Re: [ccp4bb] Experimental phasing Selenomethionine data collection etc. tips
Hi, > What if instead of images we just collected a list of x-y coordinates of > photon hits vs time? This is how the Tristan detector works, it is based on timepix3 chips and the data is a read as time stamped x-y co-ordinates + counts and then diffraction images are reconstructed from this information downstream. This means you have complete freedom about how you want to bin your data in terms of time/dose. https://ieeexplore.ieee.org/document/9875340 We’ve used the detector to test Hadamard multiplexing of time/dose bins to boost the ‘weak images’ from small bins to help with indexing and integration prior to deconvolution back into time/dose resolved data. However, this is a work in process we are waiting for some software updates to help with the image reconstruction part of the process but the detector appears to work very well for this kind of application! Briony From: CCP4 bulletin board on behalf of Guillaume Gaullier Date: Friday, 17 May 2024 at 17:07 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Experimental phasing Selenomethionine data collection etc. tips CAUTION: External Message. Use caution opening links and attachments. Hello, > What if instead of images we just collected a list of x-y coordinates of > photon hits vs time? This already exists, but for electrons: https://doi.org/10.1107/S205225252000929X This is the technology in Falcon4 detectors. The advantage is that it allows you to decide how to slice the total dose into dose fractions *after* the data collection. So, when setting up the collection at the microscope, you only need to worry about how much total dose to use. With the previous generation of detectors, during set up you have to decide how much total dose but also how many dose fractions, and if it's not optimal you can't change it once the data is collected. I don't understand detector technology enough to tell whether this should be possible for X-rays. But out of curiosity, how would you use this detector if you had one? What would it enable that you can't do now? Cheers, Guillaume From: CCP4 bulletin board on behalf of James Holton Sent: Friday, May 17, 2024 5:27:02 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Experimental phasing Selenomethionine data collection etc. tips A few follow-up questions I got out-of-band: > how did you get to the 1:1 relationship between Bijvoet ratio and dose? > I got this from fitting a straight line to Table 1 of Banu's 2004 paper: 10.1107/S0907444904007917 Is this a rough estimate based on a singular result? Of course it is! This is how we roll in radiation damage research. > > Comment: with the more modern pixel array detectors (e.g. Eiger), you > can slice your dose even more finely than 0.1s, and not worry about > the readout time. yes. With a bit of a caveat on how many photons/pixel you need for stable background subtraction. XDS starts having issues around 1 photon/pixel or less, and DIALS claims to be able to get to 0.01 photons/pixel, but I have not personally pushed it that far. Not yet. I have a plan to try and push zero-dose extrapolation to the one-photon-per-image level, but that is on another thread. > is it better to collect 360 or 720º at half the dose Nothing wrong with going longer than 360, especially if you want to do zero-dose extrapolation, because it is only by repeating the same phi range (and everything else) exactly that you get a genuinely "same" increment in dose. However, once you go past 360 the "multiplicity" you gain starts turning into what you might call a "redundancy". What I mean by that is that in the first 360 each spot and its symmetry mates generally show up on different pixels. Each pixel has about 1% to 3% calibration error associated with it (depending on the detector). So, for the 2nd 360 you will re-measure all the same spots with the same pixels again, repeating a systematic error. You will also have the same sample self-absorption, etc. But, the pixel calibration error starts to really matter for anomalous at high "redundancy". To put it another way, if a particular pixel has 1% error, then counting more than 10,000 photons with it is a waste, because the systematic error of 1% will start to dominate the total error at higher photon counts. So, for anomalous especially, I recommend moving the detector between 360s. Sliding it horizontally is best. Or you can use 2theta. But, a small change in detector distance can usually do it and is almost always an available option. The only problem with all this "dose slicing" is the images get very very weak. And that brings us back to the "weak image limit". What if instead of images we just collected a list of x-y coordinates of photon hits vs time? Anyone have a suggestion for the name to give to the program that can process such data? -James Holton MAD Scientist On 5/15/2024 3:28 PM, James Holton wrote: > > Thank you to all who provided
Re: [ccp4bb] How to compare the same protein crystallized in different conditions?
