Re: [ccp4bb] Lyophilized protein sample (purchased)
Dear Rex, for me it works in most cases. After all, vendors who sell inactive proteins usually get troubles with their customers. However, as always in crystallography, there is no guarantee that it will crystallize and in this case you should contact the vendor to get a frozen solution. If the protein you buy is not dirt-cheap (like trypsin), the price involved is such that they will do it for you. Best regards, Herman From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of REX PALMER Sent: Friday, May 06, 2011 10:01 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Lyophilized protein sample (purchased) We have purchased a 5mg commercial sample of a protein we want to crystallize. On arrival it transpired that the sample had been lyophilized. Does anyone know if this is likely to give problems and if so what can/should be done about it? Thanks in advance Rex Palmer Birkbeck College
Re: [ccp4bb] Stereo solution with Nvidia '3D vision' or '3D vision pro'
not seen a working 120 Hz stereo setup working on the Acer GD235 monitor. if you ask the Nvidia driver or the monitor, it reports 100 Hz instead This is what I encountered on Dell Alienware OptX AW2310 with Quadro FX3800, which has been fixed by nVIDIA Linux driver update (in 256.44). I don't know if the Acer monitor is compatible or not, it seems better to ask NVIDIA directly. see: http://twitter.com/#!/NVIDIAQuadro/status/65188179753435137 Takaaki Fukami - Discovery Platform Technology Dept. Gr.5 Chugai Pharmaceutical Co.,Ltd. -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Eric Bennett Sent: Saturday, May 07, 2011 8:38 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Stereo solution with Nvidia '3D vision' or '3D vision pro' We recently had issues setting up a 3D projector and have tried lots of combinations of monitors, drivers, cards, glasses, etc. The answer seems to be that interchangeability is very complicated and you won't know unless you try it. For example, with the last version of the Nvidia driver I tested, the driver refused to put out an Nvidia 3D Vision sync signal (stereo 10 in xorg.conf) unless there was a 3D capable LCD attached. I don't know of any technical reason the Nvidia 3D Vision couldn't be used with a CRT but Nvidia has apparently chosen to disable it (or at least make it hard to enable) in the Linux driver. Going the other direction, using RealD with and LCD system, it might be possible but you probably have to match your RealD emitter with RealD glasses. Older CrystalEyes glasses (CE3 and earlier) generally do not work with LCD monitors because of the polarization in the glasses. We recently got some CE4 glasses and they don't seem to have that problem although in practice we are using them with a projector, not LCD monitors. But I don't really like the CE4's, there is too much of my field of vision under the glasses that they don't cover. We've observed some really weird configurations that appear to mostly work, such as plugging in a RealD emitter and glasses when the driver is configured to output a signal for Nvidia 3D Vision (stereo 10 option under Linux). You don't say whether you are using Windows or Linux and there may be variations in the drivers, variations by card, etc. Regarding card to card variations, we've observed 3D setups in conference rooms with multiple emitters where some Nvidia cards happily drive multiple emitters with particular splitters boosters, but other Nvidia cards don't. The bottom line is if you mix hardware you might have problems and vendors are unlikely to help you. If you have CE4 glasses already, you can try it with an LCD and it may work. Otherwise, if you have to buy new glasses (ie, you have CE3 or older), you might as well get the Nvidia package with the emitter included. 