[ccp4bb] UEFI Secure Boot ( was Re: [ccp4bb] Various OSes and Crystallography)
Dear all, This discussion about OS's seems like a good time to flag up the UEFI Secure Boot issue, for any of you who haven't heard about it. Quite what it means for Linux depends on whose commentary you read, but it is just possible that the carefree days of buying any x86-based system with standard hardware and installing whatever Linux distro you like on it are coming to an end. I don't pretend to grasp all the details, but if I have understood correctly, the following scenario will become theoretically possible when Windows 8 certified hardware goes on sale around October 26: (1) You buy a Windows 8 certified machine with Windows 8 pre-installed. (2) You attempt to install a Linux distro on it, like you have done in the past with other hardware. This fails. (3) You do a bit of research, work out that Secure Boot is likely to be the problem, and that the particular Linux distro you want to install won't work with Secure Boot at all. (4) With a bit more reading, you find that Microsoft have specified as part of the Windows 8 hardware certification requirements that disabling Secure Boot should be possible for a physically present user, at least for x86-based hardware. [ARM-based hardware is another story, but that is not of general interest to crystallographers.] (5) The manufacturer of your new machine has decided that only 0.1% of purchasers of their machines are going to want to disable Secure Boot, so haven't bothered to actually implement and/or document a way of doing it. They have also gambled that Microsoft aren't committed enough to that part of their own requirements to take any action over its violation (after all, they might say to themselves, it wouldn't make any sense for Microsoft to withdraw Windows 8 certification from our machines just because a few geeks can't install Linux on them). I don't know how likely this scenario is, but disabling Secure Boot is probably not a good thing to do if you want to use the machine to dual-boot Windows 8 and Linux. If Secure Boot is a useful line of defence against Windows malware, it would be better to leave it on and have a way of booting into Linux without disabling it. Some Linux distributors have taken various steps to cope with this issue (or are at least thinking about it, with the expectation that they will have figured out something in time), but it will be something to consider when buying Windows 8 certified hardware in the future. It may be a problem if you want to install a customised or non-mainstream Linux distro. Also even if current/future Linux distro's implement ways of working with Secure Boot, installing older versions may be problematic (there are several reasons for wanting to use older OS's). I don't know how using virtual machines will be impacted by this, if at all. Please don't ask me for clarifications about all this. I am not an expert and I am only paraphrasing what other people have written. If you want to know more, these two links are reasonable starting points, and are both reasonably up-to-date: http://www.linux-magazine.com/Online/Features/No-Free-Boots http://www.zdnet.com/another-way-around-linuxs-windows-secureboot-problem-700829/ To my knowledge, RedHat/Fedora and Canonical (i.e. Ubuntu) have decided on (different) solutions, both with some attendant controversy. SUSE/openSUSE are actively working on it. I have not been able to find anything about any plans by Debian. I also don't know what the impact will be on RedHat derivatives like CentOS and Scientific Linux. Regards, Peter. On Thu, 2012-08-09 at 08:55 -0500, Jacob Keller wrote: Dear List, I guess this is somewhat of a perennial issue, but I am faced with choosing an OS for a new computer, and am curious about benefits and drawbacks with regard to crystallography. So far, I have been using windows, and have found no limitations whatsoever, but then again, maybe I don't know what I am missing. But, since so many folks out there use Macs, I am open to using one. Are there any really reasonable arguments for preferring Mac over windows (or linux) with regard to crystallography? What can Mac/Linux do that windows cannot (especially considering that there is Cygwin)? What wonderful features am I missing? Jacob -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu *** -- Peter Keller Tel.: +44 (0)1223 353033 Global Phasing Ltd., Fax.: +44 (0)1223 366889 Sheraton House, Castle Park, Cambridge CB3 0AX United Kingdom
Re: [ccp4bb] Various OSes and Crystallography
