Re: [ccp4bb] 3D passive monitor for Mac
I think one of our users recently purchased the LG D2343PBBN, but here's an official list (under monitors and monitor/tv's) : https://www.tridef.com/products/pc-licensed-products hopefully some of those are still available. On Wed, Jun 25, 2014 at 9:03 AM, Shawn Xiong shawnxiong...@gmail.com wrote: Hi: Recently my 3D Zalman monitor was burned out. All the SBGrid suggested models from Asus, LG as well as Zalmon are all discontinued. I am wondering if anyone out there have recently purchased a passive 3D monitor for Mac that is compatible with all the software commonly used in structure building and analysis. (coot, pymol, phenix ect.) Thanks Shawn
Re: [ccp4bb] Stereo monitors for use with Pymol and Coot
Thanks! we're gonna test one of the lg's from bh, one of our zalman's just died today. On Thu, Mar 6, 2014 at 6:06 PM, Shaun Lott s.l...@auckland.ac.nz wrote: Thanks to everyone who responded, on and off the list. I thought I'd post a quick summary. To clarify my question slightly (if belatedly) I'm specifically looking for a passive 3D solution to plug into my MacBook Pro whilst on sabbatical in the USA. I'll be using it for a mixture of 2D and 3D viewing, not for many hours of dedicated hand building of my 3.5A maps. Well, I hope not! ;) The LG D2343PB-BN gets honourably mentioned, and is available in several places: http://www.adorama.com/LOCD2343PBBN.html $273.50 including shipping http://www.bhphotovideo.com/c/product/1002116-REG/lg_electronics_d2343pb_bn_23_mon_led_lcd.html $273.50 + shipping Another candidate is this from AOC: http://www.amazon.com/AOC-E2352PHZ-23-Widescreen-Flicker/dp/B005LORQGG $250 including shipping The Asus VG27AH also got good reports, but is listed as either 'out of stock' or 'unavailable'. However, its kid brother, the VG23AH is available: http://www.pinnaclemicro.com/computer/dsku.php?g=VG23AHm=ASUS $251 including shipping (you need to enter the promo code SAS10 to get $10 off!) This monitor got a poor review on cnet ( http://reviews.cnet.com/lcd-monitors/asus-vg23ah/4505-3174_7-35306085.html) but much better and more thoughtful reviews elsewhere ( http://3dvision-blog.com/7861-review-of-the-23-inch-asus-vg23ah-passive-3d-ips-display) so I'm going to go with the Asus for the following very scientific reasons: 1) It's $20 cheaper than the LG 2) The colours felt a bit washed out on the only AOC monitor I've used previously 3) It has built in speakers and I don't have any on my desk My feeling is that these will all perform in a very similar fashion - I'll report back once I've plugged it in! cheers Shaun
Re: [ccp4bb] stereo emitter
Did your OS/nvidia driver get upgraded? There's a bug in all of the modern nvidia drivers that cause this on the quadro 1300/1400 series. It works fine with the older nvidia drivers, e.g. 173.14.31 (note the legacy 9x.xx.xx drivers have the same problem). We're still able to use that version of the nvidia driver with centos/rhel 6.2. If you update past that version with 6, make sure not to update any of the xorg packages. The newer xorg packages have a new ABI which will only work with newer nvidia drivers, which will then cause the stereo flipping bug. On Tue, Feb 18, 2014 at 3:59 PM, Oganesyan, Vaheh oganesy...@medimmune.comwrote: Colleagues, I was happily using my NuVision 60GX emitter with Quadro FX1400 graphics card for number of years on CRT and recently something went bad and image will flip regularly sending front to back and vice versa. First I thought the card went bad but after installing new one nothing changed. I'm suspecting the emitter now and wondering if now there are solutions better than those emitters. Hopefully it is not too off topic. Thanks in advance for suggestions. *Vaheh Oganesyan, PhD* *Antibody development and protein engineering* *1 MedImmune Way, Gaithersburg, MD 20878* *www.medimmune.com http://www.medimmune.com/* *[image: logo1]* To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. inline: image002.jpg
Re: [ccp4bb] Stereo monitor
The quadro 600 or k600 works fine, been using it for more than a year with that Asus with the built in emitter. In fact the absolute oldest and cheapest option which works is the quadro 370, but you'll want the 600 at least. On Thu, Nov 21, 2013 at 9:19 AM, mesters mest...@biochem.uni-luebeck.dewrote: Hi Andreas, the older quadro 600 (with 96 CUDA cores) features a dual Link DVI-I (do not know why they did not call it DVI-D) but if I look at the specs, NVIDIA tries to suggest (?) the k600 features a DVI-I only. No mentioning it is dual-link. It would not make sense being single-link in the first place but make sure before you buy the new k600 (with 196 CUDA cores) it is really a dual-link DVI-I *i.e.* DVI-D. Some vendors state for the k600, 1x DisplayPort, 1x *Dual Link DVI-I* (Software)... Do not know what software exactly means at this point because I have never seen that before. For the more expensive cards (2000 and up) NVIDIA state they have a DVI-D and a DVI-I. Probably they are trying to confuse us to make us buy the more expensive models.. - J. -
Re: [ccp4bb] In need of SGI computer genius
Does this help? http://www.nekochan.net/wiki/Headless Not sure, how you'd set it to output to the serial port with the commands if you can't see what you're doing in the first place though. Otherwise you'll have to look for a graphics card that'll work in an indigo, a ps/2 keyboard mouse, and a sync on green monitor. On Fri, Oct 25, 2013 at 1:14 PM, David Roberts drobe...@depauw.edu wrote: Hello all, OK - small school - old NMR (really old). We set this up around 14 years ago with an O2 system as the user interface, with an indigo system as the interface between the O2 and the NMR. This is a JEOL system, has really been a workhorse with little issues over the last 14 years. We are obviously at the end here. We are working on getting a new one - but that's a work in progress. Anyway - today the hard drive failed on the indigo system. The simple issue is this - we access the indigo strictly via telnet. I do have a backup (I believe) on tape of the indigo. What is the best way to proceed here? There is no monitor on the indigo (nor is there a keyboard). I don't even have a monitor for it (no graphics card - and I don't have an old terminal). Thanks Dave
Re: [ccp4bb] 3D graphics linux compatibility question
(a) In previous CCP4bb discussions, it was stated that only Quadro cards are compatible with Linux setups. But could someone tell me what the minimum standard really is: is it Quadro FX380, 2000, 3800 or something else ? The nVidia site lists Quadro 3700 and 3800 as the two lowest (cheapest) options compatible with Linux 3D. However, different CCP4ers have in the past mentioned the other two options as working perfectly or with little trouble. Use the 3700 with the external nvidia emitters (these require the 3 pin mini din connection from the emitter into the video card) and 120Hz LCD's that don't have built-in nvidia emitters. (b) If a monitor such as the ASUS VG278Hhttp://www.asus.com/Monitors_Projectors/VG278H/#overview , which has an in-built nVidia 3D vision emitter which takes its stereo synch from a DVI cable is used, can we even use the simpler GeForce GTX670 or 680 ? No, I've tried this with a GTX680. You cannot use a GeForce in Linux with monitors such as the Asus VG278H with built in nvidia emitters and the official nvidia drivers to get 3D. You have to have a quadro card with a G8x GPU or better. In this case the cheapest card that would work is the Quadro FX 370 (not a typo, this is a different card from the 3700). We use a Quadro 600 or K600 with our Asus VG278H to get 3D. As you might imagine, we are on a rather tight budget. Any info would be greatly appreciated! which require the 3 pin mini din port on the video card. The VG278H is not a cheap monitor. You may be able to get nvidia 3d vision kit (make sure the model # comes with the 2.5mm vesa to 3 pin mini din cable since some don't, esp. the ones bundled with 120Hz monitors) + quadro 3700 + regular 120Hz monitor for slightly less than the price of the VG278H + quadro.
