Re: [ccp4bb] Microscope camera
Dear Pat, we are facing the same problem and the most effective solution I found is to print support for smartphones, which today offer incredibly good cameras. Here are two examples of open access designs: https://www.openocular.com/ https://bioceednews.w.uib.no/2020/12/07/3d-printing-a-smartphone-holder-for-taking-pictures-on-a-microscope/ Next step is to build a low cost crystallization plate imager... Cheers, Claude Le 25/04/2024 à 10:56, Harry Powell a écrit : Hi Pat Depends on how much you want to spend. I’d start with a web search for “webcam astrophotography”, which should show options on how to remove a webcam’s lens and mount the cam (not the kens, of course!) on another optical instrument. Back in the day, I had a Philips webcam that had a screw-out lens - this device was used by amateur astronomers as a cheap way into astrophorography. Philips no longer seem to make webcams, but (from what I remember) this was plug-and-play, and used the drivers on my Mac. You could go for a mirrorless interchangeable lens camera - Nikon actually have their own webcam utility to turn your DSLR/mirrorless into a suitable device, and this would be most likely to use the SLR mount. E-Bay have Nikon bodies starting at around $200 today. Harry On 24 Apr 2024, at 22:15, Patrick Loll wrote: Greetings, hive mind, We have an old (but still useful) Nikon SMZ stereomicroscope that we use for mounting crystals. I’d like to attach a digital camera to the phototube, both to capture crystal images for archival purposes, and also to live-stream as a teaching tool. I’d be grateful for any suggestions for an inexpensive option here. When this camera was new we used it with an SLR that captured images on *film* (this is where the students gasp). We’ve since gone through one digital camera that probably still works, but the interface and software have become obsolescent. Meanwhile, the microscope keeps on truckin’; interesting to reflect on the relative lifetimes of analog vs. digital tools… Thanks in advance for any suggestions, Pat --- Patrick J. Loll, Ph. D. (he, him, his) Professor of Biochemistry & Molecular Biology Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102 USA (215) 762-7706 pjl...@gmail.com pj...@drexel.edu 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 ofwww.jiscmail.ac.uk/CCP4BB, a mailing list hosted bywww.jiscmail.ac.uk, terms & conditions are available athttps://www.jiscmail.ac.uk/policyandsecurity/ 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 ofwww.jiscmail.ac.uk/CCP4BB, a mailing list hosted bywww.jiscmail.ac.uk, terms & conditions are available athttps://www.jiscmail.ac.uk/policyandsecurity/ -- Dr Claude Sauter Directeur de Recherche Président de l'Association Française de Cristallographie Institut de Biologie Moléculaire et Cellulaire CNRS--Unistra Structure, évolution & dynamique des complexes protéine:ARNt Lab. Architecture et Réactivité de l'ARN (ARN-UPR 9002-CNRS) 2 allée Conrad Roentgen, F-67084 Strasbourg -- France tel +33 (0)388 417 109 --http://cj.sauter.free.fr/xtal 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] Early bird registration for the European Crystallography Meeting (ECM33; August 23-27)
Dear all, I forward you a message from the ECA vice-president concerning the ECM33: discover the amazing venue and exciting programme! Best regards, Claude # Dear colleagues, You can make your early bird registration for the European Crystallography Meeting (ECM33; August 23-27) in Versailles until April 18. https://www.ecm33.fr/registration After this date the registration fee increases by 50-60€. Note also that individual members of the European Crystallographic Association (ECA) receive a 50€ discount on the registration fee. You can become an individual member of the ECA (10€/year) by clicking on the following link https://ecanews.org/about-eca/membership/individual-members/ I would also like to draw your attention to the celebration of the 50th anniversary of the European Committee of Crystallography and the 25th anniversary of the European Association of Crystallography which will take place before the Gala Dinner of the Meeting. https://ecanews.org/blog/gold-and-silver-treasures-of-european-crystallography/ More details about this event can be found on the ECA and ECM33 websites. Sincerely, Arie van der Lee Vice-president of the European Crystallography Association -- Dr Claude Sauter Directeur de Recherche Institut de Biologie Moléculaire et Cellulaire (IBMC-ARN-CNRS) Biologie des ARNt et pathogénicité tel +33 (0)388 417 102 2 allée Conrad Roentgen fax +33 (0)388 602 218 F-67084 Strasbourg - France http://cj.sauter.free.fr/xtal 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] COOT running on Macbook Pro M1 chip