I completely agree with Harry's observation about the glare screen feature. I find it is quite literally an almost instant headache. There is an option with the macbook pro to pay a ransom to get a usable screen, so my wife did. On my macbook air, I found putting a dull dark grey background for a desktop helps considerably to cut down on the reflection, perhaps in part because it reflects my personality. Instead of buying iMacs, we now get mac minis and pair them with Samsung LED matte screen monitors. The improvement is considerable, and they are a lot less expensive too. Bill On Aug 9, 2012, at 11:25 PM, Harry ha...@mrc-lmb.cam.ac.uk wrote: Hi My two ha'porth. For a laptop, this is the clincher for me - if you want to use your laptop anywhere that has reasonable light levels (e.g. demonstrating to anyone in an exhibition hall), you may well find that the beautiful shiny mirror that Apple put on the front of their screens on most of their laptops makes your investment almost useless in reasonable levels of ambient light. Unless I could buy a Macbook with a matt screen I doubt I'd want to buy another one. Sometimes I wonder if my Macbook was designed in California in a cave to paraphrase what it says on the sticker on the back... It runs all the software I want it to without problems, though, including WIndows stuff via wine or VMWare. And I do *really* like OSX as an interface. On 9 Aug 2012, at 16:18, Andreas Förster wrote: Mind that if you buy a MacBook, there's only one (hefty 15) model without a mirror-coated screen. Andreas On 09/08/2012 3:58, Nat Echols wrote: On Thu, Aug 9, 2012 at 6:55 AM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: one. Are there any really reasonable arguments for preferring Mac over windows (or linux) with regard to crystallography? What can Mac/Linux do that windows cannot (especially considering that there is Cygwin)? What wonderful features am I missing? Mac vs. Linux: mostly a matter of personal preference, but I agree with Graeme. Most programs run equally well on either - with Coot a partial exception, apparently due to problems with the X11 implementation (but once you get used to these, it's not a big deal). Windows, on the other hand, simply doesn't support the full range of modern crystallography software. And in my experience, it has crippling flaws that mean some programs will always work better on Mac/Linux. I wouldn't ever endorse trying to use Windows for serious scientific computing unless you need to run an application that won't work on any other OS, and as far as I know there isn't a single (macromolecular) crystallography program that falls into this category. -Nat Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
Re: [ccp4bb] Various OSes and Crystallography
On Thu, Aug 9, 2012 at 6:55 AM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: one. Are there any really reasonable arguments for preferring Mac over windows (or linux) with regard to crystallography? What can Mac/Linux do that windows cannot (especially considering that there is Cygwin)? What wonderful features am I missing? Mac vs. Linux: mostly a matter of personal preference, but I agree with Graeme. Most programs run equally well on either - with Coot a partial exception, apparently due to problems with the X11 implementation (but once you get used to these, it's not a big deal). Windows, on the other hand, simply doesn't support the full range of modern crystallography software. And in my experience, it has crippling flaws that mean some programs will always work better on Mac/Linux. I wouldn't ever endorse trying to use Windows for serious scientific computing unless you need to run an application that won't work on any other OS, and as far as I know there isn't a single (macromolecular) crystallography program that falls into this category. -Nat
Re: [ccp4bb] Various OSes and Crystallography
OS X is a triple OS OS X, Unix, and Windows (via VM Ware Fusion or Parallels, or if you which directly booting into Windows) @original poster, you might regret the step to Mac - noticing what you have missed all the time on the other platform :-) I don't think Windows has a Beachball, that's a nifty feature of OS X - you've been missing that one for sure. Jürgen P.S. I'm running Fusion as there is one piece of software only for Windows, not even for Linux called Scrubber On Aug 9, 2012, at 10:58 AM, Nat Echols wrote: On Thu, Aug 9, 2012 at 6:55 AM, Jacob Keller j-kell...@fsm.northwestern.edumailto:j-kell...