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

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

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 th

[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

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

[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

[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 her

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 stu

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

[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

[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

[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 c

[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

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

[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). Al

[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

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% glycer

[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 conn

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 card

[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 cl

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 cris

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

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

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 >>>

[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.

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, a

[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

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 ch

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

[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

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 suspe

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

[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

Re: [ccp4bb] showing electron density on an ipad

rt 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