Re: [ccp4bb] Fedora Core 20 issues.
Thanks for all the suggestions. I think my issue is because I have a QuadroFX1400 video card and I don’t have proper drivers - the generic ones just won’t do it. I have tried and failed miserably to install the proprietary drivers from NVidea, so I’m not going to worry about it. I only use chimera to make figures, and I can do that on my MAC easy enough. If any of you have an easy to follow guide on disabling nouveau drivers I’d appreciate it - but no worries if you don’t. Thanks again Dave On Sep 30, 2014, at 7:32 AM, Adam Ralph wrote: > > I take it you have the 32bit libraries installed. They are not normally > installed > by default. Then you need to make sure the app is linked with these 32bit > libraries. > I suspect that you may have linked to the 64-bit libraries. > > > Adam > > > > > Hi all, > > > > So, I know this probably isn’t the right place, but I’m certain most of you > > here have battled/fixed > this issue. I just did a clean install of FC20 > > on an AMD dual core system. I opted for the 32 bit > version, as these > > workstations are used for multiple things (and I find that it’s just easier > > most of > the time, though 64 bit may be where I need to go eventually). > > > > Anyway - when running chimera - my computer constantly freezes. Obviously > > I’m missing something. I’m not doing anything fancy - I use Zalman > > monitors connected to generic video cards. > > > > I can run coot fine - I don’t know about ccp4i (it seems to run, but I > > haven’t challenged it in any > way). > > > > Any thoughts on where I should start here? > > > > Thanks > > > > Dave
[ccp4bb] Fedora Core 20 issues
Hi all, So, I know this probably isn’t the right place, but I’m certain most of you here have battled/fixed this issue. I just did a clean install of FC20 on an AMD dual core system. I opted for the 32 bit version, as these workstations are used for multiple things (and I find that it’s just easier most of the time, though 64 bit may be where I need to go eventually). Anyway - when running chimera - my computer constantly freezes. Obviously I’m missing something. I’m not doing anything fancy - I use Zalman monitors connected to generic video cards. I can run coot fine - I don’t know about ccp4i (it seems to run, but I haven’t challenged it in any way). Any thoughts on where I should start here? Thanks Dave
Re: [ccp4bb] Stereo monitors for use with Pymol and Coot
Every now and then I pipe on this as well. We have Zalman monitors here - I bought them about 4 years ago - when you could not buy them any more in the states. I just bought them on Ebay - they came new in the box directly from China. The person did fed-ex shipping - did not cost any extra, and at the time it was a very cheap way to get these models that were not available in the US. I don’t know if they still sell this way or not - but for me it worked great. The monitors still work, and I agree with Zhijie, the 2D applications look perfect on them. Maybe it’s because I was so used to old, dim, CRT displays. In any event - they are great monitors for normal work, and it’s nice on occasion to use 3D with them. The 3D is OK - not perfect - but I don’t think any are as good as old CRT displays. The 3D does show what you need. What I really do find with modeling (myself included) is the following: I came from a situation where I used 3D exclusively (SGI’s, CRT’s, blah blah blah). Going to the newer, brighter, faster LCD displays means that 3D isn’t as important to me anymore, and I find that I typically use 2D almost exclusively. Occasionally I do 3D, and when I do, the Zalman is fine for that. Hope that helps Dave On Mar 6, 2014, at 7:50 AM, Zhijie Li wrote: > I beg to differ on this: > "Also, passive screens have a pol-filter in place, the fine lines of which > you will observe on a white background, the more disturbing the closer the > viewing distance to the screen is. So, for general office applications > (writing text), the screens are less useful. " > > Our LG D2342P has no issue with office work. I never noticed any thin lines > on the screen. In fact I think its 2D display is excellent. I wonder if the > issue you have is related to the screen size: the pixels of 27 in screens are > bigger than our 22 in screens. > > Zhijie > > From: mesters > Sent: Thursday, March 06, 2014 3:55 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Stereo monitors for use with Pymol and Coot > > Hi, > > this is probaly due to the transition from old TFT style to new IPS panel > based monitors... Several new passive 3d monitors are hitting the market such > as AOC d2769Vh and the Philips Gioco 278G4. Both are based on 27" IPS Monitor > panels. > > A list of possible monitors can be found at Tridef (many are old but new > models are listed), https://www.tridef.com/products/pc-licensed-products. > > Problem with passive stereo is, you will half the resolution in the vertical > direction. It is a problem if you are looking at wire-models of structures in > pymol and especially fine-wire electron density mesh and models in coot as > those noticably loose resolution compared to active stereo screens. Also, > passive screens have a pol-filter in place, the fine lines of which you will > observe on a white background, the more disturbing the closer the viewing > distance to the screen is. So, for general office applications (writing > text), the screens are less useful. This is not to big a problem for viewing > full screen pictures, games and movies (increased distance to the screen...). > > Moreover, with passive monitors, as the stereo effect increases with the > screen size, the picture looks more "pixeled" compared to active stereo > screens. I personally own a AOC d2769Vh and for 3D movies it is great, for > coot not that useful if you plan longer sessions. At work, we operate an ASUS > VG278HR (active stereo and build in emitter for glasses). Many hardware > testers consider this screen the best one available on the market. > > If you mainly need it for coot, I recommend to change your priorities and buy > an active stereo screen such as Asus VG248QE or Asus VG278HR. > You do not need an expensive quadro card (600 will do fine) as the VG278HR > has build-in emitter for operation with cheap nvidia glasses. > It pays off in the long run to invest a few more dollars as you (I assume) > will spend a lot of time in front of the this device (so buy the best as you > only have one pair of eyes). > > - J. - > > > > > Am 05.03.14 23:46, schrieb Shaun Lott: >> A rather US-centric question on passive 3D monitors... >> >> I'm just getting set up in the US, and I'm surprised on how few passive 3D >> monitors seem to be around - many models seem listed as 'out of stock' when >> looking in the usual places (Amazon, NewEgg, BestBuys, Walmart etc.) >> >> The best deal I have found is for an LG D2343PB-BN >> (http://www.lg.com/us/commercial/lcd-computer-monitors/lg-D2343PB-BN) at >> US$274 >> >> Does anyone have any experience with this model, or any suggestion about >> where best to buy 3D monitors in the US? >> >> many thanks in advance >> >> Shaun > > > -- > Dr. Jeroen R. Mesters > Deputy, Senior Researcher & Lecturer > > Institute of Biochemistry, University of Lübeck > Ratzeburger Allee 160, 23538 Lübeck, Germany > > phone: +49-
[ccp4bb] In need of SGI computer genius
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] showing electron density on an ipad
