Re: [ccp4bb] FW: [ccp4bb] X-Ray versus NMR Structure

Correct, this special NMR issue of NSMB does not have any pdfs for some reason. The presubmission manuscript can be downloaded from my site: http://atbweb.stanford.edu/scripts/papers.php?sendfile=162 On Nov 18, 2008, at 8:26 PM, Kantardjieff, Katherine wrote: In regards to the reference below,

Re: [ccp4bb] Crystallographic computing platform recommendations?

Brian, There is one disadvantage with using AFP rather than wide open (potentially insecure) NFS mounts. Remote login via "ssh" into a client computer won't by default mount the user's AFP home directory. While it is possible to manually mount the AFP home directory it may preclude other

Re: [ccp4bb] Crystallographic computing platform recommendations?

Francis, From your response and others to my question about OS X server 10.5, AFP seems to be the preferred networking protocol over NFS. Yes, in our case the RAID is connected to a G5 (via firewire 800 - which provides surprisingly good transfer rates BTW) that is running OS X server 10

[ccp4bb] FW: [ccp4bb] X-Ray versus NMR Structure

In regards to the reference below, it does not appear to be in the online archive of NSMB... Those pages are mysteriously missing between volumes 10 and 11. > > You might find this review useful: X-ray Crystallography and NMR: Complementary Views of Structure and Dynamics, Nature Structural Bi

Re: [ccp4bb] R factors on Procheck and Refmac outputs

Dear Rafael -- On 19 Nov 2008, at 02:22, Rafael Counago wrote: Any ideas on why there is a difference between the Rfactors from Refmac and Sfcheck? To quote a previous posting: "Sfcheck usually does not have enough information to reproduce your full refinement. In particular, it does not rep

[ccp4bb] R factors on Procheck and Refmac outputs

Hi, I ran Sfcheck(ccp4) 7.2.02 version 6.0 and noticed a discrepancy between the R factors from Sfcheck and Refmac (the refinement program). Refmac reports: Program : REFMAC 5.2.0019 Resolution: 70.71 - 1.95 Reported R-factor : 0.171 Rfree : 0.203 and Sfcheck reports:

Re: [ccp4bb] Crystallographic computing platform recommendations?

On Nov 18, 2008, at 9:57 AM, Brian Mark wrote: Hi all, With all the talk about Mac OS X, I've not heard much mention about OS X Server and networking Macs together. Is anyone using the 10.5 server and LDAP to centrally house user directories on a RAID connected to a Mac server for exampl

Re: [ccp4bb] Crystallographic computing platform recommendations?

On Nov 18, 2008, at 11:41 AM, Anna S Gardberg wrote: 3. Eddie Snell made the point that most crystallographic software cannot take advantage of multiple processors yet. Still, as some people pointed, it is often convenient to try several refinement options at the same time, so there would

Re: [ccp4bb] Crystallographic computing platform recommendations?

The main differences aren't cosmetic, but rather free accessibility of updates and distributions, as well as attitude aka "philosophy." Advantages of Ubuntu include frequent OS updates, debian-based package management system (which admittedly is a matter of taste, but it is one of the origi

Re: [ccp4bb] Crystallographic computing platform recommendations?

Hi Anna: I think the main thing to emphasize in summary is that any of the options various people have suggested would be far more than adequate to do refinement or model building with coot. In my limited personal experience, unless you have something as big as the ribosome, you won't be

Re: [ccp4bb] Crystallographic computing platform recommendations?

Dear list, Thank you all for the helpful and thoughtful advice about crystallographic computing systems. Before I get into the (first day's) summary, I have a followup question: Has anyone worked with refinement or coot rebuilding of 1.0 Ang. structures on an iMac? If so, what was your experienc

Re: [ccp4bb] Crystallographic computing platform recommendations?

Another option is to use sbgrid's services to install every crystallography/EM/NMR-related thing on your lab computers: linux, SGI, powerpc or intel mac, and mixed labs are fine, so you are not restricted to any OS. This has the advantage of never ever thinking about how to compile anything eve

Re: [ccp4bb] Crystallographic computing platform recommendations?