Dear all, to continue on the same theme, a colleague biochemist asked me a couple of days ago if there is any incompatibility between PyMOL and other softwares used in structural biology and new mac M1 chips. Being a Linux user, I have no clue. Could mac users share their experience? Thanks Best regards, Claude Le 16/09/2021 à 09:40, WENHE ZHONG a écrit : Dear CCP4 community, The COOT is not running smoothly on my M1 chip Macbook. For example, when both model and the electron density map are displayed, the moving from one residue to the next (pressing SPACE bar) is lagging/slow (>2s). This only happened to my old computer, but I am surprised to find it happens in the newest macbook. Anyone have this problem and has a solution? Thanks. Best regards, Wim To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 -- Dr Claude Sauter Directeur de Recherche Institut de Biologie Moléculaire et Cellulaire (IBMC-ARN-CNRS) Biologie des ARNt et pathogénicité tel +33 (0)388 417 102 2 allée Conrad Roentgen fax +33 (0)388 602 218 F-67084 Strasbourg - France http://cj.sauter.free.fr/xtal To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
Re: [ccp4bb] Silicone oil for "modified microbatch"
Dear Patrick, the silicone oil you're looking for is very likely octamethyltrisiloxane (trade name BRB Silicone Oil 1 cSt): https://echa.europa.eu/substance-information/-/substanceinfo/100.003.181 You can get it from Hampton Research: https://hamptonresearch.com/product-Paraffin-Silicon-Oil-352.html or from Sigma: https://www.sigmaaldrich.com/catalog/product/aldrich/235709 Happy batch crystallization! Claude Le 19/01/2021 à 11:19, Patrick Shaw Stewart a écrit : Hi All Does anyone know where you can buy Silicone Oil Dow Corning 200/1cS nowadays? This is the silicone oil that can be mixed with regular paraffin oil to speed up evaporation in microbatch-under-oil experiments, ref below. The 1cS refers to the viscosity. We used to get this from BDH, in quite large batches, but that product is no longer available. Thx Patrick ___ D'arcy A, Elmore C, Stihle M, Johnston JE. A novel approach to crystallising proteins under oil. Journal of Crystal Growth. 1996 Oct 2;168(1-4):175-80. https://www.sciencedirect.com/science/article/pii/002202489600351X -- patr...@douglas.co.uk Douglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Patrick Shaw Stewart, Peter Baldock, Stefan Kolek http://www.douglas.co.uk Tel: 44 (0) 148-864-9090 US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 -- Dr Claude Sauter Institut de Biologie Moléculaire et Cellulaire (IBMC-ARN-CNRS) Biologie des ARNt et pathogénicité tel +33 (0)388 417 102 2 allée Conrad Roentgen fax +33 (0)388 602 218 F-67084 Strasbourg - France http://cj.sauter.free.fr/xtal To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
Re: [ccp4bb] Intergrown crystals and excess of nucleation
Le 09/09/2019 à 17:22, Nikolas a
écrit :
Dear
crystalgrowers,
I am
currently working with a protein that appeared to be
friendly but turned out it was not the case.
I found
myself to face -in the scale up- the opposite of the usual
problem of nucleation (I really love how this topic finds
new ways to make fun of me). In 24-well plates,
hanging-drop, for the same condition but in different drops
I found few big but intergrown crystals and/or a full with
microcrystals. Sometimes also in the same well, when having
more drops.
I already
decreased the concentration to less than 4mg/mL, made small
adjustments in the optimizations - both with apo and ligand
samples, used Al's oil.
I have
read about the "containerless crystallization" but since I
cannot obtain the sample myself I would like to know if
there are any experiences and/or if there are suggestions
for solving this problem.
Many
thanks!
Best
regards,
Nikolas
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Dear Nikolas,
since you have some crystal stock, I would definitely try seeding
to better control nucleation events in your drops. Then, instead
of using the containerless approach which requires two types of
oils to prepare floating drops, I suggest the crystallization in
agarose gel. Easy to perform, it favors the 3D growth of well
separated crystals in ideal convection-less conditions. In
addition, the gel provides a physical protection of your crystals
during handling, mounting and cryocooling. For more details, see "Crystal growth of proteins, nucleic acids, and
viruses in gels. Lorber et al.
Prog. Biophys. Mol. Biol. (2009),
101: 13-25."
Happy crystallization!
Claude
--
Dr Claude Sauter
Institut de Biologie Moléculaire et Cellulaire (IBMC-ARN-CNRS)
Biologie des ARNt et pathogénicité tel +33 (0)388 417 102
2 allée Conrad Roentgen fax +33 (0)388 602 218
F-67084 Strasbourg - France http://cj.sauter.free.fr/xtal
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[ccp4bb] 31st Rhine-Knee Regional Meeting on Structural Biology, September 27-29, Munster, France
The 31st Rhine-Knee Regional Meeting on Structural Biology will take place in the heart of the Vosges mountains from September 27 to September 29 at the Hotel de la Verte Vallée (http://www.vertevallee.com). Since it was established in 1987, the annual Regio-Meeting has been invaluable in facilitating discussions in the structural biology community in southwestern Germany, the Alsace region of France and an expanding area of Switzerland. It has helped establish networks for younger scientists, and highlight new strategies that can help advance projects. The scientific program of the 2017 edition includes *four keynote presentations* illustrating new developments in integrative structural biology (http://regiomeeting.eu/meeting-17/scientific-program) *New this year:* - Thanks to our sponsors, very attractive registration conditions (30 EUR only) are proposed to young scientists (PhD and postodoctoral fellows) who wish to present their research. - We also offer a few places (10-15) with special discount to highly motivated master students who whish to participate in their first international meeting. For more information: http://regiomeeting.eu/meeting-17 Email : regiomeetin...@ibmc-cnrs.unistra.fr We look forward to seeing you in September in Munster. Eric Ennifar & Claude Sauter -- Dr Claude Sauter Institut de Biologie Moléculaire et Cellulaire (IBMC-ARN-CNRS) Biologie des ARNt et pathogénicité tel +33 (0)388 417 102 15 rue René Descartes fax +33 (0)388 602 218 F-67084 Strasbourg - France http://cj.sauter.free.fr/xtal
[ccp4bb] Regio Meeting Satellite Symposium Bio-Crystallography highlights in France, Germany and Switzerland
In the context of the International Year of Crystallography and the Upper Rhine valley Regio Meeting (www.regiomeeting.eu), a symposium will take place from noon, September 23 till noon, September 24, at Mont St. Odile, Alsace, France, before the Regio Meeting and at the same place. Six renowned structural biologists, two per country, have accepted to present their latest achievements and to give an overview of on-going developments in the field of biocrystallography : Elena Conti, Department of Structural Cell Biology, Max-Planck Institute, Martinsried Structural insights into the mechanisms of RNA degradation Nenad Ban, Institute of Molecular Biology Biophysics, ETH, Zürich Beyond the prokaryotic ribosome Marc Delarue, Department of Structural Biology and Chemistry, Institut Pasteur, Paris Structural studies of pentameric ligand-gated ion channels Christoph Müller, Department of Structural and Computational Biology, EMBL, Heidelberg Structure-function studies of RNA polymerase I and III transcription Felix Rey, Structural Virology Unit, Institut Pasteur, Paris The first X-ray structure of a cell-cell fusion protein reveals homology to viral membrane fusion proteins, in spite of a different fusogenic mechanism Tilman Schirmer, Department of Structural Biology Biophysics, Biozentrum, Basel Mechanisms to regulate the cellular concentration of the bacterial second messenger c-di-GMP Online registration is open at http://www-ibmc.u-strasbg.fr/xtal2014/ Places are limited and are given in a first come, first served basis. Looking forward to seeing you in Mont Saint Odile The organizing committee -- Dr Claude Sauter Institut de Biologie Moléculaire et Cellulaire (IBMC-ARN-CNRS) Cristallogenèse Biologie Structurale tel +33 (0)388 417 102 15 rue René Descartes fax +33 (0)388 602 218 F-67084 Strasbourg - France http://cj.sauter.free.fr/xtal
Re: [ccp4bb] video that explains, very simply, what Structural Molecular Biology is about
Narayanan Ramasubbu a écrit : mb1pja wrote: Dear Fred A really nice video that would be great for giving non-crystallographers (including colleagues and 1st year students, and perhaps also friends and family) an overview of what we do. Thank you for pointing it out - and of course very many thanks to Dominique Sauter for making it. I am sure it will prove very popular. bet wishes Pete (Pete Artymiuk) On 11 Nov 2009, at 09:44, Vellieux Frederic wrote: Dear all, Thought I'd share this with you: I located this through Ms Ines Kahlaoui, from the Beja Higher Institute of Biotechnology in Tunisia (Ines has to teach and locates videos on the internet, which she then downloads and uses for teaching). Ines located this jewel: http://video.google.com/videoplay?docid=7084929825683486794ei=M3b5SvXqD6em2AK3jY33CQq=Plongee+coeur+vivant# This is the French version (explains everything about Structural Molecular Biology, but for the maths :-( , but also shows what we crystallographers have known for a long time, since the first colour ES graphics workstations in fact, that the electron are blue :-) ). Both French and English versions can be downloaded from http://cj.sauter.free.fr/xtal/Film/ No rights associated with the movie, and the Strasbourg group intends to release a higher quality version on DVD soon. Please contact them about that... I am only sharing what I thought was good for educational purposes. 18 minutes of your life, but worth it I think. So feel free to share this. Wish you all a nice day, Fred. Hi: Could someone point out the name and where to get these crystallization plates used in the video? By the way, this is a wonderful video. Subbu Dear Subbu and dear xtal lovers, the fancy plates used in the video are Nextal EasyXtal plates which are now sold by Qiagen. Concerning the video (thank you Fred for you kind advertisement!), the final version (English/French) will be available in DVD very soon, as well as divx and flash formats, we are working hard to get them ready by Christmas. This material will be released under the Creative Commons licence to make it easily accessible for all kind of education / teaching purposes. I'll keep you informed as soon as the final version is ready. Claude -- Dr Claude Sauter Institut de Biologie Moléculaire et Cellulaire (IBMC-ARN-CNRS) Cristallogenèse Biologie Structurale tel +33 (0)388 417 102 15 rue René Descartes fax +33 (0)388 602 218 F-67084 Strasbourg - France http://cj.sauter.free.fr/xtal