Re: [ccp4bb] Please recommend linux workstation
Dell Precision workstations are sold with RHEL, Ubuntu, or no OS (FreeDOS), but you can't see those options from the public websites. You need to try to get a Dell Premier account, talk to the Dell Rep for your university about that, here's a screen shot from our uni's premier site : http://i.imgur.com/NlekuSq.png We usually end up purchasing one with a Windows license though and just install CentOS over that. On Fri, Mar 15, 2013 at 11:34 AM, jie liu li...@umdnj.edu wrote: Dear All I am planning to buy a linux workstation for crystallography. It seems that Dell does not offer workstations with linux right now. Any good experience to recommend? Thank you! Jie Liu
Re: [ccp4bb] Off-topic: Best Scripting Language
Why are you dis-ing python? Seems everybody loves it... Depends on if you like the object model, some don't. In the end it really boils down to what you're used to and what you've learned to use.
Re: [ccp4bb] Nvidia 3D Vision 2 - Centos5 - Coot
Do you not need the 3 pin mini din to 2.5mm vesa cable with the 3d vision v2 emitter under linux? I haven't found a model # for this kit that comes with this cable and last I checked nvidia store was out of stock on purchasing these cables separately, so we still purchase the v1 kits. On Thu, Jun 14, 2012 at 6:55 AM, Laurent Maveyraud laurent.maveyr...@ipbs.fr wrote: Hi, on a Mandriva system, we had it working adding those two lines in the xorg.conf file, in the Section Screen : Option Stereo 10 Option Stereo AllowDFPStereo 1 The first line is mandatory with a LCD monitor. I have no idea what the second line means.. but it works with coot. hope this helps laurent Le 14/06/2012 13:19, S. Thiyagarajan a écrit : Dear CCP4 users Has anybody successfully configured NVIDIA 3D VISION-2 kit in CentOS-5.x and used COOT hardware stereo. I am currently having Quadro 4000 graphics card and a 3D compatible Alienware monitor. I could configure these easily in windows but not getting much clues for CentOS-5.x. Please point me to the right pages if this has been discussed already. Thanks for your help regards Thiyaga S. Thiyagarajan Centre of Excellence in Bioinformatics School of Biotechnology Madurai Kamaraj University Madurai - 625021 Ph: +91-9159224881 (cell) -- -- Laurent Maveyraud laurent.maveyraud AT ipbs DOT fr Université Paul Sabatier / CNRS / I.P.B.S. UMR 5089 PICT -- Plateforme Intégrée de Criblage de Toulouse Département Biologie Structurale et Biophysique BP 64182 - 205 rte de Narbonne - 31077 TOULOUSE FRANCE Tél: +33 (0)561 175 435 Fax : +33 (0)561 175 994 --
Re: [ccp4bb] DLP Link vs. IR emitter based 3D projection
1) a quadro 600 or 2000 and a DLP 3D Ready projector (3000-4000 Lumen) with DLP Link Glasses? Here's the xorg.conf for (1) since I already gave you the hardware setup : http://nopaste.info/946bd53e3e.html . Enable generic active stereo in windows. You can basically drive this with any quadro (not nvs), even a low end 370 would work.
Re: [ccp4bb] 3D projector--LG CF3D
ohh this is a passive stereo projector. what's the distance from the projector to the screen? On Wed, Jun 6, 2012 at 6:37 PM, Min, Xiaoshan x...@amgen.com wrote: Hi CCP4, I am curious if anyone has setup 3D-projector for large conference room. We have a LG CF3D projector and it is coupled to a Linux machine with Nvidia Quadro FX 3800. We haven't been able to get 3D working. If someone has experience with this projector, could you share the setting on the projector and graphic card? Thanks a lot. Xiaoshan Xiaoshan Min Amgen San Francisco 1120 Veterans Blvd. South San Francisco, CA 94080
Re: [ccp4bb] Who is using 64-bit Linux?
I tell you. Technology just doesn't work. developers and user's don't, technology is usually ok, but I feel your pain.
Re: [ccp4bb] Who is using 64-bit Linux?