On Nov 18, 2008, at 10:12 AM, Tim Fenn wrote: On Tue, 18 Nov 2008 10:21:29 + Kevin Cowtan <[EMAIL PROTECTED]> wrote: And I would give exactly the opposite advice, unless you are or have a guru who can devote time to fixing all the little things which still don't work under 64 bit OSs. (Do

Re: [ccp4bb] Crystallographic computing platform recommendations?

On Tue, 18 Nov 2008 18:04:11 + Kevin Cowtan <[EMAIL PROTECTED]> wrote: > From a system management point of view there is one very significant > benefit to Ubuntu: The LTS releases come out every 2 years and are > supported for 3 years. Compare this with Fedora: releases are only > supporte

Re: [ccp4bb] Crystallographic computing platform recommendations?

On Tue, 18 Nov 2008 10:21:29 + Kevin Cowtan <[EMAIL PROTECTED]> wrote: > And I would give exactly the opposite advice, unless you are or have > a guru who can devote time to fixing all the little things which > still don't work under 64 bit OSs. > > (Does anyone else have any clues on why 64-

Re: [ccp4bb] Crystallographic computing platform recommendations?

From a system management point of view there is one very significant benefit to Ubuntu: The LTS releases come out every 2 years and are supported for 3 years. Compare this with Fedora: releases are only supported for 18 months. Once you take into account testing and transition times, that mean

Re: [ccp4bb] Crystallographic computing platform recommendations?

I completely agree with Marius. Our (my) constraints are not $500 in price difference, but the fact that I maintain a system for scientific computing AND an X-ray system AND I am expected to be a scientist who publishes and writes grants. Thus, our approach has been to automate and minimize my

Re: [ccp4bb] Crystallographic computing platform recommendations?

For future proofing your computing platform , I would go with a 64 bit system. You will not regret it. All crystallography applications live very happily on a 64bit platform . There were a few teething troubles , but nothing an email to ccp4bb , phenixbb , coot or pymol newsgroups cant fix. We re

Re: [ccp4bb] Crystallographic computing platform recommendations?

Re: Switching from Fedora to Ubuntu. Don't. Stick with Fedora if it works for you. If you're tempted by Ubuntu because of the coolness, the bling, the color, the limited customizability or the lack of root, a Mac will get you all of this much more abundantly. If you're used to Redhat/Fedo

Re: [ccp4bb] Crystallographic computing platform recommendations?

I followed Kay's advice (after deciding that I knew better, of course, but we won't elaborate on that :-) and I am very pleased AND have had no trouble (knock on wood) to get everything working just fine. We make sure we have both 64 bit and 32 bit libraries and so far everything has worked ou

Re: [ccp4bb] Crystallographic computing platform recommendations?

Also Ubuntu, for the record... On Nov 18, 2008, at 7:55 AM, Peter Keller wrote: The same is true for SUSE distros: you don't have to recompile the NVIDIA drivers (or the ATI ones, AFAIK) on a kernel upgrade as long as you have enabled the correct package repository for the driver.

Re: [ccp4bb] Crystallographic computing platform recommendations?

I have zero experience with OS X server, but there were many changes (mostly for the better) in NFS with 10.5. I have put some information here, and as this is a wiki, I would be grateful for more contributions... http://sage.ucsc.edu/xtal/wiki/index.php/NFS On Nov 18, 2008, at 8:57 AM,

Re: [ccp4bb] Crystallographic computing platform recommendations?

On Nov 18, 2008, at 8:47 AM, Jeff Speir wrote: We also use OSX almost exclusively for our virus crystallography projects, for the same reasons given by Bill and Anastassis. Every now and then we have to spend time re-compiling some programs with larger parameters or up to 64-bit, so don't

Re: [ccp4bb] Crystallographic computing platform recommendations?

