[ccp4bb] Reminder - CCP4 Study Weekend 2015 - registration closes 14th December 2014
The CCP4 Study Weekend (7 - 9 January 2015) East Midlands Conference Centre, University of Nottingham Wednesday 7 - MX User Meeting Thursday 8 / Friday 9 - CCP4 Study Weekend Advances in Experimental Phasing We cordially invite you to participate in the 2015 CCP4 Study Weekend at the the East Midlands Conference Centre, University of Nottingham. The annual CCP4 Study Weekend is a chance to shake off the post-New Year torpor, and work hard and play hard with your fellow crystallographers. Once again, we have put together an exciting scientific programme for the Thursday and Friday, either side of the traditional conference dinner. Please also check out the satellite meetings which may be of interest. The Study Weekend is a chance to catch up with old friends, but is also a chance to meet the CCP4 staff who will be there to present and demonstrate the latest software and to answer questions - please say hello! This year, the topic for the Study Weekend is Advances in Experimental Phasing. In keeping with previous CCP4 meetings, the lectures will focus on the presentation and discussion of advanced methods and techniques developed and used by the leaders in the field. Scientific Organisers Thomas Schneider - EMBL Hamburg (Germany) Airlie McCoy - University of Cambridge (UK) Further details of the program and the registration are at http://www.ccp4.ac.uk/events/CCP4_2015 Terms and Conditions apply. Please read the cancellation policy before applying. -- Scanned by iCritical.
Re: [ccp4bb] HKL2000 Display
Hi Muhammed, It looks a lot to me like denzo thinks your detector has a larger image size than the actual number of elements in the array. However, I don't use denzo so I'm not commenting from experience. Cheers -- David On 3 December 2014 at 04:09, Muhammed bashir Khan muhammad.bashir.k...@univie.ac.at wrote: Hi All; Could somebody explain why my Display image in HKL2000 look like that. Image attached. Thanks for help in advance. Bashir Department of Biochemistry University of Alberta Edmonton Canada
[ccp4bb] Reminder: Open postdoc positions in research and scientific software development (EMBL Hamburg, Lamzin)
Just a reminder: The deadline for applications is 7 December 2014. Next Sunday! Philipp Dear colleagues, I would like to make you aware of two open positions in the Lamzin group at the EMBL in Hamburg. We are looking for two enthusiastic postdoctoral fellows in research and scientific software development: 1) The post holder will play a key role in the development of the ARP/wARP software for crystallographic structure determination and the building of macromolecular models in 3D electron density maps generated from X-ray diffraction. http://www.embl-hamburg.de/aboutus/jobs/searchjobs/index.php?newlang=1ref=HH_00072back=%2Faboutus%2Fjobs%2Fsearchjobs%2Findex.php%3Floc%3D3%26list%3D1 2) The post holder will be involved in the development of novel software approaches for free electron laser data interpretation beyond phase retrieval and imaging, towards refined models and their validation. http://www.embl-hamburg.de/aboutus/jobs/searchjobs/index.php?newlang=1ref=HH_00073back=%2Faboutus%2Fjobs%2Fsearchjobs%2Findex.php%3Floc%3D3%26list%3D1 The deadline for applications is 7 December 2014. Please apply online through www.embl.org/jobs http://ig14.i-grasp.com//fe/tpl_embl01.asp?newms=apid=53190aid=15470. Further information may be obtained from Victor Lamzin, victor[at]embl-hamburg.de Best regards Philipp -- -- Dr Philipp Heuser Senior Technical Officer EMBL-Hamburg c/o Building 25A, DESY Notkestrasse 85 22603 Hamburg phone: +49 40 89902 128 fax: +49 40 89902 149 mail:philipp.heu...@embl-hamburg.de web: www.philipp-heuser.de --
Re: [ccp4bb] Intensities and amplitudes
Dear Randy, I could not agree more. Statistical methods for phasing and refinement must be better using the observed intensities and their esds than with (c)truncated F-values. In particular one should merge intensities, not truncated Fs! To elaborate on Harry's comment, when SHELXL started refining only against intensities 22 years ago, I received many complaints from irate small molecule crystallographers whose papers had been rejected because the unweighted R-factors R2 (based on intensities) were too high. I even sent a letter to editors of the journals involved to explain why R-factors based on intensities are at least twice as high as those based on F, but to no avail. So I had to output R1 (the unweighted R-value based on F) even though the structure had been refined against intensitites, then everyone was happy. Do I correctly understand that you have developed new (better) maximum likelihood criteria for use with I rather than F? Best wishes, George On 12/02/2014 10:26 PM, Randy Read 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 t he 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 -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-33021 or -33068 Fax. +49-551-39-22582
Re: [ccp4bb] HKL2000 Display
I’ve seen this when the description in the site file does not actually match the data. // Johan On Dec 3, 2014, at 7:25, David Waterman dgwater...@gmail.com wrote: Hi Muhammed, It looks a lot to me like denzo thinks your detector has a larger image size than the actual number of elements in the array. However, I don't use denzo so I'm not commenting from experience. Cheers -- David On 3 December 2014 at 04:09, Muhammed bashir Khan muhammad.bashir.k...@univie.ac.at wrote: Hi All; Could somebody explain why my Display image in HKL2000 look like that. Image attached. Thanks for help in advance. Bashir Department of Biochemistry University of Alberta Edmonton Canada Research Specialist @ Gonen Lab Janelia Research Campus * 19700 Helix Drive Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376
Re: [ccp4bb] HKL2000 Display
Yes, it is probably the wrong detector type, or the wrong parameters, perhaps binned vs. unbinned. On 12/03/14 07:25, David Waterman wrote: Hi Muhammed, It looks a lot to me like denzo thinks your detector has a larger image size than the actual number of elements in the array. However, I don't use denzo so I'm not commenting from experience. Cheers -- David On 3 December 2014 at 04:09, Muhammed bashir Khan muhammad.bashir.k...@univie.ac.at mailto:muhammad.bashir.k...@univie.ac.at wrote: Hi All; Could somebody explain why my Display image in HKL2000 look like that. Image attached. Thanks for help in advance. Bashir Department of Biochemistry University of Alberta Edmonton Canada -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] HKL2000 Display
You are using an incorrect site file. Whatever you provided to the program as description of the detector used during data collection needs to be changed. D. Muhammed bashir Khan wrote: Hi All; Could somebody explain why my Display image in HKL2000 look like that. Image attached. Thanks for help in advance. Bashir Department of Biochemistry University of Alberta Edmonton Canada Dominika Borek, Ph.D. *** UT Southwestern Medical Center 5323 Harry Hines Blvd. *** Dallas, TX 75390-8816 214-645-9577 (phone) *** 214-645-6353 (fax)
Re: [ccp4bb] Intensities and amplitudes
Dear George, Yes, we’ve developed new likelihood functions that work with intensity data. They’re already available for the molecular replacement calculations in recent nightly-build versions of Phaser (though it’s been a while since a new nightly was released, and we’ve fixed a few problems with outliers that were more extreme than we had anticipated encountering). I’ll be presenting our work on the intensity-based SAD likelihood target at the upcoming CCP4 Study Weekend. It’s possible to define exact intensity-based likelihood functions (at least “exact” when the measurement errors are Gaussian in the observed intensity), but we haven’t found a way of evaluating them without either numerical integration (expensive) or approximation. However, we’ve got a new approximation that turns out to be excellent over the whole range from small to extremely large intensity errors, and which is very efficient to work with. Best wishes, Randy On 3 Dec 2014, at 15:07, George M. Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote: Dear Randy, I could not agree more. Statistical methods for phasing and refinement must be better using the observed intensities and their esds than with (c)truncated F-values. In particular one should merge intensities, not truncated Fs! To elaborate on Harry's comment, when SHELXL started refining only against intensities 22 years ago, I received many complaints from irate small molecule crystallographers whose papers had been rejected because the unweighted R-factors R2 (based on intensities) were too high. I even sent a letter to editors of the journals involved to explain why R-factors based on intensities are at least twice as high as those based on F, but to no avail. So I had to output R1 (the unweighted R-value based on F) even though the structure had been refined against intensitites, then everyone was happy. Do I correctly understand that you have developed new (better) maximum likelihood criteria for use with I rather than F? Best wishes, George On 12/02/2014 10:26 PM, Randy Read 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 t he 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 -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-33021 or -33068 Fax. +49-551-39-22582 -- Randy J. Read Department of
Re: [ccp4bb] HKL2000 Display
Hi All; Thanks everybody. It was wrong detector site file. Now its working. Thanks Bashir On Wed, December 3, 2014 17:19, David Schuller wrote: Yes, it is probably the wrong detector type, or the wrong parameters, perhaps binned vs. unbinned. On 12/03/14 07:25, David Waterman wrote: Hi Muhammed, It looks a lot to me like denzo thinks your detector has a larger image size than the actual number of elements in the array. However, I don't use denzo so I'm not commenting from experience. Cheers -- David On 3 December 2014 at 04:09, Muhammed bashir Khan muhammad.bashir.k...@univie.ac.at mailto:muhammad.bashir.k...@univie.ac.at wrote: Hi All; Could somebody explain why my Display image in HKL2000 look like that. Image attached. Thanks for help in advance. Bashir Department of Biochemistry University of Alberta Edmonton Canada -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu -- Muhammad Bashir Khan ** Department for Structural and Computational Biology Max F. Perutz Laboratories University of Vienna Campus Vienna Biocenter 5 A-1030 Vienna Austria Austria Phone: +43(1)427752224 Fax: +43(1)42779522
[ccp4bb] off-topic: short oligo concentrator
Hi all, We're planning to use short oligos to co-crystallize with protein. Basically we will synthesis that from company and then purified by ion-exchange then concentrate it. Does any one know a easy way or product to concentrating short oligo (such as 5nt)? The only way came to my mind, is to desalt it by dialysis first, then use SpeedVac. I will appreciate for any suggestion. Best, Xiao
Re: [ccp4bb] Intensities and amplitudes
Hi Randy, Question regarding your reply to Pavel: 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 may have misunderstood you completely, but do you mean that the Fobs's will be recalculated as the model improves (this is where French-Wilson comes into effect, right)? Or only once during refinement? Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Randy Read [rj...@cam.ac.uk] Sent: Wednesday, December 03, 2014 12:46 AM To: CCP4BB@JISCMAIL.AC.UK Subject: 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
[ccp4bb] tRNA and aminoacyl-tRNA synethetase complex question
Dear CCP4BB Members, I'm trying to design a tRNA expression system for its co-crystal structure with an aminoacyl-tRNA synthetase (class Ia, eukaryotic). My question is how a specific tRNA is chosen among tRNAs of various anticodons for co-crystallization attempts. Can codon usage be a basis of the choice? How about levels of modification? Or do I have to try every anticodon to see which works? Thank you in advance for your valuable advice, Hank
[ccp4bb] An opening for a post-doctoral position at NIMHANS, Bangalore, India
*Applications are invited for a post-doctoral position at NIMHANS, Bangalore, India.* At National Institute of Mental Health and Neuro Sciences (NIMANS), a post-doctoral / Research Associate position is available in our Structural Biology Lab. The candidate should have a Ph. D with substantial research experience in protein biochemistry. Research experience in protein crystallography is also preferable. Interested candidates may send their recent CV to: B. Padmanabhan, Ph. D Additional Professor, Department of Biophysics, NIMHANS, Bangalore, India. Email: balapa...@gmail.com Best regards, B. Padmanabhan.