3D Vision Pro uses the 2.4 GHz band instead of IR to transmit the sync signal so if you were setting up a conference room in theory the Pro version might be less likely to leave dead zones in the conference room. For a single user workstation it's very unlikely that you would get any benefit. Just to muddy the waters a bit, I have not seen a working 120 Hz stereo setup working on the Acer GD235 monitor. We have a bunch of them set up, and we put a 120 Hz mode line in xorg.conf. If you ask X11 it says it's running at 120. But if you ask the Nvidia driver or the monitor, it reports 100 Hz instead, and visually there is enough flickering that the monitor and the driver seem to have the correct number. I'm curious if anyone else here has looked in detail to make sure their Acer-based system is running at 120 and found that it is actually doing what people claim it can do. I find the 100 Hz LCD flicker annoying over long periods so I am still a neanderthal CRT user. My coworkers were convinced their LCD systems were running at 120, when they were actually only running at 100. I'm not sure if this is a driver problem or a monitor problem. -Eric On May 6, 2011, at 11:27 AM, zhang yu wrote: Dear colleagues, Sorry to present the stereo issue to the board again. Since my old SGI CRT monitor only has 75 HZ refresh rate, the flickering in stereo mode bothered me a lot. Recently, I want to update my old CRT to 120 HZ LCD. I have a Nvidia Quadro FX3800 in my workstation. I would like to make sure some issues before I make the upgrade. 1. Can I apply the previous stereo emitter (Purchased from Real D, Model #E-2) to 120HZ LCD? Although the company told me this emitter is not compatible with LCD, could some one tell me why? Is it true that the Nvidia 3D vision is the only solution for the stereo in LCD? 2. Nvidia supply two kinds of 3D emitters. One of them is 3D vision, while the other one is 3D vision pro. Which one is sufficient for crystallographier user? (3D vision pro is much more expensive than 3D
[ccp4bb] 2dx Workshop August 15-19, 2011 in Seattle
'The NIH funded network TEMIMPS will organize a Workshop for 2D crystallization of membrane proteins, electron crystallography, and all related data processing (see attached tentative schedule). The Workshop will take place from August 15-19 in Seattle at the University of Washington School of Medicine. Teachers who have confirmed their participation are: Anchi Cheng, David Stokes, Henning Stahlberg, Iban Ubarretxena, Pawel Penczek, Tamir Gonen, Vinzenz Unger, Yifan Cheng and Andreas Engel. The program can be downloaded from http://temimps.nysbc.org/TemimpsWorkshop.html Participants need to submit their application to temi...@nysbc.org by June 30, 2011. Space is limited and selection is strictly on a first come first serve basis' workshop-schedule.pdf Description: application/binary
Re: [ccp4bb] 2dx Workshop August 15-19, 2011 in Seattle
This message did not show up in my previous announcement: 'The NIH funded network TEMIMPS will organize a Workshop for 2D crystallization of membrane proteins, electron crystallography, and all related data processing (see attached tentative schedule). The Workshop will take place from August 15-19 in Seattle at the University of Washington School of Medicine. Teachers who have confirmed their participation are: Anchi Cheng, David Stokes, Henning Stahlberg, Iban Ubarretxena, Pawel Penczek, Tamir Gonen, Vinzenz Unger, Yifan Cheng and Andreas Engel. The program can be downloaded from http://temimps.nysbc.org/TemimpsWorkshop.html Participants need to submit their application to temi...@nysbc.org by June 30, 2011. Space is limited and selection is strictly on a first come first serve basis'
[ccp4bb] Thermal Ellipsoids pic
YO! I am making thermal ellipsoid plots of a highly flexibile region of a chromophore using rastep and render from the raster3D package of Merritt el al. But I cannot control the orientation. It obscures the rest of the atoms in the plane of the molecule. Does anyone know a way to orientate molecules AND get a publication quality png file? ccp4mg only produces vague traces. thanks kas -- Kenneth A. Satyshur, M.S.,Ph.D. Associate Scientist University of Wisconsin Madison, Wisconsin 53706 608-215-5207 attachment: satyshur.vcf
Re: [ccp4bb] Thermal Ellipsoids pic