Hi all, With all the talk about Mac OS X, I've not heard much mention about OS X Server and networking Macs together. Is anyone using the 10.5 server and LDAP to centrally house user directories on a RAID connected to a Mac server for example? We had this setup running with 10.4, but we

Re: [ccp4bb] Crystallographic computing platform recommendations?

Anyone out there using a current 8 core MacPro with 32GB and OSX running the usual x-tallographic programs ? Send me an email off the list if you should be such a person. Thanks, Jürgen On 18 Nov 2008, at 07:26, William G. Scott wrote: On Nov 18, 2008, at 7:01 AM, Mischa Machius wrote: F

Re: [ccp4bb] Crystallographic computing platform recommendations?

We also use OSX almost exclusively for our virus crystallography projects, for the same reasons given by Bill and Anastassis. Every now and then we have to spend time re-compiling some programs with larger parameters or up to 64-bit, so don't want the added hassle of tinkering with the har

Re: [ccp4bb] Crystallographic computing platform recommendations?

On Tue, 18 Nov 2008, Michel Fodje wrote: On Tue, 2008-11-18 at 09:40 -0500, James M. Vergis wrote: 2) Graphics Cards: I like the Nvidia cards since they provide linux drivers. ATI also does now. I would say the only thing I don't like about them is when you do a kernel update you have to rem

[ccp4bb] postdoctoral position. Laboratory of Molecular Biology, Cambridge, UK

Two postdoctoral positions are available in the group of Roger Williams at the MRC Laboratory of Molecular Biology, Cambridge, UK. One position focuses on the biogenesis of multivesicular endosomes in lysosomal sorting. The other position focuses on the molecular biology of phosphoinositi

Re: [ccp4bb] Crystallographic computing platform recommendations?

I've gone off computers completely after finding that if I stare hard enough at my diffraction pattern I can sketch the density by hand :-)! Actually it's OSX for me because I view myself as a scientist who uses computers rather than a computer expert who uses science. Linux is just that bi

Re: [ccp4bb] Crystallographic computing platform recommendations?

They're all great! - Linux offers limitless possibility with its concomitant complexity and chaos. - Mac OS X offers the design integrity, consistency, and efficiency of centralized control. - Windows guarantees lowest common denominator functionality for a rock bottom price. So why not buy

Re: [ccp4bb] Crystallographic computing platform recommendations?

On Nov 18, 2008, at 16:26, William G. Scott wrote: On Nov 18, 2008, at 7:01 AM, Mischa Machius wrote: For linux, I would recommend a commercial solution, For linux, I actually ditched the commercial solution for Ubuntu, because it was vastly easier as a non-expert to maintain. Having sa

Re: [ccp4bb] Crystallographic computing platform recommendations?

That would have saved me a lot of time and frustration! Now if only I can remember this for the next time :-) I have a 64bit Fedora 9 system running on an Lenovo Thinkstation D10 - you can buy this without the operating system. I used the 64bit option as I'm processing very high resolution

Re: [ccp4bb] Crystallographic computing platform recommendations?

On Nov 18, 2008, at 7:01 AM, Mischa Machius wrote: For linux, I would recommend a commercial solution, For linux, I actually ditched the commercial solution for Ubuntu, because it was vastly easier as a non-expert to maintain. Having said that, like you, I have found running Mac OS X to b

Re: [ccp4bb] Crystallographic computing platform recommendations?

Hi I would tend to go with a system type that you're familiar and happy with, rather than buying into someone else's idea of the best system. So if you are used to running any particular type (Windows, OSX, Linux), I'd spend a little time setting it up on what you've currently got and see

Re: [ccp4bb] Crystallographic computing platform recommendations?

On Tue, 2008-11-18 at 09:40 -0500, James M. Vergis wrote: > 2) Graphics Cards: > I like the Nvidia cards since they provide linux drivers. ATI also does > now. I would say the only thing I don't like about them is when you do a > kernel update you have to remake the driver. I would just add tha

Re: [ccp4bb] Crystallographic computing platform recommendations?

