For more information on the meeting, please contact Sonya Kiss, at sk...@bnl.gov. Note: Registration deadline is Tuesday, April 14, 2015. Organizers: Lonny Berman ABBIX Project Manager National Synchrotron Light Source II Brookhaven National Laboratory Sean McSweeney Structural Biology Program Manager Photon Sciences Division Deputy Director National Synchrotron Light Source II
[ccp4bb] Announcement - NSLS-II Early-Science Workshop for NIH-funded beamlines
Sent on behalf of the Workshop Organizing Committee The NIH-funded ABBIX structural biology beamlines at the NSLS-II are approaching completion, delivering two crystallography and one scattering beamline for biological sciences. The performance of these beamlines will present opportunities previously unattainable at synchrotron light sources, creating challenges for data collection and scientific discovery. The beamlines will provide a photon-beam flux density at least five orders of magnitude greater than that achievable at the NSLS, and orders of magnitude greater than that achievable today at any synchrotron light source. Participation in the first science undertaken at these beamlines represents a unique opportunity for scientists to help deliver on their potential. We are organizing a workshop at BNL, to occur on Jan. 28-29, 2015, to help define and develop further the priorities for the scientific commissioning of these beamlines and their entry into routine operation. Interested participants will be able to present and discuss their vision for the early science case for each beamline, thereby helping to shape the international scene for structural biology. Find workshop information at http://workshops.ps.bnl.gov/?w=ABBIXJan2015, including a draft agenda and an opportunity to register and submit an abstract.
[ccp4bb] Google Gets it Right
Check out google.com. They're announcing what would have been Dorothy Hodgkin's 104th b-day. I saw the molecule, and said to myself, My goodness, that's penicillin G, and the mouseover announced the big day. She was a great scientist and a friend to thousands of us. Bob = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Photon Sciences and Biosciences Dept Office and mail, Bldg 745, a.k.a. LOB-5 Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
[ccp4bb] AW: [ccp4bb] Twinning VS. Disorder
Dear James, I have a slightly different way to think about transverse coherence. I heard Mark Sutton give a talk about this at the APS a few years ago, and here are graphics from a similar talk given by Alec Sandy at BNL: http://www.bnl.gov/nsls2/workshops/docs/XPCS/XPCS_Sandy.ppt The eqn. he gives on figure 8 is this: L(coherence) = Lambda*(source-to-observation-point-distance) / 2*pi*sigma(source) This is the wavelength divided by the angle subtended by the source viewed by the observer, with a 2.pi in there for some reason. The way I explain it (though I cannot derive it this way) is that as you view the source, consider that your eye sees a ray coming from the top of the source, and one coming from the bottom. As you move your eye up and down, the two rays will slide back and forth against one another. The coherence length is how far you move your eye to have them slip about 1/4 of a wave. In Mark's APS example you see the horizontal is 7 microns, the vertical is 200. This reflects the fact that the typical synchrotron source is much wider than it is high. Bob From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of James Holton [jmhol...@lbl.gov] Sent: Thursday, April 24, 2014 6:59 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] AW: [ccp4bb] Twinning VS. Disorder There are two kinds of coherence length: transverse and longitudinal. Longitudinal coherence is often quoted as delta-lambda/lambda, which is easy to calculate but unfortunately completely irrelevant for diffraction from crystals. If it weren't then Laue diffraction wouldn't produce spots. Transverse coherence tends to be around 3-10 microns with 1 A x-rays, depending on the detector distance. Yes, that's right, the detector distance. Longer detector distances give you a bigger coherence length, especially when the source is very far away, like it is at a synchrotron. How this happens is easiest to picture if you consider the simplest possible diffraction situation: a point source of x-rays, two atoms, and a detector. As long as the atoms are very close together relative to the distances from the sample to the source and the detector, then you have the far field diffraction situation. This is where both atoms are within the coherence length, Bragg's diagram for Bragg's Law holds: parallel incoming rays and parallel outgoing rays. But what if the atoms are very far apart? Obviously, the scattering from two atoms on different sides of the room will just add as intensities. And if they are very close together, then Bragg's Law holds and they scatter coherently. What most people think of as the coherence length is the point of transition between these two kinds of scattering. This point is rather conveniently defined as the distance between two atoms when the path from the source to one atom to a given detector pixel becomes 0.5 wavelengths longer than the same path through the other atom. As long as both atoms lie in the Bragg plane (that's the plane perpendicular to the s vector, which is the vector difference between the incoming and outgoing beam directions), the far-field approximation tells us they should also be in phase, but if they are far enough apart the 0.5 A change in total path length is enough to change the scattering completely from constructive to destructive interference. In ordinary optics, this is called the edge of the first Fresnel zone. So, if your source is very far away, emitting 1 A x-rays, and your detector is 1 meter away, then moving one atom 10 microns away from the centerline of the beam makes the path from that atom to the detector 1-sqrt(1^2+10e-6^2) = 0.5 A longer. So that implies the coherence length is 10 microns. But if the detector is only 100 mm away, that gives you 0.1-sqrt(0.1^2+3e-6^2) = 0.5 A, so 3 um is the coherence length. Of course, this is for the ideal case of a point source very far away. In reality finite beam divergence will mess up the coherence inasmuch as a divergent source looks like an array of sources all viewing the sample through a pinhole. What you then get on the detector is the sum of the patterns from all those sources, so the coherence is not as clean. That is, you don't see the Fourier transform of the crystal shape in every spot. Mosaic spread also messes up coherence in this way. Some might even define the mosaic domain size as the inverse of the effective coherence length. But, the long and short of all this is that as long as your detector pixels are bigger than the coherence length the coherence doesn't really matter. Hope that makes sense, -James Holton MAD Scientist On Thu, Apr 24, 2014 at 2:32 PM, herman.schreu...@sanofi.commailto:herman.schreu...@sanofi.com wrote: Dear Chen, Twinning can be thought of as of two or more macro-crystals glued or grown together. The reason that the reflections often overlap is that they
[ccp4bb] Ten days left, many seats available: Apply for RapiData 2014, a course on Data Collection and Structure Solving at the NSLS.
We are offering RapiData 2014, the sixteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 27 April - 2 May 2014: http://www.bnl.gov/RapiData/. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. We encourage all students to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. In addition to MX there will be opportunity for learning about correlated MX and spectroscopy, and SAXS. You'll find the application materials on the Course Application tab at this site. For the twelfth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 27 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be an additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (no more than 30 yrs). Please apply for the course, and then contact R. Sweet (sw...@bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply yourself, or send your students to our course, Bob Sweet, Sonya Kiss, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Photon Sciences and Biosciences Dept Office and mail, Bldg 745, a.k.a. LOB-5 Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
[ccp4bb] Please apply for RapiData 2014, a course on Data Collection and Structure Solving at the NSLS.
We are offering RapiData 2014, the sixteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 27 April - 2 May 2013: http://www.bnl.gov/RapiData/. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. We encourage all students to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. In addition to MX there will be opportunity for learning about correlated MX and spectroscopy, and SAXS. You'll find the application materials on the Course Application tab at this site. For the twelfth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 27 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be an additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (no more than 30 yrs). Please apply for the course, and then contact R. Sweet (sw...@bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply yourself, or send your students to our course, Bob Sweet, Sonya Kiss, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Photon Sciences and Biosciences Dept Office and mail, Bldg 745, a.k.a. LOB-5 Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
[ccp4bb] Jerry Karle
Jerry Karle died a couple of weeks ago, and one of us here learned about it by noticing his obituary in the NY Times: http://www.nytimes.com/2013/06/15/health/jerome-karle-94-dies-nobelist-for-crystallography.html?_r=0 He's well known to those of us who started in this field when the solving of a Patterson function for a heavy atom in a structure was the only way we knew to get the structure. With Herb Hauptman, and in close teamwork with his wife Isabella who actually did crystallography, he played a major role in working out the sort of Direct Methods that allowed one to solve ordinary small-molecule structures before the days of high-speed computing. As the obituary points out, Jerry and Herb shared the 1985 Nobel Prize in Chemistry for this work. The obit. is worth reading. I suspect you'll see an even better one in Nature soon. My own tiny personal memory of Jerry Karle: When I was a grad student at the Univ. of Wisc. with Larry Dahl I made a pilgrimage to the NRL to visit Jerry and Isabella. I was trying to use direct methods to solve at least one cephalosporin structure, which eventually appeared in my thesis, and there was a feature of DM that I failed to understand. They were very patient with me, but couldn't understand what it was I didn't get. It turns out to have been essentially trivial, but that's the way it goes sometimes. Anyway he always recognized me afterwards, or pretended to. I was delighted on arriving at BNL to discover that his daughter Louise was here. Bob = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Photon Sciences and Biosciences Dept Office and mail, Bldg 745, a.k.a. LOB-5 Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
Re: [ccp4bb] PILATUS data collection
The seminal paper on actually how to collect data from detectors like this and others with negligible read-out time is this one, which I strongly recommend: Optimal Fine phi-slicing for Single-Photon-Counting Pixel Detectors Marcus Mueller, Meitian Wang, and Clemens Schulze-Briese, Acta Cryst.(2012) D68, 42-56 And you can pick up a copy of the paper from the RapiData web site: http://www.px.nsls.bnl.gov/courses/papers/Mueller_ACD68_2012.pdf The classic paper on data-collection strategies is this: Data-Collection Stragegies, Dauter, Z. Acta Cryst. (1999). D55, 1703-1717. Also available from the RapiData site: http://www.px.nsls.bnl.gov/courses/papers/dauter_strategy.pdf Then there are multiple papers on damage and its impact on your data. I suggest this one: Radiation damage in macromolecular crystallography: what is it and why should we care?, E.Garman, Acta Cryst. D66, 339-351(2010). which you can find here: http://www.px.nsls.bnl.gov/courses/papers/actad-garman-2010.pdf With this under your belt you'll be able to decide how to collect your phasing data. The bottom line is probably that you should go for SAD data. Employ multiple crystals and average them together in a judicious way, keeping only the sweeps from barely damaged x-tals. Good luck, Bob Sweet = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Photon Sciences and Biosciences Dept Office and mail, Bldg 745, a.k.a. LOB-5 Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) = On Mon, 6 May 2013, Theresa Hsu wrote: Dear crystallographers Is there a good source/review/software to obtain tips for good data collection strategy using PILATUS detectors at synchrotron? Do we need to collect sweeps of high and low resolution data separately? For anomalous phasing (MAD), does the order of wavelengths used affect structure solution or limit radiation damage? Thank you. Theresa
[ccp4bb] Seats are still available for RapiData - the deadline is in 4 days for our course on Data Collection and Structure Solving at the NSLS.
We will present RapiData 2013, the fifteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 21-26 April 2013: http://www.bnl.gov/RapiData/. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. We encourage all students to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. You'll find the application materials on the Course Application tab at this site. For the eleventh time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 21 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (under 40 yrs). Please apply for the course, and then contact R. Sweet (sw...@bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Bob Sweet, Sonya Kiss, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Photon Sciences and Biology Dept Mail Stop, Bldg 463 Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
[ccp4bb] RapiData: Seats are available - the deadline is in 10 days for our course on Data Collection and Structure Solving at the NSLS.
We will present RapiData 2013, the fifteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 21-26 April 2013: http://www.bnl.gov/RapiData/. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. We encourage all students to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. You'll find the application materials on the Course Application tab at this site. For the eleventh time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 21 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (under 40 yrs). Please apply for the course, and then contact R. Sweet (sw...@bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Bob Sweet, Sonya Kiss, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Photon Sciences and Biology Dept Mail Stop, Bldg 463 Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
[ccp4bb] 18 Days to the deadline: Please apply for RapiData 2013, a course on Data Collection and Structure Solving at the NSLS.
We are offering RapiData 2013, the fifteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 21-26 April 2013: http://www.bnl.gov/RapiData/. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. We encourage all students to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. You'll find the application materials on the Course Application tab at this site. For the eleventh time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 21 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (under 40 yrs). Please apply for the course, and then contact R. Sweet (sw...@bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Bob Sweet, Sonya Kiss, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Photon Sciences and Biology Dept Mail Stop, Bldg 463 Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
[ccp4bb] Deadline: 4 February -- Please apply for RapiData 2013, a course on Data Collection and Structure Solving at the NSLS.
We are offering RapiData 2013, the fifteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 21-26 April 2013: http://www.bnl.gov/RapiData/. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. We encourage all students to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. You'll find the application materials on the Course Application tab at this site. For the eleventh time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 21 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (under 40 yrs). Please apply for the course, and then contact R. Sweet (sw...@bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Bob Sweet, Sonya Kiss, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Photon Sciences and Biology Dept Mail Stop, Bldg 463 Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
[ccp4bb] Please apply for RapiData 2013, a course on Data Collection and Structure Solving at the NSLS.
We are offering RapiData 2013, the fifteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 21-26 April 2013: http://www.bnl.gov/RapiData/. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. We encourage all students to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. You'll find the application materials on the Course Application tab at this site. For the eleventh time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 21 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (under 40 yrs). Please apply for the course, and then contact R. Sweet (sw...@bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Bob Sweet, Sonya Kiss, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Photon Sciences and Biology Dept Mail Stop, Bldg 463 Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
Re: [ccp4bb] Off topic: Synchrotron
Good questions! I have off topic questions. Not exactly off topic. Why can't electrons continuously circulate the ring at synchrotrons instead being refilled every few hours? The electrons are traveling in pretty small packets. Eventually they get too close to one another, and they repel one another and get pushed out of the packet. Does new electrons injected into the ring affect MX data collection? If it's top-up filling, the little bumps could cause a problem. Ask the beam-line manager. If it's periodic refilling, every several hours, you don't take data during the filling time, so when you restart you'll find a new, stronger beam. That increase in intensity ought to be corrected in the scale factors when you reduce data. (There is more to it than this, and maybe you'll get more answers.) Secondly, is it impossible to have all MX beamlines with insertion device as the source and all of them tunable? Not impossible. Just takes money. Bob
Re: [ccp4bb] very informative - Trends in Data Fabrication
I thought Ethan was looking for the verb -- you know, fishing!!! On Mon, 2 Apr 2012, jens Preben Morth wrote: For the latest documentary on trolls in Norway see http://www.imdb.com/title/tt1740707/ The documentary describes both the classification system of Norwegian Trolls and why they are sensitive to sun light, i.e turn to stone. Depending in the species, some Trolls apparently prefer bridges and others caves. They all are attracted to christian blood though. cheers Preben On 4/1/12 10:42 PM, Ethan Merritt wrote: On Sunday, 01 April 2012, Kendall Nettles wrote: What is the single Latin word for troll? Kendall According to Google Translate, it is Troglodytarum. But I'm dubious. I thought trolls lived under bridges rather than in caves. Except for the ones who inhabit the internet, of course. Ethan -- = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
Re: [ccp4bb] SAXS workshop
And here's one from Brookhaven -- app. deadline is three weeks away: http://workshops.ps.bnl.gov/default.aspx?w=SAXSMar2012 http://www.chess.cornell.edu/BioSAXS%20course/index.htm Getting Started in Biological Small-Angle X-ray Solution Scattering Feb 24-26, 2012 Students will have the opportunity to collect data on CHESS beamlines using protein standards and/or their own samples. -- = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
Re: [ccp4bb] UV imaging of crystals
I'm not going to respond to the larger group, but I know one can buy LEDs that emit strongly at 280 nm, which would give tryptophan fluorescence. They're about $200, and one could build or buy a control circuit for not much more. I think this is about what the commercial tools do. You'd want front illumination. You can get the LED with a convex lens on the front, giving a focus about 1 away. At that point the light is dangerous -- don't shine it into your eye from that distance. You'd want to ask your local safety guys to check it out. We would use it at the synchrotron with a flash circuit that would be synchronized with a video camera -- I think roughly 20ms would do it. Let me know if it works. Bob = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) = On Thu, 15 Sep 2011, Harman, Christine wrote: Hi All, I was curious if any of you have tried or even know if it is possible to adapt a stereoscope (in my case an Olympus SZX10 model) so as to view protein crystals with UV illumination. Basically, I want a cheap manual version of what a Rock UV Imager does. I know this is probably a crazy dream. However, I would greatly appreciate any comments, advice or experience any of you may have. Thanks so much, Christine
[ccp4bb] Summer X-rays at the NSLS
Summer X-rays at the NSLS The PXRR operates five beamlines at the NSLS: http://www.px.nsls.bnl.gov/. Two of these are the undulator beamlines X25 and X29. The dipole beamlines X12-B and X12-C are available, and are very effective for conventional crystallography. There are efficient ALS-Style Automounters available -- 8400 crystals mounted in the last 12 months. Also, at beamline X26-C, we have a unique-in-the-US station for combined x-ray diffraction and single-crystal optical spectroscopies: http://www.px.nsls.bnl.gov/x26c/x26c_info.html Notice also our world-leading Mail-In crystallography program: http://www.px.nsls.bnl.gov/Mailin.html You may request access to any of these here: http://www.px.nsls.bnl.gov/beamtime_requests.html, and can look at the schedules for all five here: http://www.px.nsls.bnl.gov/ Stay tuned for the announcement in December of RapiData, our annual course in rapid data collection and structure solving: http://www.bnl.gov/rapidata/ Bob Sweet = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
Re: [ccp4bb] Why 0.1% bandwidth?
That's approximately the bandwidth of a Si (111) monochromator. On Wed, 9 Feb 2011, Andre Luis Berteli Ambrosio wrote: Dear ccp4bb, I sometimes find the flux of x-ray sources reported in units of “photons/s/0.1% bandwidth” instead of simply “photons/s”. Where does the “1/0.1% bandwidth” unit come from? I have also seen other percentages like 0.01% bw or 0.02% bw… Is it simply defining some degree of acceptance in energy (for example, the flux between 8 KeV +/- 8 eV for a given stored current)? Does it somehow have to do with energy resolution? Thank you in advance for your answers, -Andre Ambrosio -- = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
[ccp4bb] Ten days left to apply, and many seats available, for RapiData 2011, our course on Data Collection and Structure Solving at the NSLS.
This may be the last reminder that we are offering RapiData 2011, the thirteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 3-8 April 2011. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. All students are encouraged to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. You'll find the application materials on the Course Application tab at this site. For the ninth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 3 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (under 40 yrs). Please apply for the course, and then contact R. Sweet (sw...@bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Bob Sweet, Sal Sclafani, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
Re: [ccp4bb] See Jiang and Sweet ......Re: [ccp4bb] Structures determined: breakdown of methods
Thanks, John. Of course whatever Jiang and I put in that paper is pretty old. The PDB have been taking care of the Jiang and Sweet archive for some years. They completely rewrote the code, and they have added some searches. The catch in this case is that they are only synchrotron-based structures. Have look here. http://biosync.sbkb.org/stats.do?stats_sec=MAINstats_focus_lvl=GLBL From here choose one of the structure galleries, for example Europe: http://biosync.sbkb.org/stats.do?stats_sec=GALLRYstats_focus_lvl=RGNLstats_region=European Then choose a beamline, say ID23-1: http://biosync.sbkb.org/stats.do?stats_sec=GALLRYstats_focus_lvl=BMLNstats_site=ESRFstats_bmln=ID23-1 Then, near the top of the page, see the line Table of general information (software, resolution, R-factors, etc) in tab delimited text format http://biosync.sbkb.org/biosync_pdbtext/measureESRFID23-1.txt You'll get a table where the solution method and software follows the PDB_ID. There's a RELEASE DATE at the end on which you may sort. One catch is, this is one beamline at a time. Maybe there's a way to do a direct query on PDB to get what you want all at once. That would resolve the other catch that it's synchrotron-only structures. Bob On Sun, 16 Jan 2011, Jrh wrote: Dear Rex, A very informative and careful analysis to help your question be answered can be found In Jiang and Sweet JSR 2004, 11, 319-327. Greetings, John Prof John R Helliwell DSc On 15 Jan 2011, at 20:28, REX PALMER rex.pal...@btinternet.com wrote: Does anyone know of a statistical breakdown of successful protein structure determinations in terms of the method used? Rex Palmer Birkbeck College -- = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
[ccp4bb] Barely two weeks left to apply, and many seats available, for RapiData 2011, our course on Data Collection and Structure Solving at the NSLS.
We are offering RapiData 2011, the thirteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 3-8 April 2011. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. All students are encouraged to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. You'll find the application materials on the Course Application tab at this site. For the ninth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 3 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (under 40 yrs). Please apply for the course, and then contact R. Sweet (sw...@bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Bob Sweet, Sal Sclafani, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
[ccp4bb] Only four weeks left to apply for RapiData 2011, our course on Data Collection and Structure Solving at the NSLS.
We are offering RapiData 2011, the thirteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 3-8 April 2011. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. All students are encouraged to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. You'll find the application materials on the Course Application tab at this site. For the ninth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 3 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (under 40 yrs). Please apply for the course, and then contact R. Sweet (sw...@bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Bob Sweet, Sal Sclafani, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
[ccp4bb] Please apply for RapiData 2011, a course on Data Collection and Structure Solving at the NSLS.
We are offering RapiData 2011, the thirteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 3-8 April 2011. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. All students are encouraged to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. You'll find the application materials on the Course Application tab at this site. For the ninth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 3 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (under 40 yrs). Please apply for the course, and then contact R. Sweet (sw...@bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Bob Sweet, Sal Sclafani, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
Re: [ccp4bb] Beginning crystallography text
I like David Blow's book for beginners -- one can get the gist of things without having much math: http://www.abebooks.com/servlet/SearchResults?an=blowsts=ttn=crystallographyx=35y=6 Bernhard Rupp's book, mentioned earlier, is the current gold standard, in my view. Bob On Thu, 8 Jul 2010, Prince, D Bryan wrote: Having recently completed the CSHL Macromolecular crystallography course, I can recommend Introduction to Macromolecular Crystallography by Alexander McPherson (ISBN 987-0-470-18590-2). I am posting the link below: http://www.amazon.com/Introduction-Macromolecular-Crystallography-Alexander-McPherson/dp/0470185902/ref=sr_1_1?ie=UTF8s=booksqid=1278619717sr=1-1 Kind regards and good luck! Bryan -- Confidentiality Notice: This message is private and may contain confidential and proprietary 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 unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful. -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Peter Hsu Sent: Thursday, July 08, 2010 3:36 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Beginning crystallography text Hi all, I haven't gotten past the phase of growing the crystal, but I'd certainly still like to learn the actual theories of crystallography. Can anyone recommend a good beginner to mid-level text on macromolecular crystallography? Thanks, Peter -- = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
[ccp4bb] Another vote for PINE.
One can keep ones hands on the keyboard to do everything -- no reaching for the mouse. An added advantage is that to delete a message doesn't reqire one to find and select a small check box with the mouse cursor, then to find and select the Delete check-box, which often has scrolled off the top of the screen. A single stroke of the d key does the job. It's especially satisfying for expunging a screen full of messages with identical message subjects, like Re: [ccp4bb] attachments for example. does it. Keep the faith, George. Bob On Sat, 3 Jul 2010, George M. Sheldrick wrote: I like pine. It is especially useful if I am travelling and have a bad connection, or (as at the moment) I am at home and one or more of our children (three of whom are computer experts) are hogging our modest internet connection! And using it on the computer at the lab via ssh I dont get troubled by viruses or large attachments. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Fri, 2 Jul 2010, Ed Pozharski wrote: pine is quite handy if you can ssh to your email server (Brandeis allows that, for instance). Uses very little resources, fast, and poses zero danger of ever executing a malicious code. There is very little functionality added in other email clients. I don't use pine anymore, but there is no need to give it bad name. And you can use colors a-la-matrix :) On Fri, 2010-07-02 at 20:40 +0200, Flip Hoedemaeker wrote: Anyone still on PINE should consider a new email application :) Flip On 7/2/2010 20:29, Tim Gruene wrote: I agree to this. What are the actual reasons against attachments? If one really has a slow network connection and cannot use IMAP instead of POP3 (if I understand correctly, with IMAP one does not need to download the emails until one actually wants to read them, but I may be wrong here, too), would it be a compromise to restrict image sizes to e.g. 500kB? On Fri, Jul 02, 2010 at 01:35:57PM -0400, Douglas Jacobsen wrote: My opinion is that attached images in bb posts should be allowed: 1) Storage network bandwidth is cheap 2) Attached (even inline) images are convenient to understanding the question/issue at hand 3) Emails are very easily deleted 4) If images are to be attached via web-links, then it may not be possible to refer to them appropriately in the archives if the images are ever removed from the hosting server. - it seems to me that the archive of the bb is an excellent resource, but is diminished if the content can not be maintained centrally. -Doug On 7/2/2010 11:04 AM, Frances C. Bernstein wrote: Why not put images, maps, or data files on your own web page and then send out a link to that material? Then the e-mails are small and anyone that wants to see the files has easy access. Frances Bernstein = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339FAX: 1-631-286-1999 = On Fri, 2 Jul 2010, Tim Gruene wrote: Maybe this netiquette is a little outdated. Sending a few MB to thousands of people is probably not much more than noise compared to current net traffic. There is the IMAP protocol which overcomes the problem of modem connections, which anyhow probably only affects a very, very small amount of people nowadays, and there are plenty of mail user agents which do not have a paperclip button, e.g. mutt, pine, etc, which address the very same problem. It's is a lot easier to show a jpg-image a few kB in size than to attempt to describe what you see with words. Anyhow, the FAQ (http://www.catb.org/~esr/faqs/smart-questions.html#formats) the CCP4 netiquette (http://www.ccp4.ac.uk/ccp4bb.php#using) refers to explicitly allows MIME attachments, even though I also conside MIME outdated and am extremely glad I do not need to fiddle with uu-en/de-code anymore. Again: maybe it's time to update the CCP4 netiquette. Tim P.S.: I wonder how much traffic this email will induce ;-) On Fri, Jul 02, 2010 at 09:33:01AM -0400, Ed Pozharski wrote: Several recent posts with decently sized attachments (now in cross eyed stereo too!) prompt this (annual?) anti-paperclip-button rant. Lucky for me, I can just recycle the old messages: http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg11949.html Cheers from the self-appointed thought police, Ed. -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID =
Re: [ccp4bb] DATA COLLECTION?
On Sat, 26 Jun 2010, Sudhir Kumar wrote: Hi ALL I don't know if I'm asking the right question: What are Remote, Inflection and peak values for X ray data collection? Sorry if question is wrong or under-status. I wouldn't say it's under-status, and it's certainly a correct question. The answers you got suggest the answer, that it pertains to multi-wavelength anomalous diffraction (MAD) data collection. Also, it's part of the basic teaching these days in macromolecular crystallography. I know that sometimes it's hard to get that teaching. I'm going to refer you to the lecture notes for an all-day lecture I give once a year at our RapiData course, trying to help people brush up on fundamentals: http://www.px.nsls.bnl.gov/fundamentals_lecture/fundamentals_10_2_public.ppt Of course these are the visuals, and there's talk that goes with it. Look at graph in the upper left of image 150, which is labeled Spectrum from Phizackerly, Hendrickson, et al. Study of Lamprey Haemoglobin. That curve is derived from the absorption of, in this case a Fe atom, as a function of x-ray wavelength. Here it's in the range of 1.7 Angstroems, if you can't see the decimal point. This curve is actually the imaginary component of scattering from Fe. The inflection is the wavelength where the curve rises VERY sharply, in this case about 1.74 Ang. The peak is just that, the highest point at 1.73 Ang. Then the remote is chosen at a shorter wavelength rather arbitrarily, in this case 1.5 Ang. You still need to read more, but this should help you with that little piece of MX jargon. Watch for the announcement of RapiData, next December. Bob = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
Re: [ccp4bb] Figures
Dear Bernhard, About permissions: Written permission is required to use any of these images in publication and educational material. RapiData is coming in a few days. If I put any of your stuff into lecture notes I'll acknowledge, as you request. May I ask for permission retrospectively? Bob On Mon, 5 Apr 2010, Bernhard Rupp wrote: In response to multiple requests, all figures of my book now available for lecturers/students via the image gallery http://www.ruppweb.org/garland/image_gallery.htm Regards, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@qedlife.com bernhardr...@sbcglobal.net http://www.ruppweb.org/ - The hard part about playing chicken is to know when to flinch - -- = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
[ccp4bb] Only two weeks remain to apply for RapiData 2010. Seats are still open.
We are offering RapiData 2010, the twelfth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 11-16 April 2010. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. All students are encouraged to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. You'll find the application materials on the Course Application tab at this site. For the eighth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 11 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty. Please apply for the course, and then contact R. Sweet (sw...@bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Bob Sweet, Sal Sclafani, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
[ccp4bb] Please apply for RapiData 2010, a course on Data Collection and Structure Solving at the NSLS.
We are offering RapiData 2010, the twelfth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 11-16 April 2010. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. All students are encouraged to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. You'll find the application materials on the Course Application tab at this site. For the eighth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 11 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty. Please apply for the course, and then contact R. Sweet (sw...@bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Bob Sweet, Sal Sclafani, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
[ccp4bb] Please apply for RapiData 2010, a course on Data Collection and Structure Solving at the NSLS.
We are offering RapiData 2010, the twelvth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 11-16 April 2010. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. All students are encouraged to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. You'll find the application materials on the Course Application tab at this site. For the eighth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 11 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty. Please apply for the course, and then contact R. Sweet (sw...@bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Bob Sweet, Sal Sclafani, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
[ccp4bb] Beam time is available at the NSLS
Please visit the website at www.px.nsls.bnl.gov and select Get Access to Beam Time. The PXRR (Macromolecular Crystallography Research Resource at the NSLS) operates five beamlines for macromolecular crystallography (MX). Two of these beamlines are undulators: X29 is the most efficient MX machine east of Chicago in the US, often serving three different research groups in a day. X25 is as bright, and has counted Rod MacKinnon, Tom Steitz, and Venki Ramakrishnan among its prize-winning users. Typical beam sizes at these undulators are 50 microns. If your crystal is only 20 microns, we can give you a beam that size. There are ALS-style automounters at X29 and two of our dipole beamlines, X12-B and X12-C. We have a new station at X26-C for the coordinated measurement of optical absorption spectroscopic and x-ray diffraction data. Several publications have come from this work and many projects are underway. A Raman spectrometer is being installed now. The PXRR is funded jointly by the NIH's National Center for Research Resources and the DOE's Office of Biological and Environmental Research. = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
[ccp4bb] A workshop on macromolecular crystallography at the one-micron scale.
MX Frontiers at the One Micron Scale July 23 - July 24, 2009 Organized by Dieter Schneider of the Biology Department, and Lonny Berman and Marc Allaire, of the NSLS at Brookhaven National Lab. A web site describing the workshop is here: http://www.nsls.bnl.gov/newsroom/events/workshops/2009/mx/ We invite you to learn from the foremost structural biologists using micro-focused x-ray beams and from the most experienced designers of their beamlines about the unique scientific and experimental capabilities at the one-micron scale. We invite you to take part in discussions of these recent developments. We invite you to weigh in on how they may be translated to the design new crystallographic beamlines at NSLS-II in ways that will optimally serve your needs and fully exploit the uniquely small, stable, and brilliant beams expected to become available here by 2014. This workshop in the 'New Opportunities' series initiated by Qun Shen, the NSLS-II Experimental Facilities Director, will explore structural biology scientific opportunities made possible through the use of micro-beams. It will include studies of difficult-to-crystallize systems and systems for which only small or imperfect crystals could be grown. The impact of using such small beams on mitigating radiation damage of samples will be discussed from first principles to experimental verification. Challenges in producing and using such small beams, and working with very tiny crystals will be explored, including experimental methods that may require development. Speakers -- The following distinguished scientists have agreed to speak and lead discussions: David Eisenberg (University of California at Los Angeles) Gwyndaf Evans (Diamond Light Source, UK) Kenneth Evans-Lutterodt (Brookhaven National Laboratory) Robert Fischetti (Argonne National Laboratory) Elspeth Garman (University of Oxford, UK) Wayne Hendrickson (Columbia University) James Holton (Lawrence Berkeley National Laboartory) Antonio Lanzirotti (Brookhaven National Laboratory) Sean McSweeney (European Synchrotron Radiation Facility, Fr) Colin Nave (Diamond Light Source, UK) Christian Riekel (European Synchrotron Radiation Facility, Fr) Gebhard Schertler (MRC Laboratory for Molecular Biology, UK) Clemens Schulze-Briese (Swiss Light Source) John Spence (Arizona State University) Masaki Yamamoto (RIKEN Harima Institute, SPring-8, Japan) Format and Venue This one-day-and-a-half workshop will be held at Brookhaven National Laboratory. On the evening of July 22, an informal reception at the Brookhaven Center will encourage registration and first contacts. The workshop will convene in earnest on Thursday, July 23, and continue through midday Friday with sessions and several discussions. The Thursday evening dinner will feature an after dinner talk that is part of the workshop program and provide opportunities for more in-depth and personal discussions. The workshop agenda is focused on invited speakers and discussions. However, we welcome relevant poster contributions. Poster boards will be available outside the meeting auditorium during all coffee breaks. We will post abstracts of contributions as well as 8.5 by 11 sized pdf versions of posters on this website. Costs and Registration Please register early using the workshop registration page. The registration fee is a modest $75 and covers breakfast, lunch, and coffee breaks. The cost for dinner on Thursday night - including the after dinner talk - is $50. Sponsors The National Synchrotron Light Source II Project The National Synchrotron Light Source The National Institutes of Health NCRR The National Institutes of Health NIGMS The Department of Energy OBER
[ccp4bb] Barely one week remains to apply for RapiData, the BNL Course on Synchrotron Data Collection and Structure Solving.
The application deadline is 8AM EST Monday 9 February for RapiData 2009, the eleventh offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 19-24 April 2009. Students could be at any level from advanced undergraduate to full professor. 48 students will be accepted; 24 will bring their own specimens for data collection. Please read the course description at http://www.px.nsls.bnl.gov/RapiData2009/. You'll see that many experts in the field will be available for lectures and tutorials, and you'll find the application materials at this site. For the seventh time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 19 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty. Please apply for the course, and then contact R. Sweet (sw...@bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Alex Soares, Sal Sclafani, and Bob Sweet = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular^ (that's L Crystallography Research Resource at NSLS not 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
Re: [ccp4bb] small lines in diffraction pattern
I'm coming in late here, having only now found time to look at the images. It's facinating, isn't it? Since the lines are not arcs centered on the origin, this isn't mosaic spread. For those who haven't seen the image and the zoom, the diffraction pattern clearly shows one very long axis and a couple of much shorter ones. The rotation image is taken rotating around the long one. The small lines are perpendicular to the long axis, and run fairly uniformly, narrowly and evenly spaced at the intervals of the reflections along this axis, throughout the diffraction pattern. Also it appears that this is a rotation of about a degree; Margriet doesn't give us clues for any of this. I'm guessing that whoever said it's a diffuse scatter effect is close to the mark. I think diffuse scatter comes from the contents of each unit cell being essentially identical, but that within the molecule things are waving around a bit (where are Don Caspar and George Phillips when we need them?). I'll go a touch farther and suggest that it's really disorder -- each unit cell is well aligned to the others, but each one is different in some way. I'll guess that the RNA decamer is aligned along this long unit cell axis, but in some way either there's an opportunity for the register along the RNA axis to slip from one unit cell to the other or each is rotated slightly. On the other hand, the fact that there's a wide distribution of intensities in the Bragg spots, which are quite sharp, is confusing -- there must be a lot of contrast in the averaged structure for this to be true. Ok, it's interesting, but I have no idea. Bob On Wed, 28 Jan 2009, James Holton wrote: Hmm. I don't remember that thread. However, I personally think it is a good idea to keep the mosaic crystal as Ewald and Darwin defined it. Just because current integration software lumps things together into a mosaicity does not mean that every mechanism contributing to the rocking width of a spot should be given the same name. Especially when it is difficult to describe the mosaic crystal using any other words. Perhaps Colin could come up with a cool word for unit cell non-uniformity? Or is he waiting for us to name it after him? Nonuniform Anisotropic Variance of Elasticity? or Cells Of Loose INdex? Comments and suggestions are welcome. -James Holton MAD Scientist Jacob Keller wrote: I had thought that in a previous thread, we had all come to a consensus that actually the largest source of what is normally explained as mosaicity is really differences in unit cell size, due perhaps to uneven shrinkage in crystals upon freezing or otherwise. I believe that there was actually an acta cryst paper which investigated all of the various ingredients of mosaicity which supports this (this is why I said it.) Jacob *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu mailto:j-kell...@northwestern.edu ***
Re: [ccp4bb] small lines in diffraction pattern
I'm coming in late here, having only now found time to look at the images. It's facinating, isn't it? Since the lines are not arcs centered on the origin, this isn't mosaic spread. For those who haven't seen the image and the zoom, the diffraction pattern clearly shows one very long axis and a couple of much shorter ones. The rotation image is taken rotating around the long one. The small lines are perpendicular to the long axis, and run fairly continuously, narrowly and evenly spaced at the intervals of the reflections along this axis, throughout the diffraction pattern. They're all faint and about the same intensity, and modulated along their length only slightly. Also it appears that this is a rotation of about one degree; Margriet doesn't give us clues for any of this. I'm guessing that whoever said it's a diffuse scatter effect is close to the mark. I think diffuse scatter comes from the contents of each unit cell being essentially identical, but that within the molecule things are waving around a bit (where are Don Caspar and George Phillips when we need them?), that is, different in each unit cell. I'll go a touch farther and suggest that it's really disorder -- each unit cell is well aligned to the others, but each one is different in a more significant way. I'll guess that the RNA decamer is aligned along this long unit cell axis, but in some way either there's an opportunity for the register along the RNA axis to slip from one unit cell to the other or each is rotated slightly. On the other hand, the fact that there's a wide distribution of intensities in the Bragg spots, which are quite sharp, is confusing -- there must be a lot of contrast in the averaged structure for this to be true. Ok, it's interesting, but I have no idea. Bob On Wed, 28 Jan 2009, Jacob Keller wrote: There is something in the unit cell, aligned with the long axis of the cell, with a periodicity corresponding to ~1/5 of the long axis. This can be seen as greater intensities along the long axis every fifth spot. Without knowing the unit cell parameters, I would guess it is either the interplanar spacings of the nucleotides (probably this is too small) or the periodic twist of the helix itself. Interesting that the RNA is a decamer ( = 2 x 5). I would be curious to know what the unit cell parameters are, or more generally, what is causing that noticeable periodicity... Jacob *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** - Original Message - From: James Holton jmhol...@lbl.gov To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, January 28, 2009 12:20 PM Subject: Re: [ccp4bb] small lines in diffraction pattern Hmm. I don't remember that thread. However, I personally think it is a good idea to keep the mosaic crystal as Ewald and Darwin defined it. Just because current integration software lumps things together into a mosaicity does not mean that every mechanism contributing to the rocking width of a spot should be given the same name. Especially when it is difficult to describe the mosaic crystal using any other words. Perhaps Colin could come up with a cool word for unit cell non-uniformity? Or is he waiting for us to name it after him? Nonuniform Anisotropic Variance of Elasticity? or Cells Of Loose INdex? Comments and suggestions are welcome. -James Holton MAD Scientist Jacob Keller wrote: I had thought that in a previous thread, we had all come to a consensus that actually the largest source of what is normally explained as mosaicity is really differences in unit cell size, due perhaps to uneven shrinkage in crystals upon freezing or otherwise. I believe that there was actually an acta cryst paper which investigated all of the various ingredients of mosaicity which supports this (this is why I said it.) Jacob *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu mailto:j-kell...@northwestern.edu ***
Re: [ccp4bb] small lines in diffraction pattern (fwd)
I'm coming in late here, having only now found time to look at the images. It's facinating, isn't it? Since the lines are not arcs centered on the origin, this isn't mosaic spread. For those who haven't seen the image and the zoom, the diffraction pattern clearly shows one very long axis and a couple of much shorter ones. The rotation image is taken rotating around the long one. The small lines are perpendicular to the long axis, and run fairly continuously, narrowly and evenly spaced at the intervals of the reflections along this axis, throughout the diffraction pattern. They're all faint and about the same intensity, and modulated along their length only slightly. Also it appears that this is a rotation of about one degree; Margriet doesn't give us clues for any of this. I'm guessing that whoever said it's a diffuse scatter effect is close to the mark. I think diffuse scatter comes from the contents of each unit cell being essentially identical, but that within the molecule things are waving around a bit (where are Don Caspar and George Phillips when we need them?), that is, different in each unit cell. I'll go a touch farther and suggest that it's really disorder -- each unit cell is well aligned to the others, but each one is different in a more significant way. I'll guess that the RNA decamer is aligned along this long unit cell axis, but in some way either there's an opportunity for the register along the RNA axis to slip from one unit cell to the other or each is rotated slightly. On the other hand, the fact that there's a wide distribution of intensities in the Bragg spots, which are quite sharp, is confusing -- there must be a lot of contrast in the averaged structure for this to be true. Ok, it's interesting, but I have no idea. Bob On Wed, 28 Jan 2009, Jacob Keller wrote: There is something in the unit cell, aligned with the long axis of the cell, with a periodicity corresponding to ~1/5 of the long axis. This can be seen as greater intensities along the long axis every fifth spot. Without knowing the unit cell parameters, I would guess it is either the interplanar spacings of the nucleotides (probably this is too small) or the periodic twist of the helix itself. Interesting that the RNA is a decamer ( = 2 x 5). I would be curious to know what the unit cell parameters are, or more generally, what is causing that noticeable periodicity... Jacob *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** - Original Message - From: James Holton jmhol...@lbl.gov To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, January 28, 2009 12:20 PM Subject: Re: [ccp4bb] small lines in diffraction pattern Hmm. I don't remember that thread. However, I personally think it is a good idea to keep the mosaic crystal as Ewald and Darwin defined it. Just because current integration software lumps things together into a mosaicity does not mean that every mechanism contributing to the rocking width of a spot should be given the same name. Especially when it is difficult to describe the mosaic crystal using any other words. Perhaps Colin could come up with a cool word for unit cell non-uniformity? Or is he waiting for us to name it after him? Nonuniform Anisotropic Variance of Elasticity? or Cells Of Loose INdex? Comments and suggestions are welcome. -James Holton MAD Scientist Jacob Keller wrote: I had thought that in a previous thread, we had all come to a consensus that actually the largest source of what is normally explained as mosaicity is really differences in unit cell size, due perhaps to uneven shrinkage in crystals upon freezing or otherwise. I believe that there was actually an acta cryst paper which investigated all of the various ingredients of mosaicity which supports this (this is why I said it.) Jacob *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu mailto:j-kell...@northwestern.edu ***
[ccp4bb] Only two weeks remain to apply for RapiData, the BNL Course on Synchrotron Data Collection and Structure Solving. Many positions remain.
The application deadline is 8AM EST Monday 9 February for RapiData 2009, the eleventh offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 19-24 April 2009. Students could be at any level from advanced undergraduate to full professor. 48 students will be accepted; 24 will bring their own specimens for data collection. Please read the course description at http://www.px.nsls.bnl.gov/RapiData2009/. You'll see that many experts in the field will be available for lectures and tutorials, and you'll find the application materials at this site. For the seventh time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 19 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty. Please apply for the course, and then contact R. Sweet (sw...@bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Alex Soares, Sal Sclafani, and Bob Sweet = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular^ (that's L Crystallography Research Resource at NSLS not 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
Re: [ccp4bb] structure (factor) amplitude
Come on, Jim, even now 90% of students don't realize that boldF/bold is a phased amplitude, we think of it as a complex number, and that F(obs) or F(calc) are probably the appropriate |F|. Bob On Mon, 12 Jan 2009, Jim Pflugrath wrote: I wonder if the early use of the shortened structure amplitude is because it was a pain to do any typing, word processing, typesetting, etc before Gutenberg. But soon crystallographers will be solving all their structures on their cell phones and also just text messaging manuscripts to editors and CCP4BB. So we should probably be thinking of the newer shortened spelling of our scientific terms of the future. Jim PS: I vote for that structure factor amplitude be used in text books and |F| on cell phones. Student of 2015: You mean 'abs-F' is really pronounced 'structure factor amplitude'? I didn't know that! -- = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
[ccp4bb] Reminder: Please apply to the BNL-Biology and NSLS Course on Synchrotron Data Collection
We are offering RapiData 2009, the eleventh offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 19-24 April 2009. Students could be at any level from advanced undergraduate to full professor. 48 students will be accepted; 24 will bring their own specimens for data collection. Please read the course description at http://www.px.nsls.bnl.gov/RapiData2009/. You'll see that many experts in the field will be available for lectures and tutorials, and you'll find the application materials at this site. For the seventh time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 19 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty. Please apply for the course, and then contact R. Sweet (sw...@bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Alex Soares, Sal Sclafani, and Bob Sweet = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
[ccp4bb] The BNL-Biology and NSLS Course on Synchrotron Data Collection: Please Apply
We are offering RapiData 2009, the eleventh offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 19-24 April 2009. Students could be at any level from advanced undergraduate to full professor. 48 students will be accepted; 24 will bring their own specimens for data collection. Please read the course description at http://www.px.nsls.bnl.gov/RapiData2009/. You'll see that many experts in the field will be available for lectures and tutorials, and you'll find the application materials at this site. For the seventh time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 19 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty. Please apply for the course, and then contact R. Sweet (sw...@bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Alex Soares, Sal Sclafani, and Bob Sweet = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
Re: [ccp4bb] SUMMARY: synchrotron remote data collection
You also missed the link for the BNL / NSLS Mail-in program, where three scientists spend about one full-time equivalent of effort, employing about one full-time beamline among the six PXRR beamlines. http://www.px.nsls.bnl.gov/ -- Access to Beam Time http://www.px.nsls.bnl.gov/beamtime_requests.html -- Mail-in Program http://www.px.nsls.bnl.gov/Mailin.html It's a very busy and successful program: http://journals.iucr.org/d/issues/2006/11/00/dz5083/index.html On Tue, 22 Jul 2008, Chavas Leo wrote: Dear all -- On 22 Jul 2008, at 00:45, Tom Caradoc-Davies wrote: Beamline 3BM1 at the Australian Synchrotron I believe in Japan as well there is a remote control available, at SPring8. It is called Mail-in system. You can probably find more informations there: http://www.spring8.or.jp/en/about_us/organization/research_utilization/biology HTH Kind regards. -- Leo -- Chavas Leonard, Ph.D. @ home Research Associate Faculty of Life Sciences The University of Manchester The Michael Smith Building Oxford Road Manchester Lancashire M13 9PT Tel: +44(0)161-275-1586 e-mail: [EMAIL PROTECTED] http://personalpages.manchester.ac.uk/staff/leonard.chavas/ -- = Robert M. Sweet E-Dress: [EMAIL PROTECTED] Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
Re: [ccp4bb] UV light source for protein xtal detection
I haven't read all of these submissions. Are we talking about UV illumination to create visible light? The work we intend to emulate is this: From Cipriani and Bourgeois's groups in Grenoble -- Acta Cryst. (2006). D62, 253-261. UV laser-excited fluorescence as a tool for the visualization of protein crystals mounted in loops. The 266nm light from a laser diode stimulates blue light from W residues. Bob On Fri, 16 May 2008, James Holton wrote: It is not the light source that is expen$ive, but rather the microscope optics and the camera. Standard optical glass has a fairly high absorption in the UV. In most cases you can replace the glass with quartz by addig a 0 to the end of the price (before the decimal point). The camera is also a consideration because most CCD cameras are not very sensitive in the UV. If memory serves, Hamamatsu makes the UV sensitive camera for the Karima microscope, and that camera is a significant fraction of the price of the instrument. You can always compensate for cheap optics by using a brighter light source, but it is important to remember that UV is not just bad for your skin and eyes, but for other proteins as well. -James Li Zhijie wrote: Hello, You may want to have a look at the UV LEDs, which should be the cheapest option if you only need a specific wavelenth. I found this on google: http://www.3dzled.com/other.html. It seems that they can make 280nM LEDs. It is interesting to note that they also said these LEDs' Wavelength tolerance is usually within +/- 5 nm. For example 254 nm would be 249 nm to 259 nm and 415 nm would be 410 nm to 415 nm or 415 nm to 420 nm - apparently not as pure as those generated by monochrometers, but should be good enough for quatitating protein or exciting some fluorophores. I wonder if the microscope makers would ever consider using these instead of those multi-thousand $ light sources. One more thing: do not forget that 280nm UV is extremely harmful to human eyes and skin. Zhijie Li - Original Message - From: Torres-Larios Alfredo [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, May 14, 2008 7:59 PM Subject: [ccp4bb] UV light source for protein xtal detection Dear all, Here's another non CCP4 question: does anyone know a cheap alternative to set up a UV source at 280 nm? I'd really like to have one :), but I really don't have the $20K Dlls needed to buy a UV/white light source from the crystallographic vendors :(. Thanks so much in advance for your answers, Alfredo. Alfredo Torres-Larios, PhD Assistant Professor Instituto de Fisiologia Celular, UNAM. Ciudad Universitaria, Mexico This message was sent using IMP, the Internet Messaging Program. -- No virus found in this incoming message. Checked by AVG Free Edition. Version: 7.5.446 / Virus Database: 269.23.16/1077 - Release Date: 5/11/2008 12:00 AM -- = Robert M. Sweet E-Dress: [EMAIL PROTECTED] Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
Re: [ccp4bb] into the looking glass
I lost track. What's the date today? On Tue, 1 Apr 2008, James Holton wrote: Dear CCP4BB, I think it prudent at this point for me to announce what could be a very old, but serious error in the fundamental mathematics of crystallography. To be brief, I have uncovered evidence that the hand of the micro-world is actually the opposite of what we have believed since Bijvoet's classic paper in 1951. Those of you who know me know that I have been trying to lay down the whole of x-ray diffraction into a single program. This is harder than it sounds. We all know what anomalous scattering is, but a detailed description of the math behind translating this dynamical theory effect all the way to the intensity of a particular detector pixel is hard to find all in one place. Most references in the literature about how anomalous scattering is connected to absolute configuration point to the classic Nature paper: Bijvoet et. al. (1951). Unfortunately, since this is a Nature paper, it is too short to describe the math in detail. For the calculations, the reader is referred to another paper by Bijvoet in the Proc. Roy. Acad. Amsterdam v52, 313 (1949). Essentially, the only new information in Bijvoet et. al. (1951) is the assertion that Emil Fischer got it right in his initial (arbitrary) assignment of the R and S reference compounds for the absolute configuration of molecules. I decided to follow this paper trail. The PRAA document was hard to come by and, to my disappointment, again referenced the real calculation to another work. Eventually, however, all roads lead back to R. W. James (1946). This is the definitive textbook on scattering theory (originally edited by Sir Lawrence Bragg himself). It is extremely useful, and I highly recommend that anyone who wants to really understand scattering should read it. However, even this wonderful text does not go through the full quantum-mechanical derivation of scattering, but rather rests on J. J. Thompson's original classical treatment. There is nothing wrong with this because the the exact value of the phase lag of the scattering event does not effect anything as long as the phase lag from all the atoms is the same. The only time it does become important is anomalous scattering. Even so, changing the sign of the phase lag will have no effect on any of the anomalous scattering equations as long as all the anomalous contributions have the same sign. The only time the sign of the phase lag is important is in the assignment of absolute configuration. Unfortunately, a full quantum mechanical treatment of the scattering process DOES produce a phase lag with the opposite sign of the classical treatment. This is not the only example of this sort of thing cropping up. One you can find in any quantum text book is the treatment of tilting a quantum-mechanical spin (such as an electron). It was shown by Heisenberg that a tilt of 360 degrees actually only turns an electron upside-down. You have to tilt it by 720 degrees to restore the initial state, or get it right-side-up again. This is very counterintuitive, but true, and unfortunately a similar treatment of scattering results in a phase lag of +270 degrees to restore the electron after the scattering event, not +90 degrees as was derived classically. To be brief, there is a sign error. Perhaps the reason why noone caught this until now is not just that the quantum calculations are a pain, but that it was very tempting to accept that the large body of literature following Fischer's convention would not have to be corrected by inverting the hand of every chiral center described up to that time. Unfortunately, we now have an even larger body of literature (including the PDB) that must now be corrected. It is an under-appreciated fact in chemistry that anomalous scattering is arguably the only direct evidence we have about the hand of the micro-world. There are other lines of evidence, such as the morphology of macroscopic crystals and some recent STEM-type microscope observations of DNA. However, as someone with a lot of experience in motor control I don't mind telling you how easy it is to make a sign error in the direction of an axis. This is especially easy when the range of motion of the axis is too small to see by eye. You end up just swapping wires and flipping bits in the axis definitions until you get it right. The right configuration (we have all assumed) is the one asserted in Bijvoet et. al. (1951). Apparently, the STEM observations fell prey to such a mistake. But can you blame them? Inverting the hand of the world is going to be very hard for a lot of people to accept. Indeed, if anyone can find an error in my math, please tell me! I would really like to be wrong about this. -James Holton MAD Scientist -- = Robert M. Sweet
[ccp4bb] Five days remain to apply for the BNL-Biology and NSLS Course on Synchrotron Data Collection
There are still seats available! Please apply! We will close applications at 8AM EST Monday 4 February 2008 for RapiData 2008, the tenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 6-11 April 2008. Students could be at any level from advanced undergraduate to full professor. 48 students will be accepted; 24 will bring their own specimens for data collection. Please read the course description at http://www.px.nsls.bnl.gov/RapiData2008/. You'll see that many experts in the field will be available for lectures and tutorials, and you'll find the application materials at this site. For the sixth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 6 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty. Please apply for the course, and then contact R. Sweet ([EMAIL PROTECTED]) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. = Robert M. Sweet E-Dress: [EMAIL PROTECTED] Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
[ccp4bb] Only Five Weeks left to apply for the BNL-Biology and NSLS Course on Synchrotron Data Collection
We will close applications at 8AM EST Monday 4 February 2008 for RapiData 2008, the tenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 6-11 April 2008. Students could be at any level from advanced undergraduate to full professor. 48 students will be accepted; 24 will bring their own specimens for data collection. Please read the course description at http://www.px.nsls.bnl.gov/RapiData2008/. You'll see that many experts in the field will be available for lectures and tutorials, and you'll find the application materials at this site. For the sixth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 6 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty. Please apply for the course, and then contact R. Sweet ([EMAIL PROTECTED]) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. = Robert M. Sweet E-Dress: [EMAIL PROTECTED] Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
[ccp4bb] The BNL-Biology and NSLS Course on Synchrotron Data Collection: Please Apply
We are offering RapiData 2008, the tenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 6-11 April 2008. Students could be at any level from advanced undergraduate to full professor. 48 students will be accepted; 24 will bring their own specimens for data collection. Please read the course description at http://www.px.nsls.bnl.gov/RapiData2008/. You'll see that many experts in the field will be available for lectures and tutorials, and you'll find the application materials at this site. For the sixth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 6 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty. Please apply for the course, and then contact R. Sweet ([EMAIL PROTECTED]) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. = Robert M. Sweet E-Dress: [EMAIL PROTECTED] Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
Re: [ccp4bb] To bathe or not to bathe.
Thanks, Ron, Regarding the bathing question, these days the major source of error we find in synchrotron-based data is crystal damage. Several groups, notably the two ID23s (one each of pairs of matched canted undulators at ESRF and APS) are producing small x-ray beams, on the order of 5-10 micron diameters, and are saying that the principal use to which they're put is to shoot a single larger crystal several times. There's a certain synergy here -- each new exposure is essentially a new and undamaged tiny crystal, and the orientations of each succesive spot on the crystal are essentially identical. The orientations abut nearly precisely and various data-reduction questions are simplified. These days, where x-tals tend to be smallish and synchrotron access is pretty available, this seems to us to be an excellent strategy. Regarding absorption corrections, here at the PXRR/NSLS a whole lot of data are taken with wavelengths on the order of one Angstroem. At these wavelengths the absorption of a typical crystal in its mount, even one that is, say 3M ammonium sulfate, is nearly negligible. On the other hand, if one tries to optimize S or I anomalous with 1.7 Angstroem radiation, all bets are off. Here I'm sure you would take excellent data. About empirical corrections: to employ Tony North's method in about 1969 I took what are formally psi scans (repeat mesurements on a diffractometer of one reflection at increments of rotation about one real-lattice vector) on the trypsin/soybean-trypsin-inhibitor complex. I was using Wyckoff scans* to do this. The crystal was an orthorhombic needle, and I was rotating about the needle axis. I observed that the rocking curve varied from narrow to wide, with the extremes being separated by about 180 deg. I'd jammed the needle into a tapered capillary and it was slightly bent(!), giving a focused beam in one direction (sharp) and an unfocused one in the opposite (broad). I'm told this happens these days with frozen needles sticking out of the gob of vitreous mother liquor. * Hal Wyckoff (the inventor of the true Inverse Beam Method**) reasoned that there were three ways to integrate a reflection: one could rotate the crystal through its rocking curve (the rotation method), one could use a broad bandpass of wavelengths (the Laue method), or one could use a widely convergent source (the Wyckoff scan). To do this one increased the take-off angle of the x-ray tube (Ron knows what this is, but those of you who don't know should ask the oldest crystallographer nearby) so that the angle subtended from the crystal would fill the rocking curve. In principal the single largest measurement would equal the integrated intensity. To hedge ones bets, one did a five-point scan and summed the top three. This was how I could see the sharpness of the scans. ** Wyckoff also invented a diffractometer that had two opposing x-ray generators, literally shooting at the crystal from opposite directions, and then two opposing detectors, each on its own 2-theta arm. One detector would measure (h,k,l) at precisely the same time the other would measure (-h,-k,-l). What we do now, to flip the rotation axis by 180 degrees, seeing the (-h,-k,-l) reflections in a mirror image to the (h,k,l) ones, would better be termed the Friedel Flip. Keep those cards and letters coming, folks. Bob On Sun, 25 Nov 2007, Ronald E Stenkamp wrote: Just a few comments on consider a crystal bathed in a uniform beam. I've not fully bought into the idea that it's OK to have the beam smaller than the crystal. I learned most of my crystallography in a lab dedicated to precise structure determinations, and somewhere along the line, I picked up the idea that it's better to remove systematic errors experimentally than to correct for them computationally. (Maybe that had something to do with the computing power and programs available at the time?) Anyway, I thought the reason people went to smaller beams was that it made it possible to resolve the spots on the film or detector. Isn't that the main reason for using small beams? In practice, I guess the change in crystal volume actually diffracting hasn't been a big issue and that frame-to-frame scaling deals with the problem adequately. I'm less convinced that frame-to-frame scaling can correct for absorption very well. Due to our irregular-shaped protein crystals, before the area detectors came along, we'd use an empirical correction (one due to North comes to mind) based on rotation about the phi axis of a four-circle goniostat. It was clearly an approximation to the more detailed calculations of path-lengths available for crystals with well-defined faces not surrounded by drops of mother liquor and glass capillaries. Has anyone checked to see how frame-to-frame scaling matches up with analytical determinations of absorption corrections? It'd be interesting to determine the validity of the
Re: [ccp4bb] Why there is no C21 space group in crystal system
Just shift the origin in the C2 group and you get C21. Since they're redundant, only one is named, the simpler one. On Tue, 11 Sep 2007, wu donghui wrote: Dear all, I just get into touch with x-ray crystallography, and I made a big discovery that there is no C21 space group in monoclinic system, which system only contains P2, P21 and C2 groups. Even in the entire 65 chiral space group, there is no space for this group. I made an assumption that if there is C21 space group in monoclinic system, then the four equivalent point position could be described as: x, y, z; 1/2+x, 1/2+y, z; -x, 1/2+y, -z; 1/2-x, y, -z. However when I check the 65 chiral space group, no one is compatible with this equivalent positions. And I know I must make some mistakes. Unfortunately I can not find where the mistake stems from. I have to recourse to our expert community for your generous help. All replies are warmly welcomed and appreciated. Best regards, Donghui -- = Robert M. Sweet E-Dress: [EMAIL PROTECTED] Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
Re: [ccp4bb] Kay Diederichs Email
You will not get feedback. They do not disappear into a black hole though. Think of it as a write-only drop box on a remote file system. Someone does actually look at those things. There are certain religious analogies which may be even closer to the mark, but I hesitate to go there. Oh, go ahead. Religious analogies are appropriate for Apple users, aren't they? BS
Re: [ccp4bb] A bit of history: John W Backus obit
I'm pretty sure that the crystallographer was David Sayre. I also believe (not documented well enough for wikipedia, but perhaps for here) that IBM were so pleased with this performance that they made David an IBM Fellow, which meant that he could do anything he wanted for the rest of his life. Here's what he decided to do: He's known in crystallography for the Sayre Equation, a fundamental relationship in direct methods. Also, maybe not so well known, he was a major driving force behind the method of visualizing single molecules or cells from diffraction patterns: J. Miao, H. N. Chapman, J. Kirz, D. Sayre and K. O. Hodgson, TTaking X-ray Diffraction to the Limit: Macromolecular Structures from Femtosecond X-ray Pulses and Diffraction Microscopy of Cells with Synchrotron Radiation, Annu. Rev. Biophys. Biomol. Struct. 33, 157-176 (2004). He and I used to use adjacent darkrooms at the NSLS for developing x-ray films (the '80's). I'd meet him on the long walk, ask what he was doing, and smile sympathetically when he said he was going to image single yeast cells. Well, they're essentially doing it now. One never want's to underestimate David Sayre's ability to find phases. When David retired from IBM and his adjunct appointment at SUNY Stony Brook one of his old buddies from the FORTRAN project spoke at the symposium. Perhaps it was Backus. They both said that the period of developing that language in a small team was one of the happiest times of their lives. Don't take this as fact, but this is what I remember. Bob On Tue, 20 Mar 2007, Bart Hazes wrote: The storey also made it to the CNN business page and they add... The Fortran programming language, which was a huge leap forward in easing the creation of computer software, was released in 1957, said the report. Backus launched his research project at IBM (Charts) four years earlier, assembling a diverse team of 10, including a chess wizard, a crystallographer and a cryptographer, said the Times. Full story @: http://money.cnn.com/2007/03/20/news/newsmakers/backus/index.htm?postversion=2007032008 Bart P.Artymiuk wrote: A bit of history: NY Times obituary for John W. Backus, 82, developer of Fortran, without which CCP4 and much else would not have been possible. http://www.nytimes.com/2007/03/19/obituaries/20cnd-backus.html?ex=1332043200en=adde3ee5a1875330ei=5124partner=permalinkexprod=permalink Pete A -- = Robert M. Sweet E-Dress: [EMAIL PROTECTED] Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