On Monday, May 09, 2011 12:50:48 pm Kenneth A. Satyshur wrote: YO! I am making thermal ellipsoid plots of a highly flexibile region of a chromophore using rastep and render from the raster3D package of Merritt el al. But I cannot control the orientation. It obscures the rest of the atoms in the plane of the molecule. Does anyone know a way to orientate molecules AND get a publication quality png file? ccp4mg only produces vague traces. Simple thing to try first: cat myatons.pdb | rastep -auto | render -size 900x900 picture.png The -auto option to rastep will orient the atoms so that they are maximally spread out in the plane of the picture. More general answer: - Open the pdb file in a viewer of your choice - Orient as you please - Dump orientation matrix (exact button or command depends on the program) - Copy the matrix into the header of the raster3d file fed to render cheers, Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
[ccp4bb] Biomolecular Structure from Nanocrystals and Diffuse Scattering Workshop
Announcing a workshop on: Biomolecular Structure from Nanocrystals and Diffuse Scattering June 13-14, 2011 at Cornell University, Ithaca NY Organized by Ed Lattman (Hauptmann-Woodward Medical Research Inst.), Mavis Agbandje-McKenna (University of Florida), Keith Moffat (University of Chicago), Sol Gruner (Cornell University) FMI: http://erl.chess.cornell.edu/gatherings/2011_Workshops/details2.htm This workshop is #2 of 6 in the series Science at the Hard X-ray Diffraction Limit, devoted to science with diffraction-limited, high repetition rate, hard X-ray sources, e.g., Energy Recovery Linac and Ultimate Storage Ring. Find a summary of all the workshops at: http://erl.chess.cornell.edu/gatherings/2011_Workshops/index.htm
Re: [ccp4bb] Thermal Ellipsoids pic
On May 9, 2011, at 4:00 PM, Kenneth A. Satyshur wrote: YO! I am making thermal ellipsoid plots of a highly flexibile region of a chromophore using rastep and render from the raster3D package of Merritt el al. But I cannot control the orientation. It obscures the rest of the atoms in the plane of the molecule. Does anyone know a way to orientate molecules AND get a publication quality png file? ccp4mg only produces vague traces. Hey, you can use Chimera to orient the molecule as you like and then use Chimera's Thermal Ellipsoids tool to draw the ellipsoids. That tool lacks rastep's cut-away quadrant depiction but has all the other depictions. More info about Thermal Ellipsoids here: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/thermal/thermal.html about Chimera itself here: www.cgl.ucsf.edu/chimera --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
Re: [ccp4bb] Stereo solution with Nvidia '3D vision' or '3D vision pro'
Dear Duangrudee Thank you for your information. Is there any hardware requirement for the stereo in coot and pymol with Zalman monitor? It seems that Hign-End Nvidia graphic cards (Quadro FX 3800, FX 4800 ) are not necessary. Yu 2011/5/8 Duangrudee Tanramluk nano...@gmail.com Dear Yu, Pymol also has a Zalman option. The monitor comes with 2 pair of light-weight polarized glasses, i.e. one for clipping on your prescription glasses and another regular one. If you have the Zalman monitor and its polarised glasses, you can see this .gif movie in 3D on google chrome, just click on the picture to see in full size. http://nanonan.wordpress.com/2011/03/14/making-zalman-3d-stereoscopic-movie-with-pymol/ May be you can use this movie for trial with other 120 Hz monitor/glasses. Hope it helps, Duangrudee Duangrudee Tanramluk, Ph.D. Institute of Molecular Biosciences, Mahidol University Puttamonthon 4 Road, Salaya, Nakhon Pathom 73170 THAILAND -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
Re: [ccp4bb] Stereo solution with Nvidia '3D vision' or '3D vision pro'
Dear Yu, The graphic card I am using is Nvidia Quadro FX580. If all you want is Pymol and Coot, you don't need a high-end graphic card. Some commercial molecular viewer requires a really high-end Quadro graphic card. If you plan to use those packages on the same machine, you may want to check their websites for the high quality 3D-stereo before purchasing them. Cheers, Duangrudee ___ Duangrudee Tanramluk, Ph.D. Institute of Molecular Biosciences, Mahidol University Puttamonthon 4 Road, Salaya, Nakhon Pathom 73170 THAILAND