No, that's a limit set by the ubuntu 32 bit kernel maintainers when they configured and compiled the kernel (again, see my comment about the problem being with developers and users). I think the limit is 256 for x86, 4096 for ia64 (itanium), even old versions of RHEL supported 16 and 32 logical CPUs for x86 : http://support.bull.com/ols/product/system/linux/redhat/help/kbf/g/inst/PrKB11417 http://cateee.net/lkddb/web-lkddb/NR_CPUS.html On Fri, Apr 13, 2012 at 3:08 PM, James Stroud xtald...@gmail.com wrote: On Apr 13, 2012, at 1:24 PM, James Holton wrote: I tried downgrading the operating system to 32-bit, but that reduced the number of CPUs available in the system from 24 to 8. Still don't know why that is I'm probably wrong, but I'll guess that a 32 bit operating system can only spare 3 of those bits to address CPUs ;-) James
Re: [ccp4bb] protein structure for high schoolers
foldit doesn't do electron densities and I don't recall if there are any puzzles in it that mention active sites/docking (it's been more than a year since I played it), but it's worth a mention. Hi- I am trying to help my former chemistry teacher set up a demonstration of protein structure for her class. I'd like to include electron density maps, and maybe show an enzyme active site. Are there suggestions from the BB on the easiest way to do this? Would pymol be the program of choice, or is there a simpler program that could show electron density? Has anyone already created such a demonstration they could and have advice on it? James
Re: [ccp4bb] linux upgrade preferences for CCP4
On Wed, Dec 21, 2011 at 2:29 PM, Paul Kraft haresea...@yahoo.com wrote: hello, I'm considering upgrading my linux software from CENTOS5 to perhaps Fedora or UBUNTO. Does anyone have an opinion about the best linux version to centos 6
Re: [ccp4bb] linux upgrade preferences for CCP4
The price of stability is that you don't get all the latest stuff. In SL6.1, the current version of Firefox is 3.6.24, and the image rendering is SLOW. I am wondering if I want to go back that far in time. Not out of the box, but the latest ffx works in centos6. I think there are third party repos for ffx, but I just download and maintain that separately (e.g. in /opt or /usr/local ), which basically amounts to clicking update in the about box of ffx. Also, SL does not have their own bugzilla. If you encounter a bug, they tell you to take it to RedHat. You can imagine the finger-pointing circles that is going to lead to. Centos 6 does but it's really not that big of a help either and neither is RHAT's bugzilla unless it's something that effects the majority of servers that RHAT gets paid to support (e.g. some bug in NFS, the filesystem, or kernel)
Re: [ccp4bb] linux upgrade preferences for CCP4
FWIW, I use RHEL 5 = CentOS 5 and recently upgraded to 6. Everything I use (not crystallographic software) works fine except vmware workstation currently does not work on it, Tried upgrading to vmware workstation v8? Compat guide : http://www.vmware.com/resources/compatibility/search.php?deviceCategory=softwaretestConfig=17 says that v8 works with RHEL6/CENTOS6 as the host OS. VirtualBox is a decent alternative if you don't want to pay.
Re: [ccp4bb] OSX and stereo
On Wed, Dec 7, 2011 at 3:48 PM, Erik Martinez-Hackert e...@cns.msu.edu wrote: Can anyone positively confirm that the new Zalman monitors M240W or M215W actually work on macs and pymol/coot? Specifically, I want to put this on a new macpro with an ATI Radeon HD 5770 card, but we also have older systems. Yes, we've tested the ZM-M240W with the latest generation macbook pro and imac, both with the thunderbolt/mini displayport outputs and they work.
Re: [ccp4bb] Dennis Ritchie
The silence on this list was deafening. group is saying: OK, so he discovered fire and invented the wheel - but what has he done since?. 1983 Turing Award 1990 IEEE Hamming medal 1999 National Medal of Technology 2011 Japan Prize for Information and Communications (while he was still alive I think) Even if he hadn't done anything technologically innovative that was made public since C and UNIX, his C book (which was the first programming book I read in it's entirety) and the foundations of his OS have helped countless millions of people. I find it sad that in many undergrad computer science curricula, C is no longer being taught. If you want to understand how software works under the hood you either learn assembly or C.
Re: [ccp4bb] Dennis Ritchie
Are you saying that undergraduates do not learn to program any more, or that they use a more advanced language than C where they don't really learn what is going on? The latter. It's usually Java and .NET nowadays IIRC.
Re: [ccp4bb] Zalman displays and Macs?
I don't recall but the Zalman also has a VGA port right? Have you tried minidisplay port to VGA? Have you tried your zalman with PC or older mac hardware just to make sure it works? On Thu, Sep 22, 2011 at 4:58 AM, Adrian Goldman adrian.gold...@helsinki.fi wrote: Hi, Anybody having problems with Zalmans and the newer macs? We can't get the MACS to even _recognise_ the existence of the Zalman display using a minidisplay port -DVI adapter and also using Thunderbolt out on a new iMAC (minidisplay port) -- DVI adapter. This is a real problem if one wants to do stereo on MACS... thanks for comment and advice... Adrian Goldman
Re: [ccp4bb] Zalman displays and Macs?
Am 22.09.11 11:58, schrieb Adrian Goldman: Hi, Anybody having problems with Zalmans and the newer macs? We can't get the MACS to even _recognise_ the existence of the Zalman display using a minidisplay port -DVI adapter and also using Thunderbolt out on a new iMAC (minidisplay port) -- DVI adapter. This is a real problem if one wants to do stereo on MACS... thanks for comment and advice... Adrian Goldman Is yours a ZM-M220W which looks like is known to have pins 15 16 switched or the newer 24 ZM-M240W?
Re: [ccp4bb] Zalman displays and Macs?
Hi all, Looks like our ZM-M240W came in a few days ago and the researcher has been using it fine with a standard minidisplay port to DVI adapter off his newer imac. Zalman must have fixed the issue with pins 15 16 being switched. Unfortunately he got used to using the 3d vision setup in our graphics lab and doesn't like the quality on the zalman as much (as expected). HTH, Sabuj On Thu, Sep 22, 2011 at 8:22 AM, Sabuj Pattanayek sab...@gmail.com wrote: Am 22.09.11 11:58, schrieb Adrian Goldman: Hi, Anybody having problems with Zalmans and the newer macs? We can't get the MACS to even _recognise_ the existence of the Zalman display using a minidisplay port -DVI adapter and also using Thunderbolt out on a new iMAC (minidisplay port) -- DVI adapter. This is a real problem if one wants to do stereo on MACS... thanks for comment and advice... Adrian Goldman Is yours a ZM-M220W which looks like is known to have pins 15 16 switched or the newer 24 ZM-M240W?
Re: [ccp4bb] Zalman displays and Macs?
Hi all, I emailed the guy at Zalman to let him know that the newer ZM-M240W works out of the box with minidisplay/thunderbolt port cards. He let me know that he no longer works at Zalman (not sure why his email addr. still works) but that if anyone needs the re-wired DVI cable for the ZM-M220W that you should : ... you should call Zalman USA and request a ‘custom DVI cable for the ZM-M220W’. http://zalman.com/eng/WTB/usa.asp Don’t email to the ‘support’ email address, for the person that receives the emails is a thermal engineer proper in HQ, helping Zalman USA, but he is not familiar with 3D display related matters. Thank you, Jihoon Jo HTH, Sabuj On Thu, Sep 22, 2011 at 10:41 AM, Adrian Goldman adrian.gold...@helsinki.fi wrote: Thanks to sabuj and all who replied. We do indeed have the older monitors and clearly we will have to contact zalman for a miswired DVi adapter! Adrian Sent from my iPhone On 22 Sep 2011, at 18:27, Sabuj Pattanayek sab...@gmail.com wrote: Hi all, Looks like our ZM-M240W came in a few days ago and the researcher has been using it fine with a standard minidisplay port to DVI adapter off his newer imac. Zalman must have fixed the issue with pins 15 16 being switched. Unfortunately he got used to using the 3d vision setup in our graphics lab and doesn't like the quality on the zalman as much (as expected). HTH, Sabuj On Thu, Sep 22, 2011 at 8:22 AM, Sabuj Pattanayek sab...@gmail.com wrote: Am 22.09.11 11:58, schrieb Adrian Goldman: Hi, Anybody having problems with Zalmans and the newer macs? We can't get the MACS to even _recognise_ the existence of the Zalman display using a minidisplay port -DVI adapter and also using Thunderbolt out on a new iMAC (minidisplay port) -- DVI adapter. This is a real problem if one wants to do stereo on MACS... thanks for comment and advice... Adrian Goldman Is yours a ZM-M220W which looks like is known to have pins 15 16 switched or the newer 24 ZM-M240W?
Re: [ccp4bb] stereo
Hi, On Thu, Sep 15, 2011 at 1:55 PM, Hena Dutta hdutt...@gmail.com wrote: Hi Sabuj, Thanks for all your answers. I finally came to this plan. Please tell me if I am doing anything wrong. Option 1. HP Workstation Z400 FL998U8#ABA Desktop PC - Intel Xeon W3550 3.06GHz, 8GB DDR3, 160GB 10k RPM HDD, DVDRW, NVIDIA Quadro FX3800, Windows 7 Professional 32-bit $1000 Acer HN274H bmiiid 27 Class Widescreen 3D LED HD Monitor - 1920 x 1080, 16:9, 1:1 Dynamic, 1000:1 Native, 120Hz, 2ms, HDMI, DVI-D, VGA, NVIDIA 3D Glasses, Energy Star $670 I highly doubt this monitor will work in Linux unless you buy the 3d vision kit which comes with the emitter that you can hook into the 3 pin mini din port of your quadro (btw your quadro 3800 requires an extra 3 pin mini din bracket, more on that below). This monitor has a built in emitter that works with the pair of nvidia (these are not generic active shutter goggles) 3d vision goggles it comes bundled with : http://3dvision-blog.com/review-of-the-27-acer-hn274h-3d-vision-ready-lcd-monitor/ ...but does not have an input for the 3 pin mini din coming off a proper quadro. The latest nvidia driver for linux still mentions that you need the 3 pin mini din for nvidia 3d vision stereo in linux: http://us.download.nvidia.com/XFree86/Linux-x86_64/280.13/README/xconfigoptions.html Option Stereo integer 10 NVIDIA 3D Vision mode for use with NVIDIA 3D Vision glasses. The NVIDIA 3D Vision infrared emitter must be connected to a USB port of your computer, and to the 3-pin DIN connector of a Quadro graphics board (based on G8xGL or higher GPU) before starting the X server. Hot-plugging the USB infrared stereo emitter is not yet supported. Also, 3D Vision Stereo Linux support requires a Linux kernel built with USB device filesystem (usbfs) and USB 2.0 support. Not presently supported on FreeBSD or Solaris. Having just the USB connected to the emitter still only works in windows with the standard emitter. I also know that the windows nvidia driver explicitly checks to see what sort of monitor you have before enabling 3d vision (see the nvidia 3d vision wizard in the nvidia control panel), i.e. that's probably why you don't need a USB cable connected from your computer to this particular monitor where the emitter is housed in the bezel. So, basically if you decide to go with this monitor you'll still probably need to get the 3D vision kit with the proper emitter and you'll also need to get the 3 pin mini din bracket for your Quadro 3800 since it doesn't have the 3 pin mini din output: There's a forum about it here : http://forums.nvidia.com/index.php?showtopic=96163 which leads to this PNY part # 900-50762--000 : http://www.google.com/products/catalog?q=900-50762--000cid=17694678402912029306ei=OoVzTvKqH6mExgXwi5HRAQved=0CAkQgggwAA#scoring=tp Ofcourse I have to install linux. Do I need to buy anything else(say emiter or connector) for 3D stereo set up in linux distribution. What linux you like to suggest? I am familiar with open suse or ubuntu. Either would be fine. Lenovo IdeaCentre K330B 7747-1GU Desktop PC - Intel Core i7-2600 3.40GHz, 8GB DDR3, 1.5TB HDD, DVDRW, ATI Radeon HD 6450, Windows 7 Home Premium 64-bit $750 But, then I have to buy the right graphics card. Yes. I think buying the NVIDIA Quadro FX 3800 graphics card will be much costly than to increase the hard drive. Which one is better processor? Intel Xeon W3550 3.06GHz or Intel Core i7-2600 3.40GHz i'd say the i7 2600 @ 3.4GHz, uses less power too. If they are not big difference, I will go with the first one and increase the hard drive. What do you think? Buy the 2nd one, get a quadro 3700, get the 3d vision kit, and if you want a 120Hz 27 LED monitor, here's one : http://www.buy.com/prod/samsung-syncmaster-s27a750d-27-3d-led-lcd-monitor-16-9-2-ms-adjustable/223430191.html that doesn't have a built in emitter which as mentioned above probably isn't going to work in linux. HTH, Sabuj Many thanks for your time. Hena On Wed, Sep 14, 2011 at 5:56 PM, Sabuj Pattanayek sab...@gmail.com wrote: On Wed, Sep 14, 2011 at 3:23 PM, Hena Dutta hdutt...@gmail.com wrote: Hi, Isn't that an LCD monitor (Acer HS244HQ)? It's edge LED backlit. I don't know if there are any direct LED backlit 120Hz monitors. Couldn't find much information on those types.