Hi Murpholino, Helen Ginn is developing software to characterise changes in protein structures (especially informative when the changes are small but significant)– there is a web app and a download here: https://rope.hginn.co.uk I recommend watching the youtube tutorial. From: CCP4 bulletin board on behalf of Murpholino Peligro Date: Tuesday, 9 April 2024 at 02:39 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] How to compare the same protein crystallized in different conditions? Caution External Email: Do not click any links or open any attachments unless you trust the sender and know that the content is safe. Hi... Let's say I want to compare the same protein crystallized in different conditions. Same space group, almost same resolution. The global RMSD will be pretty small (around 0.3 Angstroms). There will be some changes in rotamers in some residues and some extra waters here and there... Besides local rsmd and contact maps (or differences in contact maps)... is there anything else to get a decent view of these small changes? Thanks a lot. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Crystallisation textbook
You can pre-order the new edition of Crystallography made crystal clear! https://blackwells.co.uk/bookshop/product/Crystallography-Made-Crystal-Clear-by-Arwen-R-Pearson-author-Nicholas-Pearce-author-Jennifer-Wierman-author/9780323910484 I’m definitely going to order a copy - along with Macromolecular Crystallization and Crystal Perfection that John has already recommended. Briony From: CCP4 bulletin board on behalf of Hough, Michael (DLSLtd,RAL,LSCI) <69715b1ac6c0-dmarc-requ...@jiscmail.ac.uk> Date: Friday, 14 July 2023 at 15:19 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Crystallisation textbook Hi all, I'd be grateful for any recommendations of a good up-to-date textbook covering macromolecular crystallisation. Currently we are using the excellent book by Terese Bergfors (2009) but would be interested if there is anything more recent with discussion around automation, micro-crystallisation and so on Many thanks in advance for your help! Kind regards, Mike -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] CCP4 NORTHERN PROTEIN STRUCTURE MEETING 2023
Dear All, The 2023 CCP4 Northern Protein Structure Workshop will be held at the University of Nottingham on the 26-27th October. Registration is FREE and this year we have a limited number of travel bursaries available so please encourage your research students and early career post-doctoral researchers to register and submit and abstract before 1st September if they wish to be considered for financial support. More information and registration can be found here: https://www.eventbrite.co.uk/e/ccp4-northern-structural-biology-meeting-tickets-664501250127?utm-campaign=social=attendeeshare=discovery=listing=cp=ebdsshwebdesktop Programme: The Key Note Lecture will be delivered by Professor Jim Naismith FRS FRSE FMedSci MAE FRSC FInstP FRSB a world leading expert in structural biology, Professor of Structural Biology at the University of Oxford and Director of the Rosalind Franklin Institute. The aim of this meeting is to encourage early career researchers from Northern England and Scotland to present and discuss their research in a friendly and supportive environment. The programme will cover all areas of structural biology and include plenty of time for networking – this year’s topic is “An integrative approach”. We plan to hold a careers panel on the last day where academics and industrial scientists will share their experiences and answer questions about careers options. Best Wishes, The organisers – Briony Yorke (b.a.yo...@leeds.ac.uk<mailto:b.a.yo...@leeds.ac.uk>) and Ivan Campeotto (ivan.campeo...@nottingham.ac.uk<mailto:ivan.campeo...@nottingham.ac.uk>) To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Post-Doctoral Research Assistant position at the University of Bradford
We are looking to recruit a post-doc with a solid background in structural biology, molecular biology or methods development (crystallography/spectroscopy) to join our team investigating the molecular mechanisms leading to the formation of cataracts. You will join myself and Dr. Yvonne Nyathi at the University of Bradford. This project is highly interdisciplinary and there are opportunities to develop your own research interests while learning new skills and applying to them to an important clinical target. This project will involve working closely with scientists at Diamond Light Source, EMBL@PetraIII and Eli-beamlines and so the ability to travel is highly desirable. The project is funded for 1 year with the possibility of an extension. Full support will be provided to candidates wishing to apply for individual post-doctoral fellowships during this time. For more information please contact myself at b.yor...@bradford.ac.uk. Full Job Description and application process can be found on the University of Bradford Website: https://jobs.bradford.ac.uk/Vacancy.aspx?ref=HR0120595 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
