Re: [ccp4bb] Dehydration treatments
Hi, Yes indeed, as Matt was kind enough to point out, we do have the HC1 installed at station I911-3 of the MAX-II ring and you are welcome to make a rapid access application. One advantage of MAX-lab might be that our wiggler beam is more merciful to the crystals at room temperature than the undulator beams at the ESRF! There are a few free days left in our spring schedule: http://cassiopeia.maxlab.lu.se/index/organiser-app Good luck Derek ___ Derek Logantel: +46 46 222 1443 Associate Professorfax: +46 46 222 4692 Dept. of Biochemistry and Structural Biology mob: +46 76 8585 707 Centre for Molecular Protein Science www.cmps.lu.se Lund University, Box 124, 221 00 Lund, Sweden www.saromics.com On May 2, 2011, at 8:11, Matthew BOWLER wrote: Dear Israel, as Martin pointed out we have a device here at the ESRF/EMBL, the HC1b, that produces a stream of air with a precisely controlled RH at the sample position that we have used with some success to monitor the effects dehydration has on diffraction quality. The same device is also available at Diamond, Max-Lab and, I believe, BESSY. The example you describe is a classic example of the sort of system that will usually benefit from controlled dehydration. Depending on the size and concentration of the LMW PEG you are using you have probably reduced the RH surrounding your crystal by ~10%. The best thing to do now is repeat these experiments using the HC1b to really define the changes in the lattice of your crystals and find the optimum dehydration conditions for your crystals. At the ESRF the device can be requested for any experimental session (just click the check box on the A form) and I presume that this will be similar at the other synchrotrons. As well as the reference describing the device we have recently published a further description of typical experimental conditions and some successful applications: http://dx.doi.org/10.1016/j.jsb.2011.03.002 And the ESRF webpage is here: http://www.esrf.fr/UsersAndScience/Experiments/MX/About_our_beamlines/ID14-2/HC1b Good luck! Matt On 01/05/2011 19:32, Israel Sanchez wrote: Hi folks, I am currently impressed by the efficiency of dehydration treatments over the diffraction capacity of our crystals in one particular condition. Without any treatment the crystals seldom diffract to 20-30A but in our last synchrotron trip the very same crystals, after been incubated with increasing concentration of low molecular weight PEGs diffracted to 6A. I was wondering if anyone has studied these effects in a systematic way. Does anyone on the ccp4bb knows references or has any experience/pseudo-religious believes that do not care to share with the community about this particular topic? Thank you very much in advance -- Israel Sanchez Fernandez PhD Ramakrishnan-lab MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK -- Matthew Bowler Structural Biology Group European Synchrotron Radiation Facility B.P. 220, 6 rue Jules Horowitz F-38043 GRENOBLE CEDEX FRANCE === Tel: +33 (0) 4.76.88.29.28 Fax: +33 (0) 4.76.88.29.04 http://go.esrf.eu/MX http://go.esrf.eu/Bowler ===
[ccp4bb] Stereo solution with Nvidia '3D vision' or '3D vision pro'
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 vision) It seems that 3D vision is for home user and powered by the Nvidia GeForce series graphic cards. While 3D vision pro is for professional user and powered by Nvidia Quardro series graphic card . 3. It looks that the Nvidia 3D glasses are very compact. Is it comfortable for someone like me already with eyeglasses? Thanks Yu -- 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'
1. No you cannot use your old stereo emitter. The 3D Vision Emitter is required for stereo on 120 Hz LCD monitors. You will also need new shutter glasses from Nvidia, but these some with the emitter. I'm not sure the reason, but I'd guess that the older emitter can't transmit the signal at the correct frequency to get 60 Hz to each eye. On a side note, consider which operating system you are running on the system to be used for stereo. You'll need the 3-pin stereo connector if you want to do stereo in Linux. For Windows it isn't required. Some computers that Dell and other manufacturers sell with FX3800 cards don't have one built in, and you will need to buy an adapter that hooks into the video card to provide the port. 2. The normal 3D Vision system uses IR signals to communicate between the emitter and the shutter glasses. 3D Vision Pro uses RF signals for communication between the glasses and the emitter and has a longer range and doesn't require line-of-sight like the IR system (hence the hefty price difference you've noticed). I don't believe the glasses from the normal 3D Vision kit are compatible with the 3D Vision Pro system due to the difference in signaling systems, but I haven't tested this. If you're going to be sitting in front of a monitor doing modeling and don't have alot of IR interference in the same room, the normal 3D Vision version will suffice for your needs. 3D Vision Pro is more geared toward having large meeting rooms and presentation halls equipped so everyone in the room can view 3D on a large screen driven by a 120 Hz DLP projector. 3. I don't wear prescription eye glasses, but I do have long modeling sessions without any discomfort wearing these. They come with several inter-changable nose-pieces so you can pick the one that fits you most comfortably. On Fri, May 6, 2011 at 11:27 AM, zhang yu ccp4f...@gmail.com 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 vision) It seems that 3D vision is for home user and powered by the Nvidia GeForce series graphic cards. While 3D vision pro is for professional user and powered by Nvidia Quardro series graphic card . 3. It looks that the Nvidia 3D glasses are very compact. Is it comfortable for someone like me already with eyeglasses? Thanks Yu -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904 -- Jim Fairman, Ph D. Post-Doctoral Fellow National Institutes of Health - NIDDK The Buchanan Lab http://www-mslmb.niddk.nih.gov/buchanan/index.html Lab: 1-301-594-9229 E-mail: fairman@gmail.com james.fair...@nih.gov
Re: [ccp4bb] Stereo solution with Nvidia '3D vision' or '3D vision pro'