@fsm.northwestern.edu wrote: one. Are there any really reasonable arguments for preferring Mac over windows (or linux) with regard to crystallography? What can Mac/Linux do that windows cannot (especially considering that there is Cygwin)? What wonderful features am I missing? Mac vs. Linux: mostly a matter of personal preference, but I agree with Graeme. Most programs run equally well on either - with Coot a partial exception, apparently due to problems with the X11 implementation (but once you get used to these, it's not a big deal). Windows, on the other hand, simply doesn't support the full range of modern crystallography software. And in my experience, it has crippling flaws that mean some programs will always work better on Mac/Linux. I wouldn't ever endorse trying to use Windows for serious scientific computing unless you need to run an application that won't work on any other OS, and as far as I know there isn't a single (macromolecular) crystallography program that falls into this category. -Nat .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu
Re: [ccp4bb] Various OSes and Crystallography
Mac OSX because of Time Machine, Illustrator and crystallographic software in one happy box. XP on a Virtual Box for emergencies (SAXS, AUC and ITC programs). Though with Microsoft and Apple both pushing towards gestures, fingertip interaction and tablets, Linux will be the only option for laptops in two/three years' time. Mind that if you buy a MacBook, there's only one (hefty 15) model without a mirror-coated screen. Andreas On 09/08/2012 3:58, Nat Echols wrote: On Thu, Aug 9, 2012 at 6:55 AM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: one. Are there any really reasonable arguments for preferring Mac over windows (or linux) with regard to crystallography? What can Mac/Linux do that windows cannot (especially considering that there is Cygwin)? What wonderful features am I missing? Mac vs. Linux: mostly a matter of personal preference, but I agree with Graeme. Most programs run equally well on either - with Coot a partial exception, apparently due to problems with the X11 implementation (but once you get used to these, it's not a big deal). Windows, on the other hand, simply doesn't support the full range of modern crystallography software. And in my experience, it has crippling flaws that mean some programs will always work better on Mac/Linux. I wouldn't ever endorse trying to use Windows for serious scientific computing unless you need to run an application that won't work on any other OS, and as far as I know there isn't a single (macromolecular) crystallography program that falls into this category. -Nat
Re: [ccp4bb] Various OSes and Crystallography
Le 09/08/2012 16:58, Nat Echols a écrit : On Thu, Aug 9, 2012 at 6:55 AM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: one. Are there any really reasonable arguments for preferring Mac over windows (or linux) with regard to crystallography? What can Mac/Linux do that windows cannot (especially considering that there is Cygwin)? What wonderful features am I missing? Mac vs. Linux: mostly a matter of personal preference, but I agree with Graeme. Most programs run equally well on either - with Coot a partial exception, apparently due to problems with the X11 implementation (but once you get used to these, it's not a big deal). Windows, on the other hand, simply doesn't support the full range of modern crystallography software. And in my experience, it has crippling flaws that mean some programs will always work better on Mac/Linux. I wouldn't ever endorse trying to use Windows for serious scientific computing unless you need to run an application that won't work on any other OS, and as far as I know there isn't a single (macromolecular) crystallography program that falls into this category. -Nat I have seen that in the last Mac Os, X11 have been removed... But can still be used with some package installation.
Re: [ccp4bb] Various OSes and Crystallography
On Thu, Aug 9, 2012 at 8:14 AM, Quentin Delettre q...@hotmail.fr wrote: I have seen that in the last Mac Os, X11 have been removed... But can still be used with some package installation. I guess it isn't distributed with the OS any more - but it is still available: http://xquartz.macosforge.org/landing/ -Nat
Re: [ccp4bb] Various OSes and Crystallography
Mountain Lion does not come with X11 preinstalled. However, as Nat states, you can very easily install Xquartz Thus far, all of the crystallography programs that were working under Snow Leopard and Lion are still working on my laptop with Mountain Lion. -Tony --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oli...@sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512 On 8/9/12 4:25 PM, Nat Echols nathaniel.ech...@gmail.com wrote: On Thu, Aug 9, 2012 at 8:14 AM, Quentin Delettre q...@hotmail.fr wrote: I have seen that in the last Mac Os, X11 have been removed... But can still be used with some package installation. I guess it isn't distributed with the OS any more - but it is still available: http://xquartz.macosforge.org/landing/ -Nat
