Re: [ccp4bb] experiences with cross-polarisers / black-white imaging vs color
Hi Tommi, Obviously for LCP glass plates, color versus black and white should make little difference. For everything else, all darker colors would look more or less the same and lighter colors similarly so not very useful, in my experience. Nagarajan V. Nagarajan JANSi On 10/1/2020 12:19 AM, Kajander, Tommi A wrote: Hi all, can I get views on imagers with with cross-polarizers and how well that works with black-and-white imaging vs color? Thank you, Tommi Tommi Kajander, Ph.D., PI Structural Biology and Biophysics Institute of Biotechnology University of Helsinki Viikinkaari 1 (P.O. Box 65) 00014 Helsinki, Finland p. +358-2-941-58904 / +358-050-4480991 tommi.kajan...@helsinki.fi <mailto:tommi.kajan...@helsinki.fi> http://www.biocenter.helsinki.fi/bi/kajander/ 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] polarizer
Hi, place a linear polarizer below the tray and one above it, rotating the top one until you get the desired view. V. Nagarajan JANSi On 8/16/2020 8:26 AM, Diana Tomchick wrote: It's my understanding that you have two polarizers on your polarizer-microscope--one in the base, and the one that attaches to the magnifying lens. When you rotate the one on the lens so that it is 90 degrees to the one in the base, no (or very little) light should pass through to your eyes, unless there is a crystal that plane polarizes the light at an angle that differs from the two on the microscope. What you have is just one polarizing lens. Not sure how that would work, even if it is a circular polarizer. Diana ** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry UT Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND10.214A Dallas, TX 75390-8816 diana.tomch...@utsouthwestern.edu (214) 645-6383 (phone) (214) 645-6353 (fax) *From:* CCP4 bulletin board on behalf of Matthias Zeug *Sent:* Sunday, August 16, 2020 9:05 AM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] polarizer EXTERNAL MAIL Hi all, The polarizer-microscope in our facility is not working properly, and I have to check my plates using a standard stereo-microscope. As a workaround, I thought about buying one at Amazon, placing it on top of the plates and rotating it to still test for birefringence. The product is linked below. Does anyone have some experience with this kind of "homemade" system? And also (this might be a stupid question), does the product even work? As far as I know, the polarizers in the microscopes are linear polarizers, whereas the product linked below is a circular polarizer. I would also be happy for product recommendations (optimally available at the German Amazon). Cheers Matthias https://www.amazon.de/dp/B00XNMXYBY/ref=cm_sw_r_cp_apa_i_5YsoFbFQXTBP9 ___ Buchmann Institute of Molecular Life Sciences Goethe University Frankfurt To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying. UTSouthwestern Medical Center The future of medicine, today. 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] Protein or DNA crystals
Hi Joseph, Could you post the UV fluorescence image? Oftentimes, UV absorbing objects that do not fluoresce (such as nucleic acid crystals) show up dark against a brighter background in UV fluorescence. V. Nagarajan JANSi On 6/19/2017 7:20 AM, Joseph Ho wrote: Dear all: I would like to seek your opinion on our crystal hits. We are working on protein/dsDNA complex. By changing different protein and DNA (14-22bp) constructs, we recently got some hits from commercial screens using sitting drop vapor diffusion (very small xtals). The precipitant is PEG and the picture of crystals are attached. In this particular condition, it is 30%PEG3350, sodium succinate pH5.5 and 100mM NaCl. The crystal seems floating and sit in the bottom. We do some test shot from other conditions and it is not salt crystals. The crystals can suck in izit dye. I do some google and it seems izit dye also turns dsDNA crystal into blue. We also do UV/Vis microscope but no Trp fluorescence (6 Trp in 256 aa). It may due to low Trp. This is our first time to work on protein/DNA complex crystals and we are not certain if this is just DNA or protein/DNA crystals. Can you provide your comments on our hits? Thank you for your help Joseph
Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...
From the Washington Post (https://www.washingtonpost.com/news/speaking-of-science/wp/2016/11/09/what-will-president-trump-mean-for-science/): Last year, Trumptold <http://www.motherjones.com/politics/2015/10/donald-trump-michael-savage-aids-nih> conservative radio host Michael Savage, “I hear so much about the NIH, and it’s terrible.” V. Nagarajan JANSi On 11/9/2016 7:17 PM, William G. Scott wrote: Dear Edward et al: I agree we shouldn’t engage in partisan arguments on the CCP4bb. However, I think it is a mistake, and perhaps a missed opportunity, to ignore politics completely. For example, Newt Gingrich is currently in the running for Sec HHS. He has previously written editorials in the NYT and Wall Street Journal advocating doubling the budget of the NIH. I think it is incumbent upon us to make our voices heard if such an opportunity arises, regardless of what one may happen to think about the individual’s political orientation, as it could potentially be of enormous benefit to the scientific community. Yours faithfully, William G. Scott Director, Program in Biochemistry and Molecular Biology Professor, Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA http://scottlab.ucsc.edu On Nov 9, 2016, at 9:02 AM, Edward Snell <esn...@hwi.buffalo.edu> wrote: As a Brexit and Trumpet affected person having a foot in both countries ,this topic is too far off the normal discussion on CCP4 and probably better taken up privately. CCP4 is not a political discussion site. With CCP4 the signal is unusually high and the noise low when compared to any discussion board. I for one would like to keep it there. Political views aside, we’re all trying to achieve the same scientific goals. Let’s remember that and keep that the focus. Edward Snell Ph.D. President and CEO Hauptman-Woodward Medical Research Institute Assistant Prof. Department of Structural Biology, University at Buffalo 700 Ellicott Street, Buffalo, NY 14203-1102 Phone: (716) 898 8631 Fax: (716) 898 8660 Skype: eddie.snell Email: esn...@hwi.buffalo.edu Heisenberg was probably here! --- This email has been checked for viruses by Avast antivirus software. https://www.avast.com/antivirus
Re: [ccp4bb] UV-transmissible plate seals 96-well format
ClearSeal film from Hampton works with our UVEX UV microscope, despite some attenuation of UV light. For hanging drops, Greiner BioOne's films are the best. V. Nagarajan JAN Scientific, Inc. http://janscientific.com -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Christoph Parthier Sent: Monday, February 02, 2009 2:25 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] UV-transmissible plate seals 96-well format Hi, Can anyone recommend any UV-transmissible (280 nm), adhesive seals (pre-cut) for 96-well crystallization plates (Greiner, MRC)? We would like to use them on an crystal imaging system with UV option (RIGAKU). I've checked seals from Zymark/Calliper Lifescience with a regular photometer and they're not UV-transmissible. The Crystal Clear tape from Hampton Research is actually UV-transmissible but it's less convenient to apply from the roll onto the plates and it has to be cut afterwards to make sure the plates fit in the plate hotel. Anyone experience with this? Thanks very much in advance, Christoph
Re: [ccp4bb] X-ray photon correlation length
From memory, correlation length is the length during which the phase of the electric field is preserved. It's typically computed by applying time (pulse width)- frequency (converted to length) uncertainty principle. V. Nagarajan JAN Scientific, Inc. -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Bernhard Rupp Sent: Thursday, January 29, 2009 9:51 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] X-ray photon correlation length I always wondered - how is the X-ray photon correlation length defined and where do I find it? This is not the interaction length, I assume. So, to the physicists: How large is the 'X-ray photon correlation length' for a given wavelength in a given material? I had the impression that the term photon correlation refers to the time correlation of the scattering such as in photon correlation spectroscopy. Best regards, BR
Re: [ccp4bb] offtopic__which crystals to harvest
Actually, UV fluorescence imaging appears to be a pretty reliable means of discriminating protein crystals, provided your protein has Trp residue(s). V. Nagarajan JAN Scientific, Inc. http://www.janscientific.com -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Artem Evdokimov Sent: Tuesday, January 13, 2009 8:10 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] offtopic__which crystals to harvest Hi, A few simple hints: (Please note that I am aware of the inexact language in the statements below but I don't have the time to write this up exactly - conversational English would have to do. Caveat emptor.) Most protein crystals will break or deform when poked with a steel needle. Most inorganic salts/minerals won't deform from a simple poke, but will break (often with an audible crack) when pushed hard against something solid (like the surface of the glass slip etc.). Many, but not all protein crystals can survive gentle prodding with a thin cat whisker. Nylon loops are a bit trickier because they can exhert different forces depending on their geometry, age of the loop, and user's manual aptitude. To make matters more complicated - crystals of organic materials (i.e. not salt but also not protein) can display properties similar to either (but will more often than not tend to behave like salts). Salt crystals sink very rapidly in most well solutions. Protein crystals often take their time (lower density). Salt crystals often display Newton rings (Newton rainbows) when viewed through a polarizer-analyzer pair (not to be confused with relatively simple gradients of birefringence colors that are also common to protein crystals!). I have seen a few crystals of proteins that had distinct Newton rings and they were all exceptionally good diffractors. Don't be confused by rainbow-like coloring that's often associated with spherolites - the latter aren't likely to diffract X-rays in a useful manner :-) If in doubt - stick your crystals into an X-ray beam. Pretty much the best way to resolve this ambiguity! The next best choice is to show the crystals to an experienced crystallographer - oftentimes it's possible to guess just by eyeballing the drops but it takes experience to learn the traits and habits. Membrane crystals (or for that matter any crystals grown in the presence of detergent) can be extremely tricky to identify correctly due to the inherently soft and nasty nature of detergent crystals and the tendency of the latter to form various quasi-crystalline artefacts. Good luck, Artem From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of deliang Sent: Tuesday, January 13, 2009 10:50 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] offtopic__which crystals to harvest Hi there, Since a lot of different forms of crystals shows, I am using a quick/simple strategy to choose crystals by applying a force on the crystal against the wall, with the nylon loop. Some can never break apart, so they are salt crystals? The others can not survive the force and lose their intact shape and sharp surface. It seems these are protein crystals, but are they bad crystals? I just came to this field, and welcome all your suggestions and experience. Thanks a lot. Deliang
Re: [ccp4bb] UV light source for protein xtal detection
We are about to release an all-LED based UV microscope for automated scanning of 96-well plates. Please contact me if you are interested. Thanks, V. Nagarajan JAN Scientific, Inc. Seattle, WA, USA. -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Li Zhijie Sent: Thursday, May 15, 2008 9:36 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] UV light source for protein xtal detection 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