Dave, thanks. There is an option for Zalman stereo in Coot. Could Zalman stereo also display properly in Pymol? Yu 2011/5/6 Dave Roberts drobe...@depauw.edu I'm very happy with Zalman passive stereo. No hardware requirements beyond Zalman monitor. Monitors cost $500ish for 21 and 700ish for 24. Any video card, any software. Glasses are the same as movie glasses ($2 per pair), no batteries, no flicker. Very nice really. Dave Sent from my iPhone On May 6, 2011, at 11:27 AM, zhang yu ccp4f...@gmail.com 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 vision) It seems that 3D vision is for home user and powered by the Nvidia GeForce series graphic cards. While 3D vision pro is for professional user and powered by Nvidia Quardro series graphic card . 3. It looks that the Nvidia 3D glasses are very compact. Is it comfortable for someone like me already with eyeglasses? Thanks Yu -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904 -- 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'
Jim, thanks. I am using Linux and with a 3-pin stereo bracket hooked to my Nvidia Quadro FX3800. It is ready to go. 2011/5/6 Jim Fairman fairman@gmail.com 1. No you cannot use your old stereo emitter. The 3D Vision Emitter is required for stereo on 120 Hz LCD monitors. You will also need new shutter glasses from Nvidia, but these some with the emitter. I'm not sure the reason, but I'd guess that the older emitter can't transmit the signal at the correct frequency to get 60 Hz to each eye. On a side note, consider which operating system you are running on the system to be used for stereo. You'll need the 3-pin stereo connector if you want to do stereo in Linux. For Windows it isn't required. Some computers that Dell and other manufacturers sell with FX3800 cards don't have one built in, and you will need to buy an adapter that hooks into the video card to provide the port. 2. The normal 3D Vision system uses IR signals to communicate between the emitter and the shutter glasses. 3D Vision Pro uses RF signals for communication between the glasses and the emitter and has a longer range and doesn't require line-of-sight like the IR system (hence the hefty price difference you've noticed). I don't believe the glasses from the normal 3D Vision kit are compatible with the 3D Vision Pro system due to the difference in signaling systems, but I haven't tested this. If you're going to be sitting in front of a monitor doing modeling and don't have alot of IR interference in the same room, the normal 3D Vision version will suffice for your needs. 3D Vision Pro is more geared toward having large meeting rooms and presentation halls equipped so everyone in the room can view 3D on a large screen driven by a 120 Hz DLP projector. 3. I don't wear prescription eye glasses, but I do have long modeling sessions without any discomfort wearing these. They come with several inter-changable nose-pieces so you can pick the one that fits you most comfortably. On Fri, May 6, 2011 at 11:27 AM, zhang yu ccp4f...@gmail.com 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 vision) It seems that 3D vision is for home user and powered by the Nvidia GeForce series graphic cards. While 3D vision pro is for professional user and powered by Nvidia Quardro series graphic card . 3. It looks that the Nvidia 3D glasses are very compact. Is it comfortable for someone like me already with eyeglasses? Thanks Yu -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904 -- Jim Fairman, Ph D. Post-Doctoral Fellow National Institutes of Health - NIDDK The Buchanan Lab http://www-mslmb.niddk.nih.gov/buchanan/index.html Lab: 1-301-594-9229 E-mail: fairman@gmail.com james.fair...@nih.gov -- 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'
Check pymolwiki for the full description of setup. It should work for coot too. http://www.pymolwiki.org/index.php/Stereo_3D_Display_Options Nian On Fri, May 6, 2011 at 10:27 AM, zhang yu ccp4f...@gmail.com 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 vision) It seems that 3D vision is for home user and powered by the Nvidia GeForce series graphic cards. While 3D vision pro is for professional user and powered by Nvidia Quardro series graphic card . 3. It looks that the Nvidia 3D glasses are very compact. Is it comfortable for someone like me already with eyeglasses? Thanks Yu -- 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'
I think all major programs used by crystallographers use Zalman option. I know that coot and chimera do as does the version of pymol I have running (which is old). I don't know about other programs, but I don't know why not. Dave Sent from my iPhone On May 6, 2011, at 12:04 PM, zhang yu ccp4f...@gmail.com wrote: Dave, thanks. There is an option for Zalman stereo in Coot. Could Zalman stereo also display properly in Pymol? Yu 2011/5/6 Dave Roberts drobe...@depauw.edu I'm very happy with Zalman passive stereo. No hardware requirements beyond Zalman monitor. Monitors cost $500ish for 21 and 700ish for 24. Any video card, any software. Glasses are the same as movie glasses ($2 per pair), no batteries, no flicker. Very nice really. Dave Sent from my iPhone On May 6, 2011, at 11:27 AM, zhang yu ccp4f...@gmail.com 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 vision) It seems that 3D vision is for home user and powered by the Nvidia GeForce series graphic cards. While 3D vision pro is for professional user and powered by Nvidia Quardro series graphic card . 3. It looks that the Nvidia 3D glasses are very compact. Is it comfortable for someone like me already with eyeglasses? Thanks Yu -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904 -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
[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] Lyophilized protein sample (purchased)
I think that's impossible to say. Some proteins lyophilize fine, some don't. Generally your chances are best if the protein is sturdy. Is also depends how it was lyophilized (any salts, buffer etc). Getting the protein in solution may be tricky; in my limited experience plain water works best (not buffered). Good luck, Bert On 5/6/11 4:01 PM, REX PALMER rex.pal...@btinternet.com wrote: 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'
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 vision) It seems that 3D vision is for home user and powered by the Nvidia GeForce series graphic cards. While 3D vision pro is for professional user and powered by Nvidia Quardro series graphic card . 3. It looks that the Nvidia 3D glasses are very compact. Is it comfortable for someone like me already with eyeglasses? Thanks Yu -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
