Re: [ccp4bb] linux question
An alternative to VMWare is virtualbox (www.virtualbox.org) which is available for free for several operating systems. Tim On Sat, Feb 27, 2010 at 10:47:42PM -0500, Jim Fairman wrote: I think a good option would be to use VMWare Player to run a flavor of Linux within Windows (http://www.vmware.com/products/player/). Using VMware player, you can run any flavor of linux or windows within a window in your native OS (be it windows, mac, or any flavor of linux). I use it to run Ubuntu in a window inside of Windows 7 for CCP4, phenix, etc and it works pretty flawless so far. You can also run as many different linuxes as you want within your native OS (ie: If you want to try out Suse, Ubuntu, Red Hat and CentOS you can install all 4 of them on your system using VMWare within your native OS). On Sat, Feb 27, 2010 at 10:10 PM, David Roberts drobe...@depauw.edu wrote: 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 -- Jim Fairman, Ph D. Post-Doctoral Fellow National Institutes of Health - NIDDK Cell: 1-865-748-8672 Lab: 1-301-594-9229 E-mail: fairman@gmail.com james.fair...@nih.gov -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
Re: [ccp4bb] linux question
You may want to consider CD-bootable Puppy Linux (http://en.wikipedia.org/wiki/Puppy_Linux). HTH, Nadir -- Pr. Nadir T. Mrabet Structural Molecular Biochemistry INSERM U-954 UHP - Nancy 1, School of Medicine 54505 Vandoeuvre-les-Nancy Cedex France Tel : +33 (0)3.83.68.32.73 Fax : +33 (0)3.83.68.32.79 E-mail : nadir.mra...@medecine.uhp-nancy.fr Selon David Roberts drobe...@depauw.edu: 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] linux question
The simplest solution is to install your favorite linux distro in a virtual machine. I use Sun's VirtualBox to install Ubuntu on my WinXP machine. Performance is reasonable even in the virtual environment. I use VBox to test install CCP4 and other crystallography software in Ubuntu before installing on my lab servers. I have also used Vbox to test windows crystallography software running in Wine under virtual Ubuntu on a WinXP machine. The only thing you won't be able to do well in a virtual machine is high-performance graphical stuff like Pymol, Coot, etc. They will run, but slowly with emulated graphics. Cheers. On 2/27/2010 10:10 PM, David Roberts wrote: 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] linux question
On 2/27/2010 10:10 PM, David Roberts wrote: 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 ?? Alternatively, he can install some xterm emulator for windows (like putty) then use it to connect to the real linux machines you already have. Any thoughts on this? Thanks Dave
Re: [ccp4bb] linux question
I have a persistent Kubuntu 8.10 on a 16Gb flash drive, on which I have been running the likes of Coot, iMosflm and CCP4. I have used my setup to process two datasets via MolRep. There are plenty of resources on the internet telling you how to set it up. e.g http://www.pendrivelinux.com/ http://www.linux-usb.org/ https://wiki.kubuntu.org/LiveUsbPendrivePersistent It was relatively quick to set up, but it took a week to work out some problems. The main one being that with limited space on the thumb drive, one cannot do a complete update of Kubuntu. Therefore many libraries are missing and dependancy errors crop up during crystallography software installation. It's not too difficult a problem to deal with if you are familiar with installing apps on linux. And by partitioning your drive with FAT32, and two ext3 partitions (one for the root, and one labelled casper-rw) before creating the linux boot-stick, you can have a bootable linux usb stick with the ability to share files with a windows machine (fat32 partition) and enough space to install those behemoth crystallography apps. And I managed to do all this with minimal linux experience. (The only issue I haven't yet resolved is with graphics drivers. Its a trivial task to install the appropriate drivers, but it seems every time I boot up Kubuntu, I have to run 'x-config' and restart the x-server to get the Nvidia drivers to work, which is necessary for Coot, at least. An inconvenience every time I start linux, but not impossible). Im not familiar with setting up or running virtual machines / emulators, but they might be a simpler, more versatile option? But at least you can run graphical applications with ease (pymol and coot run well once the nvidia drivers are working).
Re: [ccp4bb] linux question
On Feb 28, 2010, at 5:11 PM, Damon Colbert wrote: I have a persistent Kubuntu 8.10 .. it took a week to work out some problems. The main one being that with limited space on the thumb drive, one cannot do a complete update of Kubuntu. Therefore many libraries are missing and dependancy errors crop up during crystallography software installation. You might want to look at Xubuntu. It uses the rather more lightweight xfce4 windowing system, which is nice and simple and basic and lightweight and clean and responsive. I prefer it over kde and gnome, even on hardware that can easily handle the overhead of all the extra features.
Re: [ccp4bb] linux question
On Feb 27, 2010, at 7:10 PM, David Roberts wrote: 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 A slightly different approach would be to install Cygwin, and then you can do unixy things within windoze. http://www.cygwin.com/
[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] linux question
Google for knopix Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Feb 27, 2010, at 22:10, David Roberts drobe...@depauw.edu wrote: 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] linux question
I think a good option would be to use VMWare Player to run a flavor of Linux within Windows (http://www.vmware.com/products/player/). Using VMware player, you can run any flavor of linux or windows within a window in your native OS (be it windows, mac, or any flavor of linux). I use it to run Ubuntu in a window inside of Windows 7 for CCP4, phenix, etc and it works pretty flawless so far. You can also run as many different linuxes as you want within your native OS (ie: If you want to try out Suse, Ubuntu, Red Hat and CentOS you can install all 4 of them on your system using VMWare within your native OS). On Sat, Feb 27, 2010 at 10:10 PM, David Roberts drobe...@depauw.edu wrote: 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 -- Jim Fairman, Ph D. Post-Doctoral Fellow National Institutes of Health - NIDDK Cell: 1-865-748-8672 Lab: 1-301-594-9229 E-mail: fairman@gmail.com james.fair...@nih.gov