Sorry - I went back to look at that. The ipad app for pymol does not have an option to load a map. You can only load structures. I like that you can load your own structures (from a dropbox folder), that's nice. It's very powerful, and I can do a lot with it, but I would like to show electron density and can't find a way. I got good suggestions yesterday. Imolview does work well for loading pdb files. I don't have a way to get the browser that goes with it to run on my linux box. I tried it, but was unsuccessful, so I don't know if it displays density or not. The CueMol does not show density. So, both of these are nice for pdb files (I like Imolview better), but neither will easily show electron density. I just want an app that will display a pdb file and a map file. I can convert maps to whatever format is necessary (as long as it's crystallographic). That I can't seem to find. No worries. Thanks for all the suggestions Dave On 5/2/2013 2:35 AM, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Dave, could you explain what you mean by "it doesn't work"? I understand that you convert a ccp4 mtz-file to ccp4 map format (which pymol can read) and load it into pymol on your ipad which does not display. Is this correct? If so, do you get any error messages? Could you use coot instead? Best, Tim On 05/01/2013 09:56 PM, David Roberts wrote: Hello all, So, I find an ipad is a wonderful device for teaching (any tablet really - but I'm partial to the ipad). I can project it in a classroom, run pymol and a few other chemistry/biochemistry things, and really get the students interested in these subjects easily. I actually don't have a laptop - and our classrooms are such that there are computers connected to the projectors but they have standard University software packages installed on them. It would be very helpful if I could just display electron density using an ipad. The pymol app will load a map (it is an option) - but when I take a map from my linux machines it doesn't work. Any thoughts here? Has anybody done this Thanks Dave - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRggkUUxlJ7aRr7hoRAilLAJ9G2JTUu9hYnH+Hsf+LViBFHNqC6QCggGaR /r2Il4d2qklnV/IGJWxpZpw= =QOT4 -END PGP SIGNATURE-
[ccp4bb] showing electron density on an ipad
Hello all, So, I find an ipad is a wonderful device for teaching (any tablet really - but I'm partial to the ipad). I can project it in a classroom, run pymol and a few other chemistry/biochemistry things, and really get the students interested in these subjects easily. I actually don't have a laptop - and our classrooms are such that there are computers connected to the projectors but they have standard University software packages installed on them. It would be very helpful if I could just display electron density using an ipad. The pymol app will load a map (it is an option) - but when I take a map from my linux machines it doesn't work. Any thoughts here? Has anybody done this Thanks Dave
Re: [ccp4bb] Dell linux box and stereo monitor
My 0.02 on this as always. For monitors, I was worried about this at first. I replaced all my SGI units (with what was good graphics and CRT displays), and I worried about getting a new monitor and losing information with different stereo options. I bought zalman monitors, and they work fine. They have little quirks, but overall for the price it was a great deal (a one time price for the monitor, no issues with software or hardware as you can just pick up free glasses at your local 3D movie showing). Now the surprise. Going from a "dim" CRT display to any standard LCD display is really all you need to do. I find I don't use stereo a lot. The nice crispness of the LCD displays is really good enough, and the software is quick enough that one can do quick rotations and get a good feel for dimensions. I find students today don't really use stereo, and I've sort of gone away from it. But I do like the Zalmans, as they do on occasion let me use stereo if that is something I need to display As far as computers for linux - I just build them. Buy a motherboard, memory, hard drive, DVD drive, and some sort of video card and you are good to go. Costs around $300-$400 or so per computer if you do it right. I have boxes that are over 10 years old that will run a typical cns job in 10 minutes. While that is slow compared to most things now, I feel I need a 10 minute break after modeling an entire molecule (I used to get a day break, how times have changed). All modern flavors of linux are very user friendly when it comes to installing (some more than others, that's a whole different matter; I still use fedora). They don't mind hardware, and in fact they do well with almost any newer hardware Good luck Dave On 2/20/2013 2:58 PM, jlliu liu wrote: Hi All, I am about to order some linux boxes for protein crystallography use from DELL. Could you guys share the experience which model would be the best for this purpose? Also I know the stereo monitor topic has been discussed previously, but I would like to get the opinion for the current best stereo monitor available for model building in protein crystallography. Thanks so much in advance for sharing your experience. Jinyu
Re: [ccp4bb] protein crystals or salt crystals
So, if you are bored and have nothing else to do (which is how we all are at times; kidding), can you set up a control experiment with everything in the crystal dip except protein (so buffer and whatever)? I know protein plays a role in the process, but I have done this before when I had suspect conditions, and it did show that my buffer formed crystals in that situation. Sometimes it helps. But I am one that never throws a crystal away, and always just puts it in a beam before saying it's salt. Protein crystals are too precious to rule out by over thinking. Good luck Dave On 2/8/2013 9:13 AM, Edward A. Berry wrote: Raji Edayathumangalam wrote: (3) Inconclusive "no diffraction" situation, which could indicate a million things including the possibility that your cryoprotectant was sub-optimal for data collection done using flash cryocooled/flash frozen crystals in a stream of gaseous nitrogen. But before throwing it in this category, be sure to take a wide-angle oscillation, as reciprocal space is sparsely populated with small unit cell crystals and you might miss spots altogether in a 1 degree oscillation. I like to take a 5-sec 180* oscillation which gives plenty of spots in a nice pattern for a salt crystal, and I suppose records enough spacings to positively identify the mineral if anyone cared to tak the time. eab
[ccp4bb] need some suggestions for crystallization
So, I know I say this every time I post on this board, but here it goes again. I'm at an undergrad only school, and every 2 years I teach a class in protein crystallography. This year I'm being super ambitious, and I'm going to take a class of 16 to the synchrotron for data collection. It's just an 8 hour thing, to show them the entire process. I'm hoping that we can collect 5-6 good data sets while there. I would like them to grow their own crystals, and go collect data. Then we'd come back and actually do a molecular replacement (pretty easy/standard really). Just to get a feel for how it works. The protein I do research on is not one that I would push on this, as the crystals are hard to grow, they are very soft, and the data just isn't the best (resolution issues). I do have a few that will work on my proteins, but I was thinking of having others in the class grow up classic proteins for data collection. Obviously lysozyme is one, but I was wondering what other standard bulletproof conditions are out there. Can you all suggest some protein crystallization conditions (along with cryo conditions) for some commercially available proteins? I'm looking to get 6-8 different ones (and we'll just take them and see how it goes). I wouldn't mind knowing unit cell parameters as well (just a citation works, I can have them figure it out). I have about 7 weeks to get everything grown and frozen and ready to go. Any help would be greatly appreciated. It always amazes me how helpful this group is. Thank you very much. Dave
Re: [ccp4bb] 3D Monitors
I use the Zalman 21" monitor and it works great. Glasses from 3D movies work, so when students go to the movies I ask them to save a pair of glasses for me. It's easy and cheap - software controlled so works on all crystallographic packages that I've tried thus far. Frankly, since going to an LCD monitor from the old CRT displays, I find stereo is not really needed. It's cool, and occasionally nice to look at, but the display is so good that I find 2D is just fine for all modeling needs. So we really don't use the Zalman's much Dave Sent from my iPad On Jan 27, 2013, at 11:00 AM, Peng GONG wrote: > Sabine, > > I am using LG D2342P and it works fine with coot and pymol. > > Peng > --- > Peng Gong > Wuhan Institute of Virology, CAS > --- > > From: Sabine Schneider > To: CCP4BB@JISCMAIL.AC.UK > Sent: Friday, January 25, 2013 12:13 AM > Subject: [ccp4bb] 3D Monitors > > Hello everyone, > > I know there already has been discussion about 3D monitors on the Coot/CCP4bb. > However since there are a few more out there now and I am currently thinking > about buying one, I thought to get a few opinions from crystallographers > would be nice! Especially if there are people happily model building with the > cheaper LG 3D monitors? :-) > > So I am looking at the moment at: > - Zalman ZM-M215W 21,5in > - Zalman ZM-M240W 24in > - Samsung SyncMaster S27A750D 27in > - LG D2342P 23in / LG D2542P 25in > > Thanks a lot! > > Sabine > >
Re: [ccp4bb] question on metal refinement in a protein structure
Thanks for the replies. Yuri, yes, those were my exact concerns. This is a molecular replacement structure, but that was done with an apo structure, so I am certain the metal is there. My resolution is around 2.3 angstroms, which I think is OK for determining geometry. I have done omit maps as well as simply several rounds of refinement with no metal present. It always comes back, and has a certain shape (tetrahedral). I just was concerned that I was forcing a geometry by not specifying nickel properly in my pdb file. I didn't know right off how one might specify different oxidation states in a pdb file (say Nickel I vs Nickel II; that is not what I am trying to do, but it is something I'd be curious about). I haven't worked with a lot of metalloenzymes, so I just wanted to be sure. I think you are right, and I am doing things properly (the programs are of course very good). Thanks again Dave On 5/12/2012 2:49 PM, Yuri Pompeu wrote: Hi Dave, I sounds to me like you are worried about 2 separate things here. A: Am I affecting the geometry of the coordination sites with a restraint file that is innacurate? B:Are my electron density maps biased, and what I am seeing is not really there? AFAIU, if you have a restraint file that is innacurate, lets say it is defining the metal/ ligand angles to be those of a tetrahedron, that would influence the position of your atoms after refinement as the program will try to "obey" the restraint file. The electron density maps, however do not directly take into account your restraints file. With that being said, model bias can be a problem, yes. This is dependent on many factors, and if you have obtained your phases through a molecular replacement solution rather than experimentally (MAD, SAD, etc..) your maps will be particularly susceptible to bias. And if your dealing with a low resolution data set this can become even more of a problem (you dont mention your resolution). If you are working with a 1.2A data set, I would not lose sleep over it. People have spent many hours of thinking and programming to develop ways of eliminating model bias and many programs can calculate electron density maps in a way that your bias is minimized. Always check your difference map (mFo-Dfc), you can calculate omit maps, averaged kick maps, and in the case of metals even an anomalous maps sometimes. All of these would help you put your mind at ease. Hope this helps
Re: [ccp4bb] drops swelling
The following is simply a quote from a recent post by Enrico Stura. Probably has a lot to do with what you are finding: "Glycerol is also great to reduce nucleation. If you decide to add glycerol to the protein solution (for solubility, but in your case it might be for stability reasons), you also need to have a higher (double) glycerol concentration in the reservoir else you will risk finding that your drops will get biggger and not smaller. This note of caution applies to vapour diffusion set ups as equilibration can be tricky in such context: Vera,L., Czarny, B., Georgiadis, D., Dive, V., Stura, E.A. (2011) Practical Use of Glycerol in Protein Crystallization. Cryst. Growth & Des. 11 :2755–2762. http://pubs.acs.org/doi/abs/10.1021/cg101364m " Good luck Dave (but really, this is all Enrico) On 9/9/2011 7:22 AM, anita p wrote: Dear Crystallographers, I have set hanging drop trays with 2ul of protein and 2 ul of resorvior solution. I have seen in some cases the drops are swelling. My protein buffer has 15% glycerol in it. This is happening mainly when I have peg 400 or peg MME or MPD or Jeffamine in the buffer condition. Could any one suggest a remedy for this. with regards Anita
Re: [ccp4bb] Stereo solution with Nvidia '3D vision' or '3D vision pro'
Not only do you not need a high-end graphics card, you don't even need the proper graphics drivers installed. When I went to FC13 (upgrade from FC7, I don't know why), my quadro fx1400 was no longer supported. It would not work with hardware stereo (emitters/glasses of old). I went to Zalman monitors and all is great. Frankly, stereo is not needed as much in a nice bright LCD monitor (very crisp, looks great), but if you want it, Zalman is the way to go (passive stereo - light glasses, no hardware requirements beyond the monitor) Good luck Dave On 5/10/2011 12:27 AM, Duangrudee Tanramluk wrote: 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
Re: [ccp4bb] while on the subject of stereo
Thanks for the comments, I do appreciate them. I guess we went off in a direction I wasn't thinking of - related to your personal like or dislike of stereo. What I am really looking for is an answer to a simple question in that is stereo a nice thing from a pedagogy standpoint for showing students complex biomolecules. I am in a chemistry department - undergraduate only. We focus on 3-dimensional shape and the importance of shape of chemical function/reactivity/etc... With small molecules (PF5, etc...), it's easy to see how shape works by simply rotating the molecule. The molecules are small enough, the concept of 3D can be visualized easily in these systems. Furthermore, they can make a simple model using your standard organic or inorganic model kit, no worries. Now, bring in a huge protein, or a protein-protein complex. The issue of 3Dness becomes fuzzier. It's not so easy to see which hydrogen will get plucked off during a chemical reaction, even with careful zooming and mouse manipulation. So my question still is, how many of you feel stereo is important from a pedagogy standpoint (not looking at maps, just structures that are huge and complex). Is it something that we need to try to bring to the classroom, or is it just a cool toy like the 3D TV that hopefully is going nowhere and will soon fade out like the viewmaster of old. I know a large percentage of people cannot see stereo (at least the way we present it), and so it isn't for everybody. But, does it help, and if so, does it help when done in a huge classroom or when put on an individual screen. Has anybody tried to assess this (there's a horrible word for you). That's what I was wondering about. Presenting the stereo is a different issue (how is that done), but I think there are lots of avenues for that depending on your particular situation. Thanks again Dave
