[ccp4bb] SUMMARY: suggestions for UV spectrometer
On Dec 4th last year I asked for recommendations for a UV spectrophotometer to determine the concentration of protein/ [RD]NA samples. I received an enormous amount of answer emails, both to the board and privately and I am trying to summarise them as good as possible. We finally decided for a GeneQuant 1300 from GE Healthcare (http://www4.gelifesciences.com/aptrix/upp01077.nsf/Content/spectrophotometry_site~spectro_meter~spectro_mol_bio~genequant_pro?OpenDocumentparentid=80211498moduleid=167189) for the following reasons - wide wavelength range (190 - 1100 nm, 5nm bandwidth) - small display to show the spectrum - built-in (thermo) printer - no need for a controlling PC - price about 4,000 Euro - small enough to be carried between labs - It can play Tetris (;-) Following is an attempted summary of all the replies - most people (the vast majority, actually) advocated the Nanodrop 1000 (http://www.nanodrop.com/), which costs about 10,000 Euro (I believe). The main argument was that you only need 1ul and that it was fast. Several people pointed out that they found the nanodrop to be inaccurate, especially over time and repeating a measuremant would produce a considerable variation Others liked that you could re-use the sample for it was measured undiluted due to the short path length Personally I did not like the need of a controlling PC to record the measurement - The Biorad BioPhotometer Plus was in the same price range as the GeneQuant (4,000 Euro), but only measures at 9 fixed wavelengths and does not have a display to show the measured spectrum. - The Biorad Smartspec 3000 has got a wavelength range of 200-800nm, and only a 2 line matrix display. I don't know the price - The Beckman Coulter DU-730 (http://www.beckman.com/products/instrument/analytical/uvvis/duseries700_inst_dcr.asp) was recommended by one person. It seems to have similar features (both technically and in measure) as the GeneQuant although with a slightliy improved bandwidth (3nm). It includes a display that show the spectrum. I don't know how much it costs. - The Cary 50 (Varian, http://www.varianinc.com/cgi-bin/nav?products/spectr/uv/cary50/cary50cid=HFIH) was too big for our purposes. - USB2000+ (Ocean Optics, http://www.oceanoptics.com/products/usb2000+.asp) is a low-cost solution ( 3000USD) but requires a PC for control to spoil the prive. It also covers 200nm-1100nm. The Ocean Optics USB4000 was also recommended once. - The Shimadzu UV2450 (successor of UV2401) (http://www.shimadzu.com/products/lab/spectro/oh80jt001k16.html) was again a little too big for our lab since we were looking for a protable machine. I hope, but don't claim this information is complete. I am grateful to everybody who answered and hope not to disappoint the about 90% voters for the Nanodrop system for choosing a different machine. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
Re: [ccp4bb] Summary: cryoloops for X-ray data collection from protein crystals at room temperature.
hello all, I would like to thank everyone for all suggestions. Summary: 1 - MiTeGen Tools - MicroRT™ Room Temperature Mounting System - crystals slipping ? (suggestion of juan: amongst other things, problem resolved by using micromesh loops instead of using standard loops) - uses polyester capillary which scatters xrays less than the glass - works quite well - everyting is reasonably airtight - much easier to do than the old way. links: http://www.jenabioscience.com/cms/en/1/catalog/733_microrttrade_room_temperature_mounting_system.html http://mitegen.com/products/micrort/micrort.shtml 2 - coat the crystal with paratone oil and mount the crystal in a standard cryoloop - no special tools required - you can use the same crystal to collect under cryo-conditions and directly compare the impact of cooling the crystal 3 - the free mounting system (FMS) from Proteros Biostructures: a humidity control device - it does not have highly volatile components in the conditions - room temperature not too difficult links: http://www.proteros.com/articles.php?sid=18lang=de contact: kris.t...@rigaku.com 4 - the humidifier device HC1b - developed at the EMBL - available at ESRF - easy to use links: http://www.esrf.eu/UsersAndScience/Experiments/MX/special-setup technical information: weathe...@embl.fr 5 - test crystal directly on plate - japan http://journals.iucr.org/d/issues/2002/10/01/issconts.html http://www.labo.co.jp/contents/direct_ex.html contact: nobuh...@nagoya-u.jp - France, Grenoble explanations http://www.natx-ray.com/products/G-Rob_2D.html the movie http://www.natx-ray.com/products/G-Rob_2D_movie.html a prototype, commercialized by Natx-ray, is available on FIP beamline ( http://www.esrf.eu/exp_facilities/BM30/).*http://en.wiktionary.org/wiki/commercialized * contact: fer...@ibs.fr Best regards, Cédric -- Dr. Cedric Bauvois Cristallographie des protéines Institut de Recherches Microbiologiques JM Wiame -IRMW Av E. Gryzon 1, 1070 Brussels (Belgium) tél: +32 (0)2 5273634 fax: +32 (0)2 5267273
Re: [ccp4bb] temperature after 30 minutes using microscopes ?
We have both LED and cold light sources attached to our Zeiss Stemi microscopes on the beamlines at Diamond. There was some argument about not using LED lights however the solution from Zeiss is very good allowing different sections of LEDs to be used which can be moved around. This allows crystal faces to be specifically highlighted and makes crystal visualisation simple. If you were wanting to take photos of protein crystals I would probably favour a cold light source though. DIVFONT size=1 color=grayThis 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 /FONT/DIV -- Scanned by iCritical.
[ccp4bb] ARP/wARP and computer platforms
We are collecting information on computer platforms that people would like ARP/wARP to run on. To access the questionnaire please go to http://www.embl-hamburg.de/ARP/platinf_new.shtml Thank you for your cooperation. With best regards, Victor
[ccp4bb] BEAM TIME AVAILABLE FOR MACROMOLECULAR CRYSTALOGRAPHY
BEAM TIME AVAILABLE FOR MACROMOLECULAR CRYSTALLOGRAPHY AT THE TWO ID BEAMLINES OF NE-CAT AT APS. Beamline 24ID-C: Variable energy between 6-18keV, ADSC Q315 Detector, MAD Capable. Beamline 24ID-E: Equipped with MD2 microdiffractometer, delivering beam as small as 5 microns. Single energy (12662eV), ADSC Q315 Detector. Contact csalb...@anl.gov for further details. See http://necat.chem.cornell.edu for information on our beamlines and a calendar of available days.
Re: [ccp4bb] Summary: cryoloops for X-ray data collection from protein crystals at room temperature.
If you will use the Nextal device, I have also modified it something like fig.2 for checking crystals in the drop at room temperature. It is not difficult to make, too. Please see, http://journals.iucr.org/j/issues/2005/02/00/he5324/he5324bdy.html However, getting the film I have used in the note is not easy. The film was SUMILITE FS-1700 film of 50um thickness (Sumitomo Bakelite Co. Ltd). I guess I can not get it in small amounts commercially now. But you can go with any seal tape if you do not care about background, and absorption and permeability of water. Water absorption of the film is 0.01% at 313 K, 90% relative humidity, and water vapour permeability is only 0.4 g/m2/24h. http://www.sumibe.co.jp/english/products/pdf/03_10_1700.pdf I found I did not cite the histric paper in my labo-note... Nobuhisa Watanabe, PhD. === Synchrotron Radiation Research Center Department of Biotechnology and Biomaterial Chemistry, Graduate School of Engineering Nagoya University C1-3(651) Furo-cho Chikusa-ku, Nagoya 4648603 Japan Email: nobuh...@nagoya-u.jp Fax: +81-52-789-5286 On 2009/01/23, at 2:03, James Holton wrote: Something that is missing from your list is a remarkable device pictured as figure 2 in: Perutz, M. (1985) Early days of protein crystallography. /Methods in Enzymology/ *114* 3-18 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrievedb=PubMeddopt=Abstractlist_uids=4079771 . which is actually a reproduction of figure 5 from: J. D. Bernal and I. Fankuchen (1941) J. Gen. Physiol., 25, 111-146. This cell is not difficult to make. I made one using a plastic ring (to replace the brass) glued to an iron nut (to attach to the goniometer magnet), a piece of Scotch Tape for the exit window and the cover slip from the hanging drop setup of interest as the entrance window. All you do is move the cover slip from the tray to the ring and then mount it up. The excess vacuum grease from the tray makes the seal. Maybe put ~10 uL of well solution on the inner edge of the ring before closing it to keep the humidity stable. The background (especially from glass) is high but you have the advantage of never touching the crystal before shooting it. We do use this device from time to time at the beamline. I thought I had invented something new until I saw Perutz's paper. It was then that I realized that my invention was one of the FIRST mounts ever used to get diffraction from a protein crystal: J. D. Bernal and D. Crowfoot (1934) Nature (London) 133, 794. -James Holton MAD Scientist
[ccp4bb] cbuccanner.exam failed with libFFTW generated by Intel MKL