Re: [ccp4bb] stereo
Hi, On Wed, Sep 14, 2011 at 9:48 AM, Hena Dutta hdutt...@gmail.com wrote: Dear Members, Is any one using NVidia NVision 3D Setup with active stereo in linux Yes distribution for crystallographic work? Which one would be the best choice to set up, an active stereo or a passive stereo for crystallographic work? Active has better quality, greater 3D viewing area for people not sitting right in front of the monitor, but is more expensive if you have to purchase additional goggles ($70 non-nvidia online retailers - $120 currently from nvidia) Can anyone shade some details on this? I am planning to buy or build a new workstation with stereo set up. It would be great if someone can give some estimate on this. Going with the lowest prices: $300 Quadro 3700 : http://www.google.com/products/catalog?q=quadro+3700cid=5758926893192813358ei=i8FwTpqJGpGkwgXtw9H4CQved=0CAkQgggwAA#scoring=tp $320 Acer GD235HZ : http://www.google.com/products/catalog?q=acer+gd235hzhl=enum=1ie=UTF-8tbm=shopcid=114906938122589343sa=Xei=d8JwTr7TM8WgtwfFuZWJCgved=0CHsQgggwAA#scoring=tp $150 3D Vision kit with the 3 pin mini din VESA to 2.5mm stereo cable : http://www.nvidia.com/object/product_geforce_3D_VisionKit_us.html Total = $770 Passive stereo : $490 (open box) - $550 : Zalman ZM-M240W : http://www.compuvest.com/Search.jsp?Search=ZM-M240Wadvsite=frooglesku=756009288-08dp=3:CVS:51392:0:21 You can use the black RealD 3D movie theater goggles with the Zalman if you need extras. People also sell these online for a $1 + shipping. HTH, Sabuj Many thanks, Hena
Re: [ccp4bb] stereo
Hi, On Wed, Sep 14, 2011 at 10:52 AM, Hena Dutta hdutt...@gmail.com wrote: Hi Sabuj, Can I use LED monitor instead LCD? I heard the color contrast is better. If We haven't tried any, but here's an interesting 120 HZ LED monitor (Acer HS244HQ): http://www.newegg.com/Product/Product.aspx?Item=N82E16824009301nm_mc=OTC-Frooglecm_mmc=OTC-Froogle-_-Monitors+-+LCD+Flat+Panel-_-Acer+America-_-24009301 It comes with active 3D goggles, but it's noted that these only work with the 3D sync signal built into Bluray movies which I think is transmitted off the monitor. Now if this works like 3D DLP link stereo then you don't necessarily need the 3D vision stereo kit/emitter at all. In fact, we have an Infocus IN3116 projector that does 120Hz at 720p and a bunch of $50 DLP link goggles, a quadro 3700 video card in the box, and can do stereo in Windows 7 and Linux using Option Stereo 3 (standard quad buffered stereo). We use a cheap $2 DVI to HDMI converter to connect a long HDMI cable into the projector from the Quadro 3700 and that's it, no super long 3 pin mini din cable is needed. The only downside is that sometimes the left and right eye images are on the wrong sides when stereo is enabled, but most apps (e.g. pymol, chimera, and coot too probably) have an option to swap the eyes when in stereo so that's easily fixed. I buy higher level quadro graphics card (say FX 5600), will it improve the stereo quality? How big difference the prices are? Thanks for your A better card won't improve the stereo quality itself, but will improve surface, vdw, etc renderings with high polygon counts. For building models, most people are looking at wireframes/lines which you can still do for huge macromolecules on an SGI Octane. So yes, the 5600 will work with nvidia 3d vision, it has at least a G8x core (http://en.wikipedia.org/wiki/Nvidia_Quadro) and the stereo connector in the back. If you decide to go with something like that Acer HS244HQ it would be interesting to see if it can be made to work without the nvidia 3d vision kit at all. HTH, Sabuj information. Hena On Wed, Sep 14, 2011 at 11:26 AM, Sabuj Pattanayek sab...@gmail.com wrote: Hi, On Wed, Sep 14, 2011 at 9:48 AM, Hena Dutta hdutt...@gmail.com wrote: Dear Members, Is any one using NVidia NVision 3D Setup with active stereo in linux Yes distribution for crystallographic work? Which one would be the best choice to set up, an active stereo or a passive stereo for crystallographic work? Active has better quality, greater 3D viewing area for people not sitting right in front of the monitor, but is more expensive if you have to purchase additional goggles ($70 non-nvidia online retailers - $120 currently from nvidia) Can anyone shade some details on this? I am planning to buy or build a new workstation with stereo set up. It would be great if someone can give some estimate on this. Going with the lowest prices: $300 Quadro 3700 : http://www.google.com/products/catalog?q=quadro+3700cid=5758926893192813358ei=i8FwTpqJGpGkwgXtw9H4CQved=0CAkQgggwAA#scoring=tp $320 Acer GD235HZ : http://www.google.com/products/catalog?q=acer+gd235hzhl=enum=1ie=UTF-8tbm=shopcid=114906938122589343sa=Xei=d8JwTr7TM8WgtwfFuZWJCgved=0CHsQgggwAA#scoring=tp $150 3D Vision kit with the 3 pin mini din VESA to 2.5mm stereo cable : http://www.nvidia.com/object/product_geforce_3D_VisionKit_us.html Total = $770 Passive stereo : $490 (open box) - $550 : Zalman ZM-M240W : http://www.compuvest.com/Search.jsp?Search=ZM-M240Wadvsite=frooglesku=756009288-08dp=3:CVS:51392:0:21 You can use the black RealD 3D movie theater goggles with the Zalman if you need extras. People also sell these online for a $1 + shipping. HTH, Sabuj Many thanks, Hena
Re: [ccp4bb] stereo
On Wed, Sep 14, 2011 at 3:23 PM, Hena Dutta hdutt...@gmail.com wrote: Hi, Isn't that an LCD monitor (Acer HS244HQ)? It's edge LED backlit. I don't know if there are any direct LED backlit 120Hz monitors. Couldn't find much information on those types.
Re: [ccp4bb] Computer encryption matters
Hi, HIPAA and other regulations require systems which house patient identifiable data to have encrypted disks at our uni. Systems which house student data (e.g. SSN #'s, grades, etc) are also encrypted. Since we are doing mostly basic research or using de-identified data in structural biology, we are not required to encrypt our workstations and servers, which improves system performance, and is a big load off my shoulders! On Wed, Aug 17, 2011 at 2:13 PM, Jrh jrhelliw...@gmail.com wrote: Dear Colleagues, My institution is introducing concerted measures for improved security via encryption of files. A laudable plan in case of loss or theft of a computer with official files eg exams or student records type of information stored on it. Files, folders or a whole disk drive can be encrypted. Whilst I can target specific files, this could get messy and time consuming to target them and keep track of new to-be-encrypted files. It is tempting therefore to agree to complete encryption. However, as my laptop is my calculations' workbench, as well as office tasks, I am concerned that unexpected runtime errors may occur from encryption and there may be difficulties of transferability of data files to colleagues and students, and to eg PDB. Transferring data between encrypted and non-encrypted systems is seamless. Most of these applications encrypt your disk and optionally usb drives. Some require a password for boot or contact a centralized key server to get the keys required for decryption so that the system can boot. Our uni has a site license for Checkpoint's encryption app, but I've used truecrypt and they all allow transferring data between encrypted and non-encrypted systems without issues. HTH, Sabuj Does anyone have experience of encryption? Are my anxieties misplaced? If not, will I need to plan to separate office files, which could then all be encrypted, from crystallographic data files/calculations, which could be left unencrypted. If separate treatment is the best plan does one need two computers once more, rather than the one laptop? A different solution would be to try to insist on an institutional repository keeping such files. In anticipation, Thankyou, John Prof John R Helliwell DSc
Re: [ccp4bb] Stereo solution with Nvidia '3D vision' or '3D vision pro'
Hi, I tried upgrading the driver yesterday to the 270.41.06 version but it didn't make any difference, still only 100 Hz. Are you using Windows or Linux? We're using the 64-bit Linux driver. We had the same problem initially with the Asus VG236 until we went into nvidia-settings and turned off Force Full GPU Scaling for the monitor under the GPU settings. Usually this option is unchecked for standard 60 - 75Hz LCDs but I found this was checked for some reason, unchecked it and then the monitor went blank momentarily and came back. Then the refresh rate increased from 99.99Hz to 119.98Hz. The information menu in the monitor itself also showed 120Hz. This has to be applied for every user or you can copy ~/.nvidia-settings.rc to other users' directories. The system is currently using the 260.19.26 linux 64 bit driver running CentOS5. Here's the xorg.conf : # nvidia-settings: X configuration file generated by nvidia-settings # nvidia-settings: version 260.19.26 (buildmeis...@swio-display-x86-rhel47-07.nvidia.com) Mon Nov 29 01:13:18 PST 2010 Section ServerLayout Identifier Layout0 Screen 0 Screen0 0 0 InputDeviceKeyboard0 CoreKeyboard InputDeviceMouse0 CorePointer Option Xinerama 0 EndSection Section Files FontPathunix/:7100 EndSection Section Module Load dbe Load extmod Load type1 Load freetype Load glx EndSection Section InputDevice # generated from default Identifier Mouse0 Driver mouse Option Protocol auto Option Device /dev/input/mice Option Emulate3Buttons no Option ZAxisMapping 4 5 EndSection Section InputDevice # generated from data in /etc/sysconfig/keyboard Identifier Keyboard0 Driver kbd Option XkbLayout us Option XkbModel pc105 EndSection Section Monitor # HorizSync source: edid, VertRefresh source: edid Identifier Monitor0 VendorName Unknown ModelName Ancor Communications Inc ASUS VG236 HorizSync 24.0 - 140.0 VertRefresh 50.0 - 122.0 #Option ExactModeTimingsDVI TRUE # 1920x1080 @ 120.00 Hz (GTF) hsync: 138.84 kHz; pclk: 368.76 MHz Modeline 1920x1080_120 368.76 1920 2072 2288 2656 1080 1081 1084 1157 -HSync +Vsync # 1920x1080 @ 110.00 Hz (GTF) hsync: 126.61 kHz; pclk: 336.28 MHz Modeline 1920x1080_110 336.28 1920 2072 2288 2656 1080 1081 1084 1151 -HSync +Vsync # 1920x1080 @ 100.00 Hz (GTF) hsync: 114.40 kHz; pclk: 302.02 MHz Modeline 1920x1080_100 302.02 1920 2072 2280 2640 1080 1081 1084 1144 -HSync +Vsync # Monitor preferred modeline (60.0 Hz vsync, 67.5 kHz hsync, ratio 16/9, 95 dpi) #ModeLine 1920x1080 148.5 1920 2008 2052 2200 1080 1084 1089 1125 +hsync +vsync ModeLine 1920x1080 148.500 1920 2008 2052 2200 1080 1084 1089 1125 +hsync +vsync Option DPMS EndSection Section Device Identifier Device0 Driver nvidia VendorName NVIDIA Corporation BoardName Quadro FX 3700 Option Stereo 10 EndSection Section Screen Identifier Screen0 Device Device0 MonitorMonitor0 DefaultDepth24 Option TwinView 0 Option metamodes 1920x1080_120 +0+0; 1920x1080_110 +0+0; 1920x1080_100 +0+0 SubSection Display Depth 24 EndSubSection EndSection Section Extensions Option Composite disable EndSection ### I don't know if the modelines are actually necessary. The nvidia driver usually recognizes metamodes such as 1920x1080_120. HTH, Sabuj Pattanayek
Re: [ccp4bb] 3D system set up
Hi, I am about to setup a 3D system for crystallography. right now I can only think of coot and pymol software. so I might just go with Windows sytem, plus the Nvidia 3D vision kit If you're only going to use coot and pymol then perhaps a zalman will do?: http://www.google.com/products?q=ZALMAN+TRIMON+ZM-M220Waq=f I know there is a detailed list of hardware recommended. but are they compatiblility issues? can anyone recommed a set of system ( especially LCD and graphic card combo, I prefer at least 23' LCD) do we have to buy the expensive Quadro graphic card? if so, anyone can tell me which one to choose ? See this : http://www.pymolwiki.org/index.php/Stereo_3D_Display_Options The cheapest quadro that'll work with the nvidia 3d vision + pymol and coot in windows is still probably the Quadro FX 370 : http://www.google.com/products?q=quadro fx 370btnG=Search+Products There are several 120Hz LCD's that'll work (e.g. samsung 2233rz), but here are ones that are at least 23 : http://www.newegg.com/Product/Product.aspx?Item=N82E16824009222 http://accessories.us.dell.com/sna/products/Displays/productdetail.aspx?c=usl=ens=dhscs=19sku=320-8846 HTH, Sabuj Pattanayek
Re: [ccp4bb] 3D display - stereo only working in the lower half..
Only problem, using pymol or Chimera, the 3D only works in the lower half of the screen... In the top half, we see the two images superimposed and they are not separated by the shutter glasses. Surprised you got it that far. We are running it under windows. We couldn't get it to work with the linux beta driver. The graphics card is an Nvidia FX4500. It's not supposed to work in windows or linux with the quadro fx 4500. You need a quadro card with a G8x core or better, e.g. quadro 370 for windows and quadro 3700 for linux or windows, see: http://www.pymolwiki.org/index.php/Stereo_3D_Display_Options
Re: [ccp4bb] Nvidia 3D vision + 1920x1080 Desktop Displays
No, and it has nothing to do with the monitor. It's the sync signal from the nvidia emitter which isn't compatible with nuvision, crystaleyes, or edimensional goggles. On Wed, Mar 3, 2010 at 10:22 AM, Brick, Peter p.br...@imperial.ac.uk wrote: A related question: Can one use the old Crystal Eyes glasses system with the new LCD displays? And if not why not?
Re: [ccp4bb] Stereo
Yeah, only the RealD goggles, the ones that look like these and that are given out at standard (not IMAX) movie theaters: http://www.google.com/products?q=reald+3d+gogglesscoring=p will work. Several users brought back the IMAX goggles that look like these (might be yellow): http://www.3dglassesdirect.com/polarized_3d_glasses.html but these do not work. The difference is that the IMAX goggles are usually linearly polarized as mentioned in the 2nd URL above. The RealD goggles are circularly polarized which is the stereo tech that Zalman uses. HTH, Sabuj On Wed, Feb 3, 2010 at 10:42 AM, Revilleza, Maria Jamela (NIH/NIAID) [E] mariajamela.revill...@nih.gov wrote: Hello, FYI the 3D glasses distributed for viewing the Avatar movie can be used to view structures in COOT using the Zalman monitor. Regards, Jay
Re: [ccp4bb] Stereo TF - VGA to 3-pin VESA Stereo Adapter
On Mon, Jan 18, 2010 at 7:33 AM, mesters mest...@biochem.uni-luebeck.de wrote: Hi, the following information might be of use for the ones that do not have a 3-pin mini connector and are working under linux http://www.int03.co.uk/crema/hardware/stereo/ Didn't really see anything linux specific on that website but doing searches for rivatuner linux or softquadro linux mentions the nvclock utility which one might be able to use to mod a geforce into a quadro before you try the hard hacks mentioned above.
Re: [ccp4bb] 3D fitting
The Matchmaker utility in Chimera is another good one: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html On Sun, Jan 17, 2010 at 12:54 PM, Miri Hirshberg m...@ebi.ac.uk wrote: Sun., Jan. 17th 2010 EBI Greetings, I am looking for a 3D structure superposition program which takes two structures and superpose them based only on the coordinates X,Y,Z regardless of of residue/atoms name. (both files are in PDB format) Thanks Miri
Re: [ccp4bb] Stereo TFT
Hi, I thought FX3700 would work. Good to hear confirmation from you. It would be nice a Linux driver is available to allow USB based stereo sync. Yeah, it won't happen anytime soon. This details which cards are supported for 3D vision and which have a 3 pin mini-DIN stereo connector. That page says cards without the connector can be used via USB, but I am not sure if that applies to Linux or just to Windows. Again, USB stereo only works with Windows. They did not put the USB stereo code into the Linux binary driver :( . FX1400 and FX3500 not working - are you just saying that because they do not appear on the list, or have you personally verified it? Those happen to be the cards I currently have. We have also verified that both the 1400 and 3500 do not work and also that the Quadro 370 works with Windows using the USB stereo but does not work with Linux. Thus, the cheapest way to go on Linux for hardware stereo is with the Quadro 3700. Someone posted a link for the release notes of the 195.30 beta driver last week. I can't find the link right now, but I believe it said that to be supported for 3D vision, the card has to be G82XL or newer. The Core designations for Quadro cards can be found at Wikipedia: http://en.wikipedia.org/wiki/Nvidia_Quadro It only works with a G8x based card or better (see stereo option 10 in the 195.22 driver readme ftp://download.nvidia.com/XFree86/Linux-x86/195.22/README/README.txt). We've been using 195.22 with Stereo 10 without problems, here's an xorg.conf for Centos5: http://forums.nvidia.com/index.php?showtopic=91072st=0p=968627#entry968627 HTH, Sabuj Pattanayek
Re: [ccp4bb] Zalman LCD availability
Hi, http://www.provantage.com/zalman-tech-trimonzm-m220w~7ZALM03E.htm As someone mentioned still showing 4 in stock. That's where we got ours from. HTH, Sabuj Pattanayek
Re: [ccp4bb] Best 3D stereo combination
This chart: http://www.nvidia.com/object/IO_11761.html combined with the CCP4 wiki's advice (that the card should say stereo under display connectors) imply that we need to spend at least $760 on the video card alone. Is that really true??? EEK!! Uhhh no you don't. The Quadro FX 1400 is more than adequate for crystallography. We purchase new Dell Precisions with low end NVS cards and then switch them out with this model if we need stereo. We usually buy ours from http://www.compuvest.com . Do a search for quadro 1400 in their search box and you'll see ones starting at $80 (wow, looks like it dropped $20 since we bought these last!). If you want even cheaper deals see: http://www.google.com/products?q=quadro+1400scoring=psa=Nstart=0 These are usually refurbished but we've had several of these for almost 2 years without any problems. if anything goes bad it'll probably be the fan which can easily be replaced. HTH, Sabuj