[ccp4bb] while on the subject of stereo
Hi again, I'd like to ask a question about the pedagogy of stereo. That is, using stereo with students in the classroom. Do you all find that, after setting up these elaborate stereo devices, students really use the stereo or do they tend not to? I am a huge fan of stereo - and frankly here we have quite a few options for doing stereo - from the active Nvidia systems that people have recently been discussing to passive zalmans. I went from SGI systems and crystaleyes to linux systems using nuvision glasses, and finally have settled for Zalman stereo - as I think it is the best thing out there. Zalman is passive - go to the movies and get a free pair of glasses (realD glasses work fine), and you don't have to have any video card requirements (I haven't tried using it with onboard stereo - I do have graphics cards, but I have a feeling onboard stereo wouldn't be bad). When in a classroom - we project using glasses that work on an emitter based system (so it's active stereo - we are thinking of going passive in the classroom as well). When we use stereo in a classroom, we find you take just as much time telling students they need to look forward as we do talking about active sites. In some cases, the stereo may be distracting. Many can't get it to work - and when they do I don't know how effective it is. I teach a crystallography class, and for that I have a linux lab setup with 6 computers equipped with Zalman stereo (recent, it was active nuvision before). Students have to fit a map and build a MIR structure (from scratch totally) using coot. It's a great experience, but I find that I have to constantly get them to put on stereo glasses to get the best fit of their model in the map. They tend to not do it, and so I'm trying to see if it's the type of stereo used (as I said, I had a few options, and this class actually has their range of devices) or if it's just that they can do it good enough without stereo. They do prefer the LCD monitor over a CRT display (and that is a brightness thing I think - they are just crisper and newer). When on the CRT's, they will use stereo (active), but when on the LCD displays stereo is not necessarily used (they don't seem to need it as much). As I mentioned, I like stereo a lot, but really projecting on a nice bright lcd monitor also has it's advantages, and with the ease of moving things using the mouse (or whatever device you use), the overall need for stereo seems to be decreasing. I don't know - I just wonder what peoples views are out there for the actual "need" for stereo. It's incredibly cool - and I think is a very powerful way to show things - but I'm wondering if we focus too much on it because it's cool and not because it's pedagogically necessary. Just wondering, no worries. Thanks Dave
[ccp4bb] linux flavors
Hello all, Quick question on linux varieties. For years (and years) I have used fedora (after Ultrix of course). In fact, most of my computers are running FC7 (that long ago), it's very stable and works fine. However, since it is no longer supported, I'm toying with upgrading. I upgraded one machine to FC13. However, this nouveau driver thing is killing me, and getting my nvidia drivers installed is hopeless (I have followed every thread on this and I simply give up - it's not worth it). With a Zalman monitor it doesn't matter - nouveau works fine and my stereo is good - so I don't really care (or do I). The question is this - what flavors of linux out there are simplest to install - work instantly with various hardwares, and run stereo seamlessly (either Zalman stereo or hardware stereo with an emitter). For zalman anything works - which is why I'm going that way - but I still need hardware stereo on a few machines. So, for hardware, I need my nvidia drivers to install easily. I'm downloading ubuntu - is that a good choice? Can I run different flavors of linux with nfs and share drives in a local network (so one has fc7, one has fc13, and another has ubuntu)? Thanks Dave
Re: [ccp4bb] Liquid nitrogen resistant flooring
We went through a building renovation and this has been a problem for us too. In the old days, our building was simply sealed concrete - and you could do anything with it with no issues. Now, it's an epoxy floor, but really what happens is the liquid nitrogen cools it down and breaks the seal between the epoxy and the concrete - causing cracks and ugliness. We use a series of throw rugs and large containment pans to hold the nitrogen. It doesn't really work - so every now and then we simply repaint the floor. It's only in a few places that we use this, so it's not too bad. I do have 1 room that they put the wrong floor down first. It's a spongy floor - designed to not carry a static charge. Instead of removing the covering (which they can't do), they just went over that floor with an epoxy coating. Oddly enough - that room doesn't crack when I pour liquid nitrogen on the floor. So maybe that's the trick - put a cushion between the concrete and the epoxy. They wouldn't leave sealed concrete because it looked bad (we did a renovation, not a new building). Too bad Dave On 2/16/2011 7:32 AM, Richard Edward Gillilan wrote: This has been a problem for us too. Sorry, I don't have a solution to offer except, recently, we have provided metal buckets filled with a layer of aquarium gravel at each station and encouraged users to dump their excess nitrogen there instead of on the floor. Richard On Feb 16, 2011, at 7:20 AM, Nicholas Keep wrote: Can anyone recommend a floor coating that passes category 2 containment (ie not wood) that is resistant to liquid nitrogen. Ie you can fill dewars on without cracking. Various solutions our estates people have fitted have all proved unsatisfactory. Bets wishes Nick --
[ccp4bb] NUVISION 60GX glasses/emitters
Is there anybody out there who has a use for these glasses/emitters that would be willing to purchase some for a reduced fee? I have 16 pair (I think, I need to go check closely, but I have a lot of them), plus 6-7 emitters. I just need to go away from this type of system, probably to a mixed bag of zalman passive and strict 2D. Not all of the glasses work (3 of them do not), but I think the problem is just a small microswitch, and NuVision will repair them for next to nothing (I just haven't had time to deal with that issue). Sorry to make this board into a garage sale, but it seems like this group is the best place to put these. I would give them away if I could afford it, but I'm trying to use proceeds from this to get a couple of higher end monitors. Thanks. Feel free to contact me off list if interested (drobe...@depauw.edu) Dave
Re: [ccp4bb] which Linux workstation for crystallography to buy?
I think people have answered this correctly. As one who did this several years ago - I built my workstations with top end hardware (at the time). I used an AMD dual core system (top end for the money - I'm OK with AMD), built it from scratch (so I bought the fastest processor available for the money at the time), loaded it with memory, got a video card that met my needs, and the rest is there. The systems still work great, do a typical CNS run in under 5 minutes, can do a PHASER run in 10 or so minutes, so they still work fine (that's enough time to go down the hall, stretch and get coffee, and then come back and do coot). I only have 4 Gig memory per computer - but for me that's enough. My systems are obviously no longer top of the line, but they still run great, 6 years later. Just swap out a motherboard every now and then and we are set to go. The biggest thing you need to do is make some key decisions on what you need (and then stick with it): 1. Do you need stereo (biggest issue - if so you need to pay attention to video cards, etc...) 2. Do you care if you have to upgrade your system often - free linux such as fedora is very nice, but requires a lot of maintenance (which isn't hard, but you have to stay on it). The hardware can handle it, it's just in picking your OS 3. Are you going to run more than one monitor/display? 4. Disk space is now incredibly cheap (has been for awhile, but this used to be a crunch). Buy one smallish disk and use it solely for your OS (whatever OS you choose). Then use a separate disk for data (user disk, whatever you want to call it). You can buy several small disks ($25 each, can't go wrong here), put different systems on them (even windows), and use the bios switch as your bootloader (hit the F11 key on startup and pick the disk to boot - don't bother with a dual boot system and boot-loader as those can go bad, screwing up both systems). Go with SATA drives, they are cheap and easy to come by now. Try different flavors of linux this way (FC13, ubuntu, whatever - each on their own disk). It's easy I'm sure the list is longer - but really most software will work with whatever system you get. They all are very good now, come with packages pre-compiled, and simply work when you put them on your system. Good luck. Dave On 10/12/2010 9:03 AM, Paul Smith wrote: Stefano, I second the previous posts. Essential is a solid NVIDIA graphics card - quadro or geforce and not something low end. Vendors don't matter so much, we use both Dell and Hp and both are fine (essentially the same hardware inside). Also, linux version doesn't matter. We use both Suse and Ubuntu (and, yes, you can have a root account on Ubuntu, just use the "sudo su" command to log in as root, set a password, and Bob's your uncle). For laptop, I recommend the Dell precision portable workstation in i5/nvidia configuration. For desktop, I recommend HP proliant quad-core servers with a third-party nvidia graphics card. Avoid AMD hardware - often the linux drivers aren't stable. Feel free to contact me if you would like more specifics. --Paul --- On Tue, 10/12/10, Benini Stefano (P) wrote: From: Benini Stefano (P) Subject: [ccp4bb] which Linux workstation for crystallography to buy? To: CCP4BB@JISCMAIL.AC.UK Date: Tuesday, October 12, 2010, 4:28 AM Dear All, I need to buy a Linux workstation to run crystallographic software and graphics like ccp4, mosflm, coot., etc., Could you please suggest me a good combination of hardware and which linux operating system to install (ubuntu?)? I can spend about 1500€ Technology evolves so fast that I really want to be up to date not to be already late! Thank you very much in advance Stefano Stefano Benini, Ph.D. Assistant Professor http://pro.unibz.it/staff2/sbenini/ Bio-organic Chemistry Laboratory Faculty of Science and Technology Free University of Bolzano Piazza Università, 5 39100 Bolzano, Italy Office (room K2.11): +39 0471 017128 Laboratory (room E.012): +39 0471 017901 Fax: +39 0471 017009 ***
Re: [ccp4bb] stereo (again - sigh)
Thank you all for the quick replies. I did leave out some specs, but I really wanted to know what others have found. Sadly, it's no different than my findings. I am at a small undergrad only university - low on resources but big on ideas for teaching students. This is not research based, so I don't have a grant to buy one system for research (I do solve structures and I can buy one system, but I need more for a class). Instead, I'm trying to teach a class - we have 6 workstations that are shared among the students. We solve a crystal structure as part of this class. Stereo is nice but not necessary - though as a teaching tool it's invaluable. Switching to the nvidia system works - we have that here for one classroom - the problem being active stereo is a nuisance. It can flicker - looking away can cause problems (with a larger classroom), and it's just not the way to go (the glasses are expensive, I can go on and on). I think passive stereo is the beat all end all - but I can't buy a zalman monitor to save my life (I have literally had 3 of these in shopping carts - and one went as far as to charge my card only to refund me 3 days later due to lack of stock). That does make me worry as to replacing it later in life should I get 6 and they crap out on me. When I was at Argonne, they have a polarizing filter that fits on the front of a monitor. You can turn it on and see stereo through that, I think it's basically a Zalman filter. Does that sound right - and if so - is that something somebody out there has? Thanks again - your help is invaluable. By the way - if I ever do replace this, is anybody in the market for some old emitters, video cards, and glasses (I have 14 pair of the 3D glasses - crystal eyes knock-offs, sorry the company escapes me at the moment, but they are good glasses). Dave On 10/5/2010 12:25 PM, Ben Eisenbraun wrote: Hello Dave, I would like to replace the CRT's with some sort of LCD thing. You have two options for stereo on linux. The Zalman passive stereo route, which you tried, or the active stereo route, which means an Nvidia 3d Vision emitter/glasses combo and a 120 Hz LCD. The glasses/emitter kit is here: http://www.nvidia.com/object/product_GeForce_3D_VisionKit_us.html And you need an Nvidia Quadro FX 3700 or higher to run them on linux: http://www.nvidia.com/object/quadro_pro_graphics_boards_linux.html There are several 120 Hz LCDs available right now. Some links to models and additional info on set up are on our website: http://sbgrid.org/wiki/install/stereo I hope this helps. -ben -- | Ben Eisenbraun | Software Sysadmin | | Structural Biology Grid | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |
[ccp4bb] stereo (again - sigh)
I hope for everybody this is the last time with this. I know it has been asked (even partially by me), and I know people talk about it often - but I am really trying to solve this problem once and for all, and am having a very hard time. Past and present set-up for this: Started out with SGI's running active stereo with classic emitters/crystaleyes glasses (or the equivalent) Moved to linux boxes with quadroFX-1400 video cards. Still have CRT's/emitters I would like to replace the CRT's with some sort of LCD thing. I have tried several times via at least 5 different web buyers to buy a Zalman monitor. I can't get one (I just received a rebate for a purchase I thought I made last week - out of stock). I would love to go Zalman with all passive stereo - seems like the best way to me, but it just isn't happening. Has anybody used these 3D tv monitors with active stereo with a FX1400 video card? If not, can you just let me know what video card/monitor combo are needed on a linux station to run 3D (using a classic emitter/crystaleyes). I would like to stay with my video card - but it's possible that I have to upgrade that as well. I just need to get away from CRT's, as they are fading and purchasing them is getting tougher and tougher (and really, I don't want them anymore). Thanks much Dave
[ccp4bb] mol rep help needed
Hi all, I'm relatively new to using CCP4 (I've done most of my crystallography using x-plor, phases, etc...). But, I like ccp4, and so I'm using it in concert with amore (which I know is part of the ccp4i build now) for molecular replacement. I have a protein that I'm working on with data collected from Argonne. There are many forms, and I have several of these forms collected (metal bound, apo, mutants, etc...). I have a solution for a wild-type form, and am presently working on solving a mutant form. For molecular replacement, I used the wild type structure (obviously). It's a homodimer, so I tried using both the monomer and the dimer form of the protein (it's possible that the mutant is conformationally different from the wild type, so it's not a clear-cut problem). Furthermore, they both crystallize in the same space group (P212121), but unit cells are different (I don't have the exact numbers now, but the general idea is the wild type is 30/60/120, while the mutant is 60/70/120). As a result, the wild type has 2 monomers per asu while the mutant has 4 (I think). When I look at results from mol rep (ccp4i, auto-molrep routine), I get 4 molecules per asu with the monomer as a search. 2 of the molecules I think are right (map is good - they form a good dimer, etc...), while I think 2 are incorrect (the dimer overlaps, and it just doesn't look good). My question - finally - how can I run automolrep with one dimer fixed, looking for the location of the other 2 monomers (so basically I want to fix a dimer as part of my solution, and then search for the other 2 molecules in the asu). I know it's probably simple and possible, but it's not a world I am very familiar with (I seriously have just done MIR structures, they are easy for me, I have had very little work with mol rep). Could I do this with Amore as well (so fix 2 molecules and then look for an additional 2 using amore). Thanks for the help. Have a great week-end Dave
[ccp4bb] Zalman monitor
Hi all, I'm sorry, I know this has been extensively discussed, but does anybody know right now where one can buy a zalman monitor (either the 22" or 24", or whatever sizes they are). I am a crystallographer at an Undergrad only university, and it appeals to me that passive stereo devices exist for 3D viewing (active glassware is nice, but expensive for me to maintain). I'd simply like to try one out - I'll buy it from Europe if necessary, I'd really just like to see it and see how well it works. With that, do we really have to buy Zalman glasses, or do movie glasses work (I assume if they don't work that it's just an inverted stereo thing, but that could be very wrong). I'm curious to hear from those with Zalman monitors, is the stereo crisp and is it something that one can easily stare at for say an hour or so at a time (maybe longer)? That was my main love for the emitters, in the sense that one could stare at it for hours and your eyes didn't fatigue or ache. I don't use stereo so much anymore due to the great improvements in graphics by all of these programs, however, it is still nice to do, and when teaching it's an incredible tool, but only if it works well. If I get this up and running, would anybody be interested in 7 emitters and about 16 pair of glasses (I think 10 work well, the other 6 just need a slight repair, very cheap compared to the price of the glasses). The glasses cost around $500 or so each (new), and the emitters are around $100 each (that's just for reference, not something I'm charging). I may have to get some compensation here - but I haven't thought about that yet (I'd consider trading for 7 Zalman monitors once I assured myself that it works). Thanks for you help on this. Dave Roberts drobe...@depauw.edu
[ccp4bb] linux question
I have a quick question about linux for all. Is there anybody running a windows pc with linux on a bootable cd or bootable drive/flash drive/??? that works for crystallography apps? I have a colleague who does molecular dynamics calculations and he needs some conversion programs that are unix based (not pc based - they just haven't been ported and that's not my area). We have linux computers that he can use, but I thought in the end it might be easiest if he could just boot up a linux flash drive to run his conversion, then go back to his pc and windows. Something like "damn small linux" or ?? Any thoughts on this? Thanks Dave
Re: [ccp4bb] dial box
I have a few of these if people are interested. Please just let me know off list. The ones I have are the 8 dial boxes connected to an old SGI workstation (they work in linux as well I believe - with O). I simply don't use these anymore and wouldn't mind parting with them. Thanks Dave >>> Tobias Krojer 07/01/09 1:19 PM >>> Dear all, does someone still have a couple of functional dial boxes and wants to sell them? I guess one cannot buy them anymore?! Thanks, Tobias
Re: [ccp4bb] suggestions for UV spectrometer
Wow, that's like putting a pool in your backyard so you don't have to pay the $3.00 admission every day (I'm kidding). In any event, Ocean Optics has some very nice, small, and portable units that would run around $3000 total. These connect to the USB port in a computer and produce data that can be manipulated easily via any spreadsheet manipulation program (open office, whatever). They are diode array, and so they take quick, continuous spectrum. We use these in our intro chem classes (sorry, small University, we can't afford the nanodrop) and they work great. I believe it's the USB2000 if you go to the Ocean Optics website. And, for those who find cuvettes as expensive as a nanodrop system, you can purchase polyacrylate ones that are good down to around 250 nm or so. They are marketed as disposable, but work well with several washings. They seem to be consistent from batch to batch, and we do use them for simple 280's on things (though of course we pull out the lock and key and get the quartz ones for those 2 special readings we take every year). Now, the specs you get are good and reliable (even though we use them with undergrads). They are not high end Cary's, but I don't think you need that sort of system for simple 280's. These detectors work as good cheap fluorimeter sources as well with some modifications on the light source (again, look around if that's something you are interested in). We use the Vernier system here, which allows us to connect spectrophotometers (mentioned above), drop counters, pH probes, temperature probes, and a whole variety of ion selective probes to a computer for data collection using almost any device. It's quite nice actually (vernier.com I believe). Good luck with that Dave Michael Giffin wrote: We also like the Nanodrop. Very fast, no cuvettes (breaking, washing, cleaning, uh nitric acid bath anyone?), and the .ndv data file is a delimited text file. Open in a text editor, copy and paste into a spreadsheet, and you have a convenient record of all of your stocks, including date, sample name, concentration, and full spectra. It is expensive, but so are good cuvettes. Mike Michael Giffin The Scripps Research Institute Department of Molecular and Experimental Medicine 10550 North Torrey Pines Road, MEM-131 La Jolla, CA 92037 email: [EMAIL PROTECTED] lab: 858-784-7758 On Thu, Dec 4, 2008 at 7:16 AM, Tim Gruene <[EMAIL PROTECTED]> wrote: Dear all, we would like to purchase a UV spectrometer for measuring protein concentrations (280nm), and I would like to here your comments and especially recommendations. We don't need anything fancy, a small, fast device would be sufficient. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
Re: [ccp4bb] Crystallographic computing platform recommendations?
A few years back I built 6 machines for $8000 total, and it should be as cheap if not cheaper now. I bought my video cards on ebay (there are lots of people who part out old leased machines and so it is very cheap really, and I haven't had a card fail yet, knock on wood). I'll try to itemize below: I used an AMD dual core (though quad is the way to go now). My specs are 6600, though I'm not sure what that number means (it was high end at the time). It's plenty fast enough (amazingly fast to be honest) Nice case/power supply/fans. I believe I bought a gaming case for this (high air flow). When I did this, I purchased a bare bones computer from a company in Indiana (3Btech.net I believe). I added memory, hard drive, video card, and peripherals. I have 2 hard drives (standard IDE actually). One is for the OS and the other is for data. Easier to troubleshoot and backup in my mind if you keep them separate, but to each his own. 4 Gig of DDR-3 memory (though this could be upped using todays standards with no worries). If you don't want stereo, you can put in whatever monitor you want. I have old 21" CRT that work great and give a nice crisp display. To these I have emitters and stereo, no worries (very nice, no headaches). Fedora core is my preference. I have core 7 on there now, but am planning on going to core 9 soon just for fun (why not). It's all pretty standard and simple really. I used this for a class of 12 undergrad students (with no computer expertise), and it went well, though I did use Paul a lot at the beginning to get over my own personal cootisms. It's very stable now, fast and reliable. I'd do it again in a heartbeat. All sorts of programs are running just fine (most of the xtal suite, though probably not all, just what I needed for MIR stuff at nominal resolutions, say 2.1 A). Good luck Dave Artem Evdokimov wrote: Dear Anna, Here’s my personal list of preferences for a fast and pretty inexpensive Linux workstation for crystallography. I can provide exact specs if desired. This assumes that you or someone in your group has basic computer hardware skills to put the workstation together*. Dual or quad core Pentium, depending on the budget. No need to go for the ‘extreme’ editions J Motherboard with a fast bus e.g. one of the recent Intels (but not the absolute latest version – give Linux developers time to catch up with drivers etc. – this makes a huge difference!) Make sure that your MoBo has multiple PCI-Express and a couple of older PCI slots, just in case. 4GB of dual DDR-3 memory Some sort of a fatty hard drive or two (depending on whether you have RAID for data storage and backup or not). Don’t be seduced by the ‘insanely cheap’ 1TB single drives – it is often safer to get a couple of really cheap high-quality 250GB drives. Linux can use as many drives as you want in a single logical volume anyway (or set up RAID). NVIDIA Quattro – in my opinion a mid-range Quattro (i.e. one of the slightly older series) is more than enough for our use Dual 21-inch monitors. (seriously, it’s very nice to have one monitor with say Coot main window and the other one with all the buttons etc.) Fedora core linux (at work we use Enterprise RedHat but that costs money) or whatever recent Linux flavor that you are familiar with Metal case and a souped-up CPU fan ( 4-core CPUs under full load tend to run a little hot with stock Intel fans) All of this should cost at ~$2000 if you buy components online and are aware of sites like pricewatch.com and suchlike. Good luck, Arte, * Additional bonus – if you build the system yourself you can choose to install various tricked-out (modded) components for added wow factor. From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Anna S Gardberg Sent: Monday, November 17, 2008 4:01 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Crystallographic computing platform recommendations? Dear list, I haven't seen the "crystallographic computing platform" thread come up for a while, and I've got a chance to upgrade my desktop to a workstation, so I thought I'd ask the CCP4BB for advice on: 1. Mac vs. Linux (which flavor?) vs. Windows 2. Graphics cards 3. Displays 4. Processors - multiple processors, multiple cores? Speed? About half of what I do involves ~1.0 A X-ray structures - data processing, rebuilding in Coot, refinement, and so forth - so my current desktop (Optiplex GX745, Radeon X1300) machine drags on graphics sometimes. I don't seem to need stereo these days, for what it's worth. Anybody have suggestions or specs they'd like to share? Thanks in anticipation of your advice. Regards, Anna Gardberg
Re: [ccp4bb] 3D model building without CRT monitor
Title: Message I've had good luck with refurbished monitors off the web. Just do a google search for a sun monitor (for example) and it should come up. Otherwise, go to pricewatch.com and search for crt monitors there. They may have some external case dents, but the monitors are usually crisp and last being on for at least 2-3 years. They are all refurbished monitors. Their cost is generally $30 for the monitor (or something ridiculously cheap) and then around $100 to ship (unfortunately). Not a bad overall price if you want stereo. I will say, I teach a class on crystallography to undergrad students. In the past I had SGI's, with dial boxes and stereo. When I switched to linux, I changed to coot, and away went the dial boxes (but I do still do stereo). In the past, students only used stereo and really liked the dial boxes. Now, with the graphics of coot and it's fitting algorithms, the real need for stereo was nothing more than an oddity, and so they did use stereo at times but it wasn't used as much. I do think stereo has a great purpose, especially in the education part and the final evaluation, but I'm not sure it's needed as much for the actual model building. Cheers Dave Krojer,Tobias wrote: Dear all, recently some of our CRT monitors broke down and we realized that these monitors are no longer produced. However, we would still like to continue model building in 3D which is apparently not possible with current TFT displays. Beside the possibility of getting old CRT monitors at ebay, I was wondering how other groups solved this problem. Thank you very much for suggestions! best wishes, Tobias Tobias Krojer, PhD IMP (Research Institute of Molecular Pathology) Dr. Bohr-Gasse 7 1030 Vienna Austria Tel.: +43-1-797303358 Fax.: +43-1-7987153
[ccp4bb] While on the subject of stereo
OK, so we weren't on this subject, and all of you are tired of me asking. However, the following link came to me and I wanted to see some programmers opinions on this one. The thing I'm wondering is, what needs to be done on the programming end to make this something that we could use in a classroom to show molecules in stereo. It seems like it would be fun, and I actually think it would work well, though I don't know if it would work with more than one person looking at the screen at a time (now that I really think about it, probably not - nevermind). If it only works with one person, can we use this for modeling? Just curious www.ted.com/index.php/talks/view/id/245 Dave
Re: [ccp4bb] stereo with Nvidia Quadro
Just check out the cards on the back - it should have the small round port that a 60GX plug would fit into. The NuVision site has a list of cards that are compatible with their emitters. I don't remember them all right off, but it's fairly straightforward. By the way, I buy all my video cards and memory on e-bay. Those quadro FX cards are often packaged in Dell systems that are leased to companies, and when the leases are up, the cards get parted out. I've purchased at least 7 this way, only paying 1/3 or so for each (compared to retail prices). I haven't had an issue with any thus far (until today that is - I'm sure something will happen now). Be sure to check the vendors out, but it is a source that isn't too crazy. I don't remember the prices I paid, but it was small compared to buying them new online somewhere. As I furnished 6 computers at once, I looked for package deals (they were even better). Good luck with that. Dave Tim Gruene wrote: Dear David, thank you for your answer. Do you (or anyone on the list) know if any FX-card would work with NuVision 60GX (like FX370, FX570), or only the dear ones (FX1400 and above)? Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Thu, 8 May 2008, David J. Schuller wrote: The nVidia cards used for stereo are the Quadro FX series. The Quadro NVS series are for running multiple monitors, but not fancy 3D graphics. You can explore the manufacturer's web site for details. - === With the single exception of Cornell, there is not a college in the United States where truth has ever been a welcome guest - R.G. Ingersoll === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University [EMAIL PROTECTED] On Thu, 2008-05-08 at 15:01 +0200, Tim Gruene wrote: Good day, I have been trying to enable stereo mode on a PC (SuSE10.1) with an NVIDIA NV37GL [Quadro FX 330/Quadro NVS280] graphics card (according to Xorg.0.log). (--) PCI:*(5:0:0) nVidia Corporation NV37GL [Quadro FX 330/Quadro NVS280] rev 162, Mem @ 0xdd00/24, 0xc000/28, 0xde00/24, BIOS @ 0xdfc0/17 (II) NVIDIA(0): NVIDIA GPU Quadro NVS 280 PCI-E at PCI:5:0:0 (GPU-0) Accroding to some web page about O, the options are set to (**) NVIDIA(0): Option "Stereo" "3" (**) NVIDIA(0): Option "NvAGP" "1" (**) NVIDIA(0): Option "IgnoreEDID" "false" (**) NVIDIA(0): Option "UseEdidFreqs" "true" Yet, the log file says (WW) NVIDIA(0): Stereo is only available on Quadro cards (II) NVIDIA(0): Disabling stereo. I was wondering whether anyone could explain what is so un-Quadro about this card? (Currently, the display is an LCD, but the same messages came up when the display was a CRT) Thank you for your help, Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
[ccp4bb] projecting 3d stereo
Hey there, I know this was recently rehashed, but of course I wasn't thinking too much about it at the time (and now somebody has made me interested). In any event, a colleague (go figure) of mine saw an article on projecting stereo for a classroom. The way it works uses a dlp projector connected to some sort of gaming graphics card (this was not for crystallography but instead used for playing games). There is an emitter connected to an inverter, and stereo glasses costing around $100 each. The overall system sounds cheap (in a good way), and it seems to be a reasonable way to do things. Now, I of course want to be even cheaper and use as much of my present systems as possible, and maybe just hook up the projector. Has anybody tried to hook up a dlp projector to a linux box and if so, does it project stereo as is (just as a crt monitor)? And, if so, do we need the inverter thing or does a standard emitter used on our systems (any of the usual flavors of emitters) do the job well. My thought is to just buy the projector and try it (and then buy extra pieces if needed), but I wanted to ask if anybody else has had success doing something similar to this. By the way, while on the subject, how do most emitters work (is it radio frequency or ?). I ask because I was playing with that the other day and found that I could sit a far distance from my computer (over 15 feet, which is the extent of the room) and still see in stereo. Does one need to look towards the emitter to have it work (they sit on top of our monitors now and so I never really thought about it) or could one possibly just have the emitter in the room and have people looking towards a wall that is on the opposite side of the room as the emitter? This obviously relates to having a computer project from one side of the room and look at a stereo figure on the other side (with an emitter - where do I need to put it - I don't have a long enough cable at present). I know there are issues with people using multiple workstations in the same room, but it seems possible to me that if they are all at the same frequency that it wouldn't matter. I've never had issues with multiple computers, all right next to each other, but I've heard rumors :) Thanks. If anybody is interested I'll dig up the web site where my friend found this. It has to do with projecting 3D gaming applications to a group of people. Dave Roberts
Re: [ccp4bb] cryoprotectant for crystals in isopropanol
Not that all proteins are created alike, but we had a protein crystallize in a similar situation (PEG/20%IPA). I don't remember the exact details, but we did have good luck using just glycerol as a cryoprotectant. That is, I made up the well buffer and added to that well buffer 20-25% glycerol (in addition to IPA/PEG), and moved the crystal into that. We had no issues with cracking or anything, and data collection went well. The first thing I tried worked, so I don't have a lot of trial information for you. You could probably reduce the glycerol a bit with no worries, but I don't know. Good luck Dave shivesh kumar wrote: Dear all, The question is regarding the cryoprotectant.We have crystallized a protein in 20% PEG 500 with 10% isopropanol.What should be the cryo we should try for data collection.Also,what percentage of PEG 500 is sufficient enough as a cryo for data collection. We are also trying to crystallize it with higher PEG's also like 1K, 2K, 4K.Lets C.Since the condition is having isopropanol also and it is reported that mounting with isoprop is very difficult and it evaporates as soon as we open the slides. Thanx in advance... Shivesh Kumar
[ccp4bb] coot question for any/all?
Hello, So sorry to post this here but I'm at wits end and am just hoping that somebody here has had a similar problem (and subsequent fix). Here goes. I have 7 systems, close to identical, all running FC7. For all, I used the autobuild script on the ccp4 website to generate the entire ccp4 package (including coot0.3.1). As I don't want to deal with network problems, I install the programs on every computer following the same build methods. I know I could do this differently, but for now I don't want to change methods. Now, everything appears to be running normally with no issues. However, I just recently tried building a model from scratch, using the baton-mode and then CAatoms - > mainchain button. One one computer, this works great, and I can build, combine fragments, renumber, blah blah blah and get a structure. For the other 6 machines, I can do the baton mode (and it seems to work), but when I hit the CA - > mainchain button, nothing happens (it just spins for a few seconds then appears to work but there are no new atoms on the screen). I tried downloading the newest ccp4 with no luck, and also the newest coot (from the coot website). They seem to run fine, but again get stalled when I try to do what I state above. It just doesn't work (though coot appears to be working normally - I can display molecules/maps and move things around and such). The problem is, I don't even know where to start here. I would gladly replace/uninstall/reinstall, but what is it that is broken and needs fixing? Like I said, I tried several different reinstalls today with no luck at all (even the new coot gave the same problem). I went to the coot faq and did the soft-link of the reference-libraries (which is an old fix but you never know) and it had no effect. I will say the one machine that is working is my one at home, and so I can't simply share that directory via nfs and see if it works on the other machines (not trivial). All were built the same way, but obviously I missed a file/link or something that is not allowing this important part of the program to work. Any helpful tips? Thanks so much. Dave Roberts [EMAIL PROTECTED]
[ccp4bb] SGI Indigo II question
Hi all, I have several (5 at least) SGI Indigo II systems that I used for crystallography for years. I'm looking to see if anybody needs them for parts/use? I'm not looking to make money here, but I don't want to pay anything either (so you pay shipping/packaging and you can have them). Also, I really don't want to throw them away, though that may be an option of course. I do have monitors, but they are probably not worth the shipping cost so I'm not offering them unless you really need them. Of course if you live near Indiana you can simply come by and pick them up :) Anybody interested? They are working, and were up and running until about a year ago (they have been in boxes on the shelves until I was sure I didn't need anything on them). I may also have some dial boxes, but for those I would need a little reimbursement. I've grown fond of coot and using a mouse, so dials have sort of gone away for me, but I hesitate to totally get rid of them. I have 4 of the newer type dials (gray boxes), and 2 of the older ones (brown colored), no buttons. All cables are included of course. E-mail me if you need specifics on a system (memory, hard drive sleds, etc...). Thanks much and sorry for the ad (just thought this was a good place to donate these computers). Dave Roberts [EMAIL PROTECTED]