Re: [ccp4bb] Various OSes and Crystallography
On Thu, Aug 09, 2012 at 10:29:10AM -0500, Jacob Keller wrote: Question--do macs have multiple-button mice? Last I checked they had only one button, which seemed almost criminal. You're about 7 years behind the times on that one: http://en.wikipedia.org/wiki/Apple_Mighty_Mouse -b -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |
Re: [ccp4bb] Various OSes and Crystallography
you can use your favourite 24 button mice from windows on a Mac as long as it has USB. And I highly recommend Bill Scott's Crystallography on OS X website. Jürgen On Aug 9, 2012, at 11:29 AM, Jacob Keller wrote: Are there no closet windows-users on this list to respond? Shall we have a coming-out day? Question--do macs have multiple-button mice? Last I checked they had only one button, which seemed almost criminal. JPK On Thu, Aug 9, 2012 at 10:14 AM, Quentin Delettre q...@hotmail.frmailto:q...@hotmail.fr wrote: Le 09/08/2012 16:58, Nat Echols a écrit : On Thu, Aug 9, 2012 at 6:55 AM, Jacob Keller j-kell...@fsm.northwestern.edumailto:j-kell...@fsm.northwestern.edu wrote: one. Are there any really reasonable arguments for preferring Mac over windows (or linux) with regard to crystallography? What can Mac/Linux do that windows cannot (especially considering that there is Cygwin)? What wonderful features am I missing? Mac vs. Linux: mostly a matter of personal preference, but I agree with Graeme. Most programs run equally well on either - with Coot a partial exception, apparently due to problems with the X11 implementation (but once you get used to these, it's not a big deal). Windows, on the other hand, simply doesn't support the full range of modern crystallography software. And in my experience, it has crippling flaws that mean some programs will always work better on Mac/Linux. I wouldn't ever endorse trying to use Windows for serious scientific computing unless you need to run an application that won't work on any other OS, and as far as I know there isn't a single (macromolecular) crystallography program that falls into this category. -Nat I have seen that in the last Mac Os, X11 have been removed... But can still be used with some package installation. -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edumailto:j-kell...@northwestern.edu *** .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu
Re: [ccp4bb] Various OSes and Crystallography
Yes, you can define 3 buttons on a MagicMouse with this free software: http://magicprefs.com/ or simply attach a mouse with 3 real buttons... -Luca Luca Jovine, Ph.D. Assistant Professor EMBO Young Investigator Karolinska Institutet Department of Biosciences and Nutrition Center for Biosciences Hälsovägen 7, SE-141 83 Huddinge, Sweden Voice: +46.(0)8.524-81136 FAX: +46.(0)8.6081-501 E-mail: luca.jov...@ki.se W3: http://jovinelab.org On Aug 9, 2012, at 17:29 , Jacob Keller wrote: Are there no closet windows-users on this list to respond? Shall we have a coming-out day? Question--do macs have multiple-button mice? Last I checked they had only one button, which seemed almost criminal. JPK On Thu, Aug 9, 2012 at 10:14 AM, Quentin Delettre q...@hotmail.fr wrote: Le 09/08/2012 16:58, Nat Echols a écrit : On Thu, Aug 9, 2012 at 6:55 AM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: one. Are there any really reasonable arguments for preferring Mac over windows (or linux) with regard to crystallography? What can Mac/Linux do that windows cannot (especially considering that there is Cygwin)? What wonderful features am I missing? Mac vs. Linux: mostly a matter of personal preference, but I agree with Graeme. Most programs run equally well on either - with Coot a partial exception, apparently due to problems with the X11 implementation (but once you get used to these, it's not a big deal). Windows, on the other hand, simply doesn't support the full range of modern crystallography software. And in my experience, it has crippling flaws that mean some programs will always work better on Mac/Linux. I wouldn't ever endorse trying to use Windows for serious scientific computing unless you need to run an application that won't work on any other OS, and as far as I know there isn't a single (macromolecular) crystallography program that falls into this category. -Nat I have seen that in the last Mac Os, X11 have been removed... But can still be used with some package installation. -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Various OSes and Crystallography
How critical is stereo visualization for you? Macs are great with Zalman, but have fallen behind (again) with active stereo (ie. shutter glasses). I will disclaim that I haven't revisited stereo visualization in about 1 year so my info is dated. HTH, Chris From: Jacob Keller j-kell...@fsm.northwestern.edumailto:j-kell...@fsm.northwestern.edu Reply-To: Jacob Keller j-kell...@fsm.northwestern.edumailto:j-kell...@fsm.northwestern.edu Date: Thursday, August 9, 2012 10:29 AM To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Various OSes and Crystallography Are there no closet windows-users on this list to respond? Shall we have a coming-out day? Question--do macs have multiple-button mice? Last I checked they had only one button, which seemed almost criminal. JPK On Thu, Aug 9, 2012 at 10:14 AM, Quentin Delettre q...@hotmail.frmailto:q...@hotmail.fr wrote: Le 09/08/2012 16:58, Nat Echols a écrit : On Thu, Aug 9, 2012 at 6:55 AM, Jacob Keller j-kell...@fsm.northwestern.edumailto:j-kell...@fsm.northwestern.edu wrote: one. Are there any really reasonable arguments for preferring Mac over windows (or linux) with regard to crystallography? What can Mac/Linux do that windows cannot (especially considering that there is Cygwin)? What wonderful features am I missing? Mac vs. Linux: mostly a matter of personal preference, but I agree with Graeme. Most programs run equally well on either - with Coot a partial exception, apparently due to problems with the X11 implementation (but once you get used to these, it's not a big deal). Windows, on the other hand, simply doesn't support the full range of modern crystallography software. And in my experience, it has crippling flaws that mean some programs will always work better on Mac/Linux. I wouldn't ever endorse trying to use Windows for serious scientific computing unless you need to run an application that won't work on any other OS, and as far as I know there isn't a single (macromolecular) crystallography program that falls into this category. -Nat I have seen that in the last Mac Os, X11 have been removed... But can still be used with some package installation. -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edumailto:j-kell...@northwestern.edu ***
Re: [ccp4bb] Various OSes and Crystallography
Can you explain to me what the difference in stereo is ? I like my Zalman's and the visual stereo effect is pretty impressive. I have no idea if active stereo would improve the perception of the 3D effect or not. Jürgen On Aug 9, 2012, at 11:47 AM, Colbert, Christopher wrote: How critical is stereo visualization for you? Macs are great with Zalman, but have fallen behind (again) with active stereo (ie. shutter glasses). I will disclaim that I haven't revisited stereo visualization in about 1 year so my info is dated. HTH, Chris From: Jacob Keller j-kell...@fsm.northwestern.edumailto:j-kell...@fsm.northwestern.edu Reply-To: Jacob Keller j-kell...@fsm.northwestern.edumailto:j-kell...@fsm.northwestern.edu Date: Thursday, August 9, 2012 10:29 AM To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Various OSes and Crystallography Are there no closet windows-users on this list to respond? Shall we have a coming-out day? Question--do macs have multiple-button mice? Last I checked they had only one button, which seemed almost criminal. JPK On Thu, Aug 9, 2012 at 10:14 AM, Quentin Delettre q...@hotmail.frmailto:q...@hotmail.fr wrote: Le 09/08/2012 16:58, Nat Echols a écrit : On Thu, Aug 9, 2012 at 6:55 AM, Jacob Keller j-kell...@fsm.northwestern.edumailto:j-kell...@fsm.northwestern.edu wrote: one. Are there any really reasonable arguments for preferring Mac over windows (or linux) with regard to crystallography? What can Mac/Linux do that windows cannot (especially considering that there is Cygwin)? What wonderful features am I missing? Mac vs. Linux: mostly a matter of personal preference, but I agree with Graeme. Most programs run equally well on either - with Coot a partial exception, apparently due to problems with the X11 implementation (but once you get used to these, it's not a big deal). Windows, on the other hand, simply doesn't support the full range of modern crystallography software. And in my experience, it has crippling flaws that mean some programs will always work better on Mac/Linux. I wouldn't ever endorse trying to use Windows for serious scientific computing unless you need to run an application that won't work on any other OS, and as far as I know there isn't a single (macromolecular) crystallography program that falls into this category. -Nat I have seen that in the last Mac Os, X11 have been removed... But can still be used with some package installation. -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edumailto:j-kell...@northwestern.edu *** .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu
Re: [ccp4bb] Various OSes and Crystallography
Hi Jurgen, I am using the term active stereo to refer to shutter glass stereo. This was originally implemented with CRT monitors and more recently with LCD monitors and Nvidia 3D vision. It is usually implemented using OpenGL. The advantage of active stereo over Zalman stereo is that the text in the window or on the screen is not half resolution when viewing through the stereo glasses. Some may argue about the stereoscopic effect, but I find them both to be quite useful. Chris From: Bosch, Juergen jubo...@jhsph.edumailto:jubo...@jhsph.edu Date: Thursday, August 9, 2012 10:51 AM To: Christopher Colbert christopher.colb...@ndsu.edumailto:christopher.colb...@ndsu.edu Cc: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Various OSes and Crystallography Can you explain to me what the difference in stereo is ? I like my Zalman's and the visual stereo effect is pretty impressive. I have no idea if active stereo would improve the perception of the 3D effect or not. Jürgen On Aug 9, 2012, at 11:47 AM, Colbert, Christopher wrote: How critical is stereo visualization for you? Macs are great with Zalman, but have fallen behind (again) with active stereo (ie. shutter glasses). I will disclaim that I haven't revisited stereo visualization in about 1 year so my info is dated. HTH, Chris From: Jacob Keller j-kell...@fsm.northwestern.edumailto:j-kell...@fsm.northwestern.edu Reply-To: Jacob Keller j-kell...@fsm.northwestern.edumailto:j-kell...@fsm.northwestern.edu Date: Thursday, August 9, 2012 10:29 AM To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Various OSes and Crystallography Are there no closet windows-users on this list to respond? Shall we have a coming-out day? Question--do macs have multiple-button mice? Last I checked they had only one button, which seemed almost criminal. JPK On Thu, Aug 9, 2012 at 10:14 AM, Quentin Delettre q...@hotmail.frmailto:q...@hotmail.fr wrote: Le 09/08/2012 16:58, Nat Echols a écrit : On Thu, Aug 9, 2012 at 6:55 AM, Jacob Keller j-kell...@fsm.northwestern.edumailto:j-kell...@fsm.northwestern.edu wrote: one. Are there any really reasonable arguments for preferring Mac over windows (or linux) with regard to crystallography? What can Mac/Linux do that windows cannot (especially considering that there is Cygwin)? What wonderful features am I missing? Mac vs. Linux: mostly a matter of personal preference, but I agree with Graeme. Most programs run equally well on either - with Coot a partial exception, apparently due to problems with the X11 implementation (but once you get used to these, it's not a big deal). Windows, on the other hand, simply doesn't support the full range of modern crystallography software. And in my experience, it has crippling flaws that mean some programs will always work better on Mac/Linux. I wouldn't ever endorse trying to use Windows for serious scientific computing unless you need to run an application that won't work on any other OS, and as far as I know there isn't a single (macromolecular) crystallography program that falls into this category. -Nat I have seen that in the last Mac Os, X11 have been removed... But can still be used with some package installation. -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edumailto:j-kell...@northwestern.edu *** .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu
Re: [ccp4bb] Various OSes and Crystallography
Thanks Chris, I really prefer the 30g Zalman glasses versus 400 g shutter glasses that have troubles (at least the old ones) when people are sitting next to each other in terms of interference of the signal. Half resolution ? 1600 x 1040 on a Zalman I think is full but I have not counted the pixels when looking at them and I might be wrong. Dr. Coot might know more about that what happens when turning on stereo on Zalmans. Jürgen On Aug 9, 2012, at 12:10 PM, Colbert, Christopher wrote: Hi Jurgen, I am using the term active stereo to refer to shutter glass stereo. This was originally implemented with CRT monitors and more recently with LCD monitors and Nvidia 3D vision. It is usually implemented using OpenGL. The advantage of active stereo over Zalman stereo is that the text in the window or on the screen is not half resolution when viewing through the stereo glasses. Some may argue about the stereoscopic effect, but I find them both to be quite useful. Chris From: Bosch, Juergen jubo...@jhsph.edumailto:jubo...@jhsph.edu Date: Thursday, August 9, 2012 10:51 AM To: Christopher Colbert christopher.colb...@ndsu.edumailto:christopher.colb...@ndsu.edu Cc: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Various OSes and Crystallography Can you explain to me what the difference in stereo is ? I like my Zalman's and the visual stereo effect is pretty impressive. I have no idea if active stereo would improve the perception of the 3D effect or not. Jürgen On Aug 9, 2012, at 11:47 AM, Colbert, Christopher wrote: How critical is stereo visualization for you? Macs are great with Zalman, but have fallen behind (again) with active stereo (ie. shutter glasses). I will disclaim that I haven't revisited stereo visualization in about 1 year so my info is dated. HTH, Chris From: Jacob Keller j-kell...@fsm.northwestern.edumailto:j-kell...@fsm.northwestern.edu Reply-To: Jacob Keller j-kell...@fsm.northwestern.edumailto:j-kell...@fsm.northwestern.edu Date: Thursday, August 9, 2012 10:29 AM To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Various OSes and Crystallography Are there no closet windows-users on this list to respond? Shall we have a coming-out day? Question--do macs have multiple-button mice? Last I checked they had only one button, which seemed almost criminal. JPK On Thu, Aug 9, 2012 at 10:14 AM, Quentin Delettre q...@hotmail.frmailto:q...@hotmail.fr wrote: Le 09/08/2012 16:58, Nat Echols a écrit : On Thu, Aug 9, 2012 at 6:55 AM, Jacob Keller j-kell...@fsm.northwestern.edumailto:j-kell...@fsm.northwestern.edu wrote: one. Are there any really reasonable arguments for preferring Mac over windows (or linux) with regard to crystallography? What can Mac/Linux do that windows cannot (especially considering that there is Cygwin)? What wonderful features am I missing? Mac vs. Linux: mostly a matter of personal preference, but I agree with Graeme. Most programs run equally well on either - with Coot a partial exception, apparently due to problems with the X11 implementation (but once you get used to these, it's not a big deal). Windows, on the other hand, simply doesn't support the full range of modern crystallography software. And in my experience, it has crippling flaws that mean some programs will always work better on Mac/Linux. I wouldn't ever endorse trying to use Windows for serious scientific computing unless you need to run an application that won't work on any other OS, and as far as I know there isn't a single (macromolecular) crystallography program that falls into this category. -Nat I have seen that in the last Mac Os, X11 have been removed... But can still be used with some package installation. -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edumailto:j-kell...@northwestern.edu *** .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.eduhttp://lupo.jhsph.edu/ .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu
Re: [ccp4bb] Various OSes and Crystallography
For me, Windows would be my last choice for crystallographic software. Most of the popular packages are developed for *nix in the first place, so you know you will be able to run it. Not everything is compiled for Windows. Programs will run faster and with less hardware in *nix than in Windows, and backups and file shares are both easier to set up and more secure in *nix than in Windows. And scripting (yes, it's still necessary on occasion) is less clumsy in *nix than Windows. The command shell in Windows is a pale imitation of tcsh or bash, and the freely available editors leave something to be desired. (Textpad is awesome, though.) For the random Windows-only stuff (CrysalisPro still runs only in Windows) there is Wine or a virtual box. The choice for me is really Mac or Linux. Linux is much less expensive, especially if you build your own boxes. I've not experienced driver hell since the early versions of Fedora. In Ubuntu 12.04 Nvidia drivers install seamlessly, and I've had no trouble with wireless or Bluetooth, audio hardware, etc. Just don't buy bleeding edge hardware. Roger Rowlett On Aug 9, 2012 9:55 AM, Jacob Keller j-kell...@fsm.northwestern.edu wrote: Dear List, I guess this is somewhat of a perennial issue, but I am faced with choosing an OS for a new computer, and am curious about benefits and drawbacks with regard to crystallography. So far, I have been using windows, and have found no limitations whatsoever, but then again, maybe I don't know what I am missing. But, since so many folks out there use Macs, I am open to using one. Are there any really reasonable arguments for preferring Mac over windows (or linux) with regard to crystallography? What can Mac/Linux do that windows cannot (especially considering that there is Cygwin)? What wonderful features am I missing? Jacob -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