Re: [ccp4bb] hkl2000 license
home computers. I do have the current def.site from biocars downloaded. The error that keeps coming up is No valid license for un-mar165. ERROR CODE 5. We tried getting an additional license (from HKL2000) for the particular detector but it still doesn't seem to work. Any suggestions/help will be greatly appreciated. I'd talk to hkl-xray. We've processed data using that hardware (not the same beamline) and were able to see and process the frames using v0.98.695b (not even the latest greatest I think). This is the list of licensed detectors we have for hkl2000: mar Mar345 unsup unsup210 unsup315 un-mar un-mar165 un-brand
Re: [ccp4bb] PDB protein strucutrues as screen saver
But as a biophysics student I would like to appreciate and feel happy to have pdb structures as my computers screen savers than to have some funny and fancy stuffs. And it may help me as a motivator to solve my own structures in future http://74.125.47.132/search?q=cache:_WRPDpKtbtcJ:ubuntuforums.org/showthread.php%3Ft%3D291503+linux+pdb+screen+saverhl=enct=clnkcd=1gl=us Ubuntu forums was down so there's the google cache page. I'm sure you can port the directions to your distro of Linux, if that's what you're running.
Re: [ccp4bb] Mac pro
with Unix on the Mac. There are also options for virtualization of Windoze and Linux via the software Parallels although I have yet to test this out. If you're trying to purchase a Mac so that you can run MS Office or other Windows only products without dual booting this is no longer necessary if you've got a Windows installation CD and a Linux system. I run Windows in Linux using Virtualbox (http://www.virtualbox.org) which is pretty much like a free version of VMWare Workstation. Do all of your research/graphics/modeling work on Linux and put it together using Adobe/MS publishing software in Windows running in VirtualBox. You can even share folders between the host Linux system and the guest Windows system without manually setting up a Samba server in Linux. VirtualBox doesn't support Direct3D so most Windows games won't work. I haven't tried OpenGL apps, but what's the point when you can just run these in Linux. HTH, Sabuj Pattanayek
Re: [ccp4bb] Mac pro
I assume you are waiting for today's announcements of the i7 core MacPro's ? If not wait another 6 hours before deciding to buy something. hrmm, I was hoping store.apple.com was down due to modifications for this new item, it's back up but no new i7 mac pro ..
Re: [ccp4bb] stereo with Nvidia Quadro
The 3500 series is moderately expensive. If you are on a budget maybe you could snag an older used card online somewhere. You can still buy new 1400's (OEM) for less than $160. Go to compuvest.com and search for quadro 1400.
Re: [ccp4bb] HKL2000 and gcc4
Hi, Have you installed the compatibility libraries compat-libstdc++-33 and libstdc++296? This is easily accomplished using yum if it is installed, e.g., $ yum -y install compat-libstdc++-33 compat-libstdc++-296 These libraries are required for programs compiled using GCC 3.x Those packages don't provide libg2c but they are good to have. You need yum install compat-libf2c-34 for libg2c.so.0 assuming you're using RHEL5 or greater. In any case, we're using v0.98.698d and it doesn't seem to need libg2c: % ldd `which hkl2000` linux-gate.so.1 = (0x4000) libX11.so.6 = /usr/lib/libX11.so.6 (0x00ada000) libm.so.6 = /lib/libm.so.6 (0x00a7) libdl.so.2 = /lib/libdl.so.2 (0x00a99000) libc.so.6 = /lib/libc.so.6 (0x0092e000) libXau.so.6 = /usr/lib/libXau.so.6 (0x00acd000) libXdmcp.so.6 = /usr/lib/libXdmcp.so.6 (0x00ad2000) /lib/ld-linux.so.2 (0x0090d000) which version of HKL2000 are you using that requires libg2c?
Re: [ccp4bb] cns map in coot
attempting to read CNS map: /Users/rajadey/yong/cns/coot/excl_comp.map CNSMAPfile: can't get number of header lines WARNING:: failed to read /Users/rajadey/yong/cns/coot/excl_comp.map DEBUG:: Erasing the back molecule 1 which says that it has molecule number 1 Read map /Users/rajadey/yong/cns/coot/excl_comp.map failed What does head /Users/rajadey/yong/cns/coot/excl_comp.map show? I just loaded 2fofc and fofc maps generated by cns 1.2 into coot 0.4.1 You should probably also post to the coot list specifically.
Re: [ccp4bb] stereo emitter sync issues (linux/quadro 4500/nuvision 60GX)
Peter Adrian Meyer wrote: I've tested the emitter on another system, and it works fine there. I've also tried the drivers from the ubuntu repositories and directly from nvidia (both behave the same way). What's the video card in the other system? Are you using the same driver version on the other system if it is nvidia? Can you take the 4500 out of the system where it doesn't work and put it in the system that where the emitter does work and test it there? if the 4500 works in the other system with the same driver/setup then there's something wrong with your motherboard or power supply on the system where it doesn't work.
Re: [ccp4bb] Linux Crystallography PC with Core 2 Duo CPU?
linwoo kang wrote: Dear all: I try to build a new linux crystallography pc with most updated CPU. Is there anyone using Core 2 Duo CPU on your linux system? works great, Xeon version too (5xxx) series
[ccp4bb] OT: turbo frodo keys?
Hi, Has anyone recently been able to get Turbo Frodo keys? Thanks, Sabuj