Dear all, I tried to build CCP4 6.1 with Intel Compiler Intel Math Kernel Library(MKL) on Fedora 8. I used MKL as LAPACK and FFTW libraries. The building processes have been completed successfully, but all tests passed except cbuccaneer.exam (core dumped). Log: --- % ./cbuccaneer.exam or make runtest (snip.) Cycle: 1 C-alphas after finding:5 C-alphas after growing:5 ./cbuccaneer.exam: line 12: 23479 Aborted cbuccaneer -mtzin-ref $CLIBD/reference_structures/reference-1tqw.mtz -pdbin-ref $CLIBD/reference_structures/reference-1tqw.pdb -mtzin-wrk $CCP4_SCR/toxd_phase_mir_pirate1.mtz -pdbout-wrk $CCP4_SCR/toxd_phase_mir.pdb -colin-wrk-fo '/NATIVE/NATIVE/[FTOXD3,SIGFTOXD3]' -colin-wrk-hl '/*/*/[pirate.ABCD.A,pirate.ABCD.B,pirate.ABCD.C,pirate.ABCD.D]' -find -grow -join -link -prune (core dumped) - In case of compiling with Intel Compiler and default fftw libraries (bundled by CCP4), building and all test processes passed. Building process: % mkdir ccp4-intel % cd ccp4-intel % tar xvf CCP4-6.1.0.src.tar (CCP4 core source package) % setenv XLDFLAGS -lmkl -liomp5 -lguide % setenv COPTIM -O -ip % setenv FFTW_LIBS -lfftw2xc_intel -lmkl -liomp5 -lguide -lpthread % setenv FFTW_CXXFLAGS -I/opt/intel/Compiler/11.0/074/mkl/include/fftw % ./install.sh (building x-windows programs - no) (building fftw library - no) Any suggestions? Thanks, Nobuo OKAZAKI
Re: [ccp4bb] cbuccanner.exam failed with libFFTW generated by Intel MKL
Dear Nobuo: I should let the experts answer definitively, but I think this might be because the clipper-related stuff (and coot) need single-precision s[r]fftw libraries. I had to do something like this: LDFLAGS=-Wl,-dylib_file,/sw/lib/libsfftw.2.0.7.dylib:/sw/lib/ libsrfftw.2.0.7.dylib It will probably be a bit different on Fedora (linux uses .so instead of .dylib suffixes). The main point is to force-feed it the single- precision libraries. In practice it is probably just easier just to let ccp4 build its own, unless you need the mpi versions. Single precision makes the calculation go faster and you can't see the difference in the maps, in my experience. HTH, Bill William G. Scott contact info: http://chemistry.ucsc.edu/~wgscott On Jan 22, 2009, at 10:32 PM, Nobuo OKAZAKI wrote: Dear all, I tried to build CCP4 6.1 with Intel Compiler Intel Math Kernel Library(MKL) on Fedora 8. I used MKL as LAPACK and FFTW libraries. The building processes have been completed successfully, but all tests passed except cbuccaneer.exam (core dumped). Log: --- % ./cbuccaneer.exam or make runtest (snip.) Cycle: 1 C-alphas after finding:5 C-alphas after growing:5 ./cbuccaneer.exam: line 12: 23479 Aborted cbuccaneer -mtzin-ref $CLIBD/reference_structures/reference-1tqw.mtz -pdbin-ref $CLIBD/reference_structures/reference-1tqw.pdb -mtzin-wrk $CCP4_SCR/ toxd_phase_mir_pirate1.mtz -pdbout-wrk $CCP4_SCR/toxd_phase_mir.pdb - colin-wrk-fo '/NATIVE/NATIVE/[FTOXD3,SIGFTOXD3]' -colin-wrk-hl '/*/*/ [pirate.ABCD.A,pirate.ABCD.B,pirate.ABCD.C,pirate.ABCD.D]' -find - grow -join -link -prune (core dumped) - In case of compiling with Intel Compiler and default fftw libraries (bundled by CCP4), building and all test processes passed. Building process: % mkdir ccp4-intel % cd ccp4-intel % tar xvf CCP4-6.1.0.src.tar (CCP4 core source package) % setenv XLDFLAGS -lmkl -liomp5 -lguide % setenv COPTIM -O -ip % setenv FFTW_LIBS -lfftw2xc_intel -lmkl -liomp5 -lguide -lpthread % setenv FFTW_CXXFLAGS -I/opt/intel/Compiler/11.0/074/mkl/include/ fftw % ./install.sh (building x-windows programs - no) (building fftw library - no) Any suggestions? Thanks, Nobuo OKAZAKI
[ccp4bb] Caution - 120 Hz LCDs: Not CRT killers yet...
Stereo 3D Users: I tested out the Samsung Syncmaster 2233RZ / NVIDIA 3D Vision bundle today ($599 for a 120 Hz LCD display with one pair of glasses). Unfortunately, the 2233RZ display is clearly not yet a drop-in replacement for your stereo-3D-capable CRT: The display is very nice, and the stereo quality is excellent (as good as a CRT!), but only provided that you: 1. Run Microsoft Vista. 2. Install a high-end GeForce 3D card (9800 GT or similar). 3. Have DirectX-based software than has been modified to support nVidia's consumer-grade stereo API. 4. Use nVidia's 3D Vision glasses and sync emitter (a USB-based device). In other words, despite the high stereo image quality, this is not yet a servicable stereo 3D solution for professional use. Rats! I was very much hoping that this new display would nevertheless also work with existing nVidia Quadro-based Mac or Linux systems with existing emitters and glasses running existing OpenGL software. Sadly, this does not seem to be the case due at least in part to the fact that the phase of the sync signal coming out of the Quadro card does not match the update phase of the LCD display. In addition, light from the display itself seems to corrupt the sync signal for StereoGraphics glasses. So, in summary, it seems we are out of luck until nVidia does a bit more work. Reportedly, there is a driver update coming that will target use of nVidia's 3D vision glasses with Quadro-based graphics cards, so stay tuned. Cheers, Warren