After having dealt, over the years, with several dozens of 'crystallographic computing platforms' and having setup and maintained quite a few myself, I would recommend to not be cheap. I would recommend to go with well supported hardware and OS. For linux, I would recommend a commercial sol

Re: [ccp4bb] Crystallographic computing platform recommendations?

I have no problem calculating maps with my 64-bit version of coot. I posted on the cootbb how I was able to compile coot on CentOS 5.2 since I couldn't get the autobuild script to work for me. Also I couldn't get the gtk2 version to compile (but it may now) so I compiled a gtk1 version. I was ab

Re: [ccp4bb] Crystallographic computing platform recommendations?

Hi 1. Mac vs. Linux (which flavor?) vs. Windows Ubuntu - just works(TM). Gentoo - install only if know vi :-) 2. Graphics cards any NV quadro series. Buy at least one year old card so that linux will have drivers. Intel integrated cards also work well and have good drivers (Coot/ono shows go

Re: [ccp4bb] Crystallographic computing platform recommendations?

Am 18.11.2008 um 11:43 schrieb Kevin Cowtan: My understanding is that 32 bit coot runs on 64 bit systems with the appropriate compatibility libraries. yes, that's true. Regards, Dirk. *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximili

Re: [ccp4bb] Crystallographic computing platform recommendations?

Hi Kevin, there are several different ways to make 32 and 64bit coexist under Linux. I only know the RedHat way (I think the same as SuSe's) with its separation of /lib for 32bit and /lib64 for 64bit. This is completely painless because all your 32bit applications run without changes. There a

Re: [ccp4bb] Crystallographic computing platform recommendations?

Actually 4GB is fine for 32 bit Linux: http://www.linux.com/feature/119287 (You can actually go up to 64G with the proper kernel config, although beyond 4G I would switch to a 64 bit OS) My understanding is that 32 bit coot runs on 64 bit systems with the appropriate compatibility libraries.

Re: [ccp4bb] Crystallographic computing platform recommendations?

Kevin, Ouch, didn't know about that! Slightly worrying as I am about to take delivery of a new machine with 4GB of ram, and hence will *need* a 64 bit OS :o( Will a 32 bit compiled coot work on this system? Here's hoping, Graeme 2008/11/18 Kevin Cowtan <[EMAIL PROTECTED]>: > And I would give e

Re: [ccp4bb] Crystallographic computing platform recommendations?

And I would give exactly the opposite advice, unless you are or have a guru who can devote time to fixing all the little things which still don't work under 64 bit OSs. (Does anyone else have any clues on why 64-bit compiled coot can't calculate a map? I need to look into it, but have a huge b

Re: [ccp4bb] Crystallographic computing platform recommendations?

Dear Anna, you didn't ask about that, but I would definitely recommend a 64bit operating system. My specific recommendations are mostly in the articles "Computer_hardware" and "CentOS", to be found under the more general topic "Xtal_computing" of the CCP4 wiki (

Re: [ccp4bb] Crystallographic computing platform recommendations?

Hi Folks, Appropos to the comments below - if the folk who bundle CCP4 in this way would be kind enough to send the packages to me, I can test them the same way as we test our own binary builds, to make sure they work correctly. Saves me trying to search them out on the web. Many thanks, Graeme

Re: [ccp4bb] Crystallographic computing platform recommendations?

the high-end iMac is certainly a suitable computer, but a MacPro has more processors, which I find useful in running different applications in parallel or the same one with different parameters (i.e. refmac with different weights, phaser with different starting models or copy numbers). I ad

Re: [ccp4bb] iMosflm 1.0.0

Hi Jan, Thanks for the message - At the moment there is the imosflm tutorial on website under Documentation http://www.mrc-lmb.cam.ac.uk/harry/imosflm/ - There is no equivalent of the old mosflm parameter file ... yet. - When loading images imosflm loads all the images with the same template. How