Re: [ccp4bb] Problems installing CCP4 6.2 on Mac OS X 10.7.3
1, Check your directory permission. Make sure you have the read and execute permission for that directory (sometimes like this* drwxr-xr-x*). 2, Try to install CCP4 package by *fink*. There's already a stable version for Lion. (http://pdb.finkproject.org/pdb/package.php/ccp4) On Tue, May 22, 2012 at 12:44 AM, Terry Lang wrote: > Hey Everyone, > >I am having some problems getting CCP4 up and running on a laptop > with Mac OS X 10.7.3. I have downloaded the .dmg and run the installation > with no errors. However, when I try to set up my Project directory, I run > into some problems. It seemingly won't let me access my directory tree. > When I click on Users, for example, the Browse window does not enter the > directory and frequently just closes without an error message. Any ideas? > > Thanks, > Terry > > -- > Paula Therese Lang > Postdoctoral Scholar > Alber Lab > UC Berkeley/QB3 > -- Xiaoguang Xue, PhD student Utrecht University Crystal & Structural Chemistry Padualaan 8. Room N807 3584 CH Utrecht The Netherlands Tel. +31-30-253-2383
Re: [ccp4bb] Setup pymol in Mac OS X 10.7
As I know, you have 3 choices: 1, You can apply a free educational-use-only MacPymol from the company, Schrodinger, LLC. This is the easiest way, just move the MacPymol program into your Program Folder. 2, I think you still can try to install Pymol by Fink. Just follow the wiki page of Pymol.(http://www.pymolwiki.org/index.php/MAC_Install). But there is a compatible problem between Fink and Lion. There is a Lion upgrade notes written by William Scott( http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Lion_upgrade_notes). Maybe it can help you. 3, If Fink doesn't work. I think you can try to use MacPorts. It looks like there is no compatible problem between MacPorts and MacOS Lion. The install process is very simple (http://www.macports.org/install.php). I found MacPorts still contain Pymol package, also include apbs plugin. But there is no other protein xtallography software packages, like CCP4 and coot. And It is impossible to install MacPorts and Fink at the same time. So If you also want install CCP4 or coot from source code, it will be very inconvenient. Best! Xiaoguang Xue On Wed, Sep 21, 2011 at 11:04 AM, Mecy Shi wrote: > Dear members, > > I want to setup pymol in Mac OS X 10.7, but I didn't do this before. > > Who can tell me how to setup and tell me the detail setup procedure. > and if need other programs to setup this. > > Thank you very much! > -- Xiaoguang Xue, PhD student Utrecht University Crystal & Structural Chemistry Padualaan 8. Room N807 3584 CH Utrecht The Netherlands Tel. +31-30-253-2383
Re: [ccp4bb] Lion kills moleman (and all other USF programs on the Mac)
Can I use the Linux version under Xterm (from Macports)? I noticed that the Fink repository will not run on the Lion system, but it looks like Macports is OK, because they have a new branch for Lion. And they also have a dmg install file for Lion. On Fri, Jul 22, 2011 at 12:59 PM, Gerard DVD Kleywegt wrote: > Hi all, > > Just a heads-up - if you upgrade to OSX Lion, your trusty old USF > executables will no longer work. > > Help is on its way - in the near future the indefatigable and intrepid > Lion-taming heroes of the USF will release a distribution kit that includes > source code. However, for now you may want to postpone upgrading to Lion if > your will to live would be compromised by not being able to run Moleman, > Mapman, Lsqman, etc. > > --Mr Anchovy (Proud owner of a lion taming hat. A hat with 'lion tamer' > written on it. And it lights up saying 'lion tamer' in big red neon letters, > so you can tame them after dark when they're less stroppy.) > > PS: > http://www.youtube.com/watch?**v=XMOmB1q8W4Y<http://www.youtube.com/watch?v=XMOmB1q8W4Y> > > ** > Gerard J. Kleywegt > >http://xray.bmc.uu.se/gerard/ mailto:ger...@xray.bmc.uu.se > ** > The opinions in this message are fictional. Any similarity > to actual opinions, living or dead, is purely coincidental. > ** > -- Xiaoguang Xue, PhD student Utrecht University Crystal & Structural Chemistry Padualaan 8. Room N807 3584 CH Utrecht The Netherlands Tel. +31-30-253-2383
Re: [ccp4bb] Pymol question
Firstly, I think in Pymol there is no true electrostatic potential calculator, but only a "charge-smoothed" surface presentation ( http://www.pymolwiki.org/index.php/Protein_contact_potential). So, If you want to calculate the real electrostatic potential in Pymol (by Possion-Boltzman method), you have to install a plugin such as APBS or Delphi. Personally, I prefer Delphi, because there is a good and simple tutorial written by James Stroud from USC ( http://structure.usc.edu/howto/delphi-surface-pymol.html). And you also can read the man page of Delphi where describe the details how it works ( http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:DelPhi). On Thu, May 26, 2011 at 12:51 PM, Tim Gruene wrote: > Dear Maher, > > as far as I know pymol uses the APBS (http://www.poissonboltzmann.org) for > the > calculations and your question is answered in the FAQ: > > http://www.poissonboltzmann.org/apbs/frequently-asked-questions/what-are-the-units-of-electrostatic-potential > (kT/e) > > I don't know if this also answers your second question, but you could let > us > know in case it does. > > Tim > > On Wed, May 25, 2011 at 03:58:17PM -0700, Maher Alayyoubi wrote: > > Hi everyone, I have two questions: > > > > 1- Does anybody know what are the units on the display ruler after you > > calculate the vaccum electrostatics using pymol? > > > > 2- What are the default kT/e values used by pymol? > > > > Thank you, > > > > > > > > > > Maher > > -- > -- > Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > phone: +49 (0)551 39 22149 > > GPG Key ID = A46BEE1A > > > -BEGIN PGP SIGNATURE- > Version: GnuPG v1.4.10 (GNU/Linux) > > iD8DBQFN3jDOUxlJ7aRr7hoRAuONAJ9/PlFL6WgLhiw44GrofkSibUw8IgCfRQxh > YhReBu+gIxwpBm/7PHQwW4w= > =dLaZ > -END PGP SIGNATURE- > > -- Xiaoguang Xue, PhD student Utrecht University Crystal & Structural Chemistry Padualaan 8. Room N807 3584 CH Utrecht The Netherlands Tel. +31-30-253-2383
Re: [ccp4bb] CCP4 for iphones
Well, maybe building a distributed computing network （Like Fold@Home) by iphone is an improvement of the clusters. Let's think about a phenomenon, the most common functions of our iphone are calling, playing music, and maybe gaming, so most of the time the phone is idle. Why don't we try to use these idle computing time to help us doing some more important and interesting things, like determining the proteins structures? I also noticed that there is some progress in grid computing on iphone and PS3. So I think it's possible to apply this technique to structural biology. http://www.sciencedaily.com/releases/2010/04/100413072040.htm Xiaoguang On Fri, Feb 25, 2011 at 10:01 PM, Tommi Kajander wrote: > why, If we are lucky they will all just vaporize and disappear... > (...sorry couldn't resist...) > > tommi > > > On Feb 25, 2011, at 10:51 PM, Xiaoguang Xue wrote: > > But I don't know what will happen if we make a cluster by hundreds and >> thousands of iphones. >> >> On Fri, Feb 25, 2011 at 9:25 PM, Xiaoguang Xue wrote: >> Hi, >> >> Your idea is very cool, but i think it's difficult to run CCP4, Coot or >> Phenix on iphone/itouch. Because the CPU of iphone/itouch is very slow and >> the graphics engine is also not good enough for these programs. >> >> But I think we can install an SSH client app on iphone/itouch/ipad, such >> as iSSH, then we can control our server or workstation by iphone/itouch, and >> we can run these 'big' software remotely. If this can be considered working >> on an iphone, I think we can do that. >> >> Nice weekend! >> >> Xiaoguang >> >> >> >> >> On Fri, Feb 25, 2011 at 8:54 PM, Jacob Keller < >> j-kell...@fsm.northwestern.edu> wrote: >> Hello All, >> >> is there a ccp4 app for iphones yet? Has any structure been solved on >> an iphone? I know BR uses an iphone to drive his robots, but what >> about structures? >> >> (A question for Friday afternoