Re: [ccp4bb] how to dump diffraction image header info?
Dear all,
Thank you all giving a valuable information.
I wanted to get the header info in my script, and from images not only in the
.cbf format,
though I didn’t write so. Thanks Harry for giving me a list of formats which
have a text header.
Unfortunately, I couldn’t find a way to print out the header information by
Mosflm.
Although dxtbx.print_header is nice, it doesn’t write a collection date/time in
the header,
which I also want to know. I can’t dig out a method to get the date/time in
dxtbx.
Clemens introduced me the ‘imginfo’ tool in autoPROC, and it gave me all what I
wanted.
Thanks again for your kind helps.
Takaaki
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Graeme
Winter
Sent: Monday, December 1, 2014 10:46 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] how to dump diffraction image header info?
Dear All,
dxtbx.print_header /path/to/image should work
Graemes-MacBook-Pro:~ graeme$ dxtbx.print_header
data/i04-BAG-training/th_8_2_0001.cbf
=== data/i04-BAG-training/th_8_2_0001.cbf ===
Using header reader: FormatCBFMiniPilatusDLS6MSN100
Beam:
wavelength: 0.97625
sample to source direction : {0,0,1}
divergence: 0
sigma divergence: 0
polarization normal: {0,1,0}
polarization fraction: 0.999
Goniometer:
Rotation axis: {1,0,0}
Fixed rotation: {1,0,0,0,1,0,0,0,1}
Setting rotation:{1,0,0,0,1,0,0,0,1}
Detector:
Panel:
pixel_size:{0.172,0.172}
image_size: {2463,2527}
trusted_range: {-1,161977}
fast_axis: {1,0,0}
slow_axis: {0,-1,0}
origin: {-210.76,205.277,-265.27}
Scan:
image range: {1,1}
oscillation: {82,0.15}
Total Counts: 1437712
Best wishes Graeme
On Mon Dec 01 2014 at 12:40:09 PM David Waterman
dgwater...@gmail.commailto:dgwater...@gmail.com wrote:
Dear Takaaki,
dxtbx provides a way to do this (see
http://journals.iucr.org/j/issues/2014/04/00/jo5001/jo5001.pdf). It is
available in ccp4-python (try 'import dxtbx'), however there is no script
currently in CCP4 that uses this to print the header information. One could
write such a script easily though, and I would be happy to provide one off-list
if you are interested. Scripts like this already exist in the DIALS project
(http://dials.sourceforge.net/ - try e.g. dials.import /my/images/*.cbf;
dials.show_models datablock.json).
Note that the dxtbx way is not giving you direct access to header values, but
will print information about experimental models constructed from the headers.
Usually this is what you want. If not, ADXV
(http://www.scripps.edu/tainer/arvai/adxv.html) is a useful tool that can
display image header values, but I don't know if this can be scripted to print
to console.
Cheers
-- David
On 1 December 2014 at 11:22, Takaaki Fukami
fukami...@chugai-pharm.co.jpmailto:fukami...@chugai-pharm.co.jp wrote:
Dear all,
I'd like to dump header information of a diffraction image file.
CCP4 diffdump is a good tool, though it outputs the same angle
for both oscillation start and end for .cbf image. (bug?)
Are there any other tools to get diffraction image header info?
Regards
-
Takaaki Fukami
(mailto:fukami...@chugai-pharm.co.jpmailto:fukami...@chugai-pharm.co.jp)
Discovery Research Dept. (Biostructure Gr.)
Chugai Pharmaceutical Co.,Ltd.
[ccp4bb] 29th European Crystallographic Meeting
Dear ccp4bb users, I am delighted to tell you the registration for the 29th European Crystallographic Meeting is open. Just to remind you ECM29 (August 23-28, 2015) is taking place in beautiful city of Rovinj in Croatia. You can find more information on our web site, and please visit and share our Facebook page! I hope I will see you all there! Web: http://ecm29.ecanews.org/ Facebook: https://www.facebook.com/29thEuropeanCrystallographicMeeting?ref=hl Sincerely, Igor [1] IGOR SABLJIĆ _Social networks editor_ Ruđer Bošković Institute Division of Physical Chemistry Bijenička cesta 54, 1 Zagreb, CROATIA http://ecm29.ecanews.org [1] Facebook [2] home [3] Links: -- [1] http://ecm29.ecanews.org [2] http://www.facebook.com/29thEuropeanCrystallographicMeeting [3] http://www.irb.hr/eng/Research/Divisions-and-Centers/Division-of-Physical-Chemistry/Laboratory-for-chemical-and-biological-crystallography/Igor-Sabljic
[ccp4bb] PhD in structural biology of membrane protein complexes, IST Austria
Applications are invited for the PhD course in IST Austria, with specialisation in structural biology of large membrane protein complexes, in particular complex I. Complex I is central to bioenergetics – it is the first and largest enzyme of the respiratory chain in mitochondria and bacteria. It is also involved in a wide range of human diseases. Sazanov lab uses the bacterial enzyme as a ‘minimal’ model of the more elaborate mammalian complex I. We have determined, by X-ray crystallography, all currently known atomic structures of complex I, starting with the hydrophilic domain (Science 2005, 2006), followed by the membrane domain (Nature 2010, 2011) and, finally, the recent (Nature 2013) structure of the entire Thermus thermophilus complex (536 kDa, 16 subunits, 9 Fe-S clusters, 64 TM helices). Structures suggest a unique mechanism of coupling between electron transfer in the hydrophilic domain and proton translocation in the membrane domain, via long-range (up to ~200 Å) conformational changes. Future studies are aimed at the elucidation of this mechanism and the determination of the structure of much larger mitochondrial enzyme, as well as other related complexes (https://ist.ac.at/research/research-groups/sazanov-group/). We use both X-ray crystallography and the most advanced single particle cryo-EM methods. The Institute of Science and Technology is located near Vienna on a dedicated campus. IST Austria is a new institute dedicated to basic research, providing world-class research environment and benefits. PhD program at the IST lasts 4-5 years and involves 1 year Phase 1 with rotations in 3 different groups, followed by Phase 2 conducting research in the selected group. Further information is available at https://ist.ac.at/graduate-school/phd-program/. The deadline for applications is 15th of January 2015. Informal queries should be forwarded to Dr. Leonid Sazanov (saza...@mrc-mbu.cam.ac.uk).
[ccp4bb] BCA Biological Structures Group (BSG) Winter Meeting, 15-17Dec 2014.
Dear All Please support the BCA winter meeting this year which, in a break from convention, is being held at ESRF/ILL, Grenoble, France - as you know, a major centre for structural biology research and infra-structure. This is an experiment for the BSG committee, really, being in the spirit of the International Year of Crystallography, etc, and is perhaps a one-off event. However, registrations from the UK are low so please register, publicise the meeting and encourage your group members to attend, if at all possible. There is some urgency in this and I can't put it better than one of the local organisers: ...it needs to be done soon and it needs to have as many people as possible trying to get it going. We are trying hard to mobilise people at this end... The BSG is extremely appreciative of the hard-working organisers in Grenoble who have put together an excellent programme covering: Research Infrastructures: State-of-the-Art and Impact for Structural Biology, Future Opportunities for UK Structural Biology in Grenoble, Combining X-rays Neutrons in Structural Biology, Structural Biology on the EPN Campus, Emerging Techniques in Structural Biology. Registration and all other details are available at this link: http://bsg.crystallography.org.uk/index.html We look forward to seeing you there. Best wishesJon Cooper
[ccp4bb] Postdoctoral Position at the Institute for Bioscience and Biotechnology Research
Dear crystallographic community The Institute for Bioscience and Biotechnology Research (IBBR) at the University of Maryland is seeking a highly motivated postdoctoral fellow. We are seeking an individual with an interest in protein engineering and structural biology to participate in a new IBBR initiative in conjunction with the Center for Biomolecular Therapeutics (CBT). IBBR is a joint research institute, which brings together partner institutions including the University of Maryland College Park (UMCP), University of Maryland Baltimore (UMB) and the National Institute of Standards and Technology (NIST), and is geographically located at the nexus of these institutions and in the hub of Maryland's biotechnology corridor (www.ibbr.umd.edu). The mission of IBBR is to conduct groundbreaking biomolecular and measurement science research to generate innovative technologies and solutions for medical and public health applications. IBBR is committed to providing an exceptional environment for specialized training and to mentoring tomorrow's biotechnology workforce. Interested applicants can apply at the following link: https://ejobs.umd.edu/postings/30999 Regards, Eric _ Eric A. Toth, Ph.D. Assistant Professor University of Maryland School of Medicine Department of Biochemistry and Molecular Biology Marlene and Stewart Greenebaum Cancer Center Section Leader, Structural Biology Center for Biomolecular Therapeutics 9600 Gudelsky Drive Rockville, MD 20850 Email: et...@som.umaryland.edu Phone: x-240-314-6516 Faculty Profilehttp://medschool.umaryland.edu/FACULTYRESEARCHPROFILE/viewprofile.aspx?id=8032 _ Eric A. Toth, Ph.D. Assistant Professor University of Maryland School of Medicine Department of Biochemistry and Molecular Biology Marlene and Stewart Greenebaum Cancer Center Section Leader, Structural Biology Center for Biomolecular Therapeutics 9600 Gudelsky Drive Rockville, MD 20850 Email: et...@som.umaryland.edu Phone: x-240-314-6516 Faculty Profilehttp://medschool.umaryland.edu/FACULTYRESEARCHPROFILE/viewprofile.aspx?id=8032
Re: [ccp4bb] Intensities and amplitudes
Dear Mohamed, At the moment, a lot of programs require amplitudes, but I believe that they should all eventually be updated to use intensities. In fact, we’re in the end stages of a large project to switch Phaser from using amplitudes to using intensities. There are a number of reasons why, in principle, it’s better to work in terms of intensities. One is that it’s perfectly reasonable to have a negative observed intensity, which can come from subtracting a background estimate with measurement errors from a very weak peak with its own measurement errors. That, of course, is where the French and Wilson algorithm comes in, allowing an amplitude to be estimated without simply taking a square root. However, the problem with the French and Wilson algorithm is that it loses information, i.e. you can’t reconstruct the intensity and its standard deviation. What you get out of French Wilson depends on the estimate of the expected intensity for a reflection, which is typically taken from the mean in the resolution shell but should vary with direction for crystals suffering from anisotropic diffraction and should be modulated for crystals with translational non-crystallographic symmetry. Another reason it’s better to work in terms of intensities is that it’s reasonable to assume that the measurement errors for intensities are Gaussian, but then less reasonable to assume that for amplitudes (particularly with the problem that amplitudes can’t be negative). For now, you need amplitudes for a lot of purposes and then the French Wilson algorithm is useful. But what I would strongly recommend is that you hang on to the intensities and you make sure that the intensities are deposited at the PDB. It’s a pity that many PDB depositions only have amplitudes that have been through French Wilson, so that new procedures based on intensities won’t be able to be applied with their full power. Best wishes, Randy Read - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical ResearchTel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk On 1 Dec 2014, at 20:49, Mohamed Noor mohamed.n...@staffmail.ul.ie wrote: Dear crystallographers Is there any reason for using one data type over the other? Are there any errors associated with the French and Wilson I-to-F conversion step? Thanks. Mohamed
Re: [ccp4bb] Intensities and amplitudes
Hi Randy, I can see all good reasons for using intensities! What about maps and R-factors? I guess you still need F to compute them (I realize you can compute R(I) but this is not what people are used to do in general), and if that's the case then I-F is still inevitable (at least for some purposes). Thanks, Pavel On Tue, Dec 2, 2014 at 1:26 PM, Randy Read rj...@cam.ac.uk wrote: Dear Mohamed, At the moment, a lot of programs require amplitudes, but I believe that they should all eventually be updated to use intensities. In fact, we’re in the end stages of a large project to switch Phaser from using amplitudes to using intensities. There are a number of reasons why, in principle, it’s better to work in terms of intensities. One is that it’s perfectly reasonable to have a negative observed intensity, which can come from subtracting a background estimate with measurement errors from a very weak peak with its own measurement errors. That, of course, is where the French and Wilson algorithm comes in, allowing an amplitude to be estimated without simply taking a square root. However, the problem with the French and Wilson algorithm is that it loses information, i.e. you can’t reconstruct the intensity and its standard deviation. What you get out of French Wilson depends on the estimate of the expected intensity for a reflection, which is typically taken from the mean in the resolution shell but should vary with direction for crystals suffering from anisotropic diffraction and should be modulated for crystals with translational non-crystallographic symmetry. Another reason it’s better to work in terms of intensities is that it’s reasonable to assume that the measurement errors for intensities are Gaussian, but then less reasonable to assume that for amplitudes (particularly with the problem that amplitudes can’t be negative). For now, you need amplitudes for a lot of purposes and then the French Wilson algorithm is useful. But what I would strongly recommend is that you hang on to the intensities and you make sure that the intensities are deposited at the PDB. It’s a pity that many PDB depositions only have amplitudes that have been through French Wilson, so that new procedures based on intensities won’t be able to be applied with their full power. Best wishes, Randy Read - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical ResearchTel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk On 1 Dec 2014, at 20:49, Mohamed Noor mohamed.n...@staffmail.ul.ie wrote: Dear crystallographers Is there any reason for using one data type over the other? Are there any errors associated with the French and Wilson I-to-F conversion step? Thanks. Mohamed
Re: [ccp4bb] Intensities and amplitudes
Hi Pavel, We were chatting with Phil Evans the other day about things like this, and generally we were in agreement that any programs that need amplitudes (and you’re right of course, you have to have some sort of amplitude to calculate a map!) should be able to compute them on the fly. That may well involve the French Wilson algorithm, but can take advantage of whatever is understood by the program (e.g. anisotropy and translational non-crystallographic symmetry, both of which in principle can be modeled better as the atomic model improves). I haven’t really worried about R-factors. We could learn to embrace the R-factor on intensity that small molecule crystallographers are comfortable with but, as you say, people are not used to these. If we compute amplitudes on the fly, with a French Wilson algorithm that is calibrated better as the model improves, the R-factors will be calculated with a changing set of Fobs. This would probably be a minor effect, but it’s slightly disconcerting. Randy - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical ResearchTel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk On 2 Dec 2014, at 21:44, Pavel Afonine pafon...@gmail.com wrote: Hi Randy, I can see all good reasons for using intensities! What about maps and R-factors? I guess you still need F to compute them (I realize you can compute R(I) but this is not what people are used to do in general), and if that's the case then I-F is still inevitable (at least for some purposes). Thanks, Pavel On Tue, Dec 2, 2014 at 1:26 PM, Randy Read rj...@cam.ac.uk wrote: Dear Mohamed, At the moment, a lot of programs require amplitudes, but I believe that they should all eventually be updated to use intensities. In fact, we’re in the end stages of a large project to switch Phaser from using amplitudes to using intensities. There are a number of reasons why, in principle, it’s better to work in terms of intensities. One is that it’s perfectly reasonable to have a negative observed intensity, which can come from subtracting a background estimate with measurement errors from a very weak peak with its own measurement errors. That, of course, is where the French and Wilson algorithm comes in, allowing an amplitude to be estimated without simply taking a square root. However, the problem with the French and Wilson algorithm is that it loses information, i.e. you can’t reconstruct the intensity and its standard deviation. What you get out of French Wilson depends on the estimate of the expected intensity for a reflection, which is typically taken from the mean in the resolution shell but should vary with direction for crystals suffering from anisotropic diffraction and should be modulated for crystals with translational non-crystallographic symmetry. Another reason it’s better to work in terms of intensities is that it’s reasonable to assume that the measurement errors for intensities are Gaussian, but then less reasonable to assume that for amplitudes (particularly with the problem that amplitudes can’t be negative). For now, you need amplitudes for a lot of purposes and then the French Wilson algorithm is useful. But what I would strongly recommend is that you hang on to the intensities and you make sure that the intensities are deposited at the PDB. It’s a pity that many PDB depositions only have amplitudes that have been through French Wilson, so that new procedures based on intensities won’t be able to be applied with their full power. Best wishes, Randy Read - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical ResearchTel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk On 1 Dec 2014, at 20:49, Mohamed Noor mohamed.n...@staffmail.ul.ie wrote: Dear crystallographers Is there any reason for using one data type over the other? Are there any errors associated with the French and Wilson I-to-F conversion step? Thanks. Mohamed
[ccp4bb] Postdoctoral Positions Available
Postdoctoral Positions at Indiana University School of Medicine My lab will have two postdoc positions available, one immediately and the other in April 2015. A summary of what we do can be found at http://snri.iusm.iu.edu/people/primary-investigators/quyen-q-hoang-ph-d/ http://snri.iusm.iu.edu/people/primary-investigators/quyen-q-hoang-ph-d/ No particular skill sets are required. We use a wide range of techniques including computational chemistry, molecular biology, protein biochemistry, enzymology, X-ray crystallography and other biophysical methods, yeast genetics, cell biology, and a little bit of C. elegans. I will show you these techniques as they become applicable to your project(s), but you must come with a desire to learn and a passion to understand the biological systems at the molecular level. If you are interested, please email your CV and 3 reference letters to qqho...@iu.edu mailto:qqho...@iu.edu. Cheers, Quyen
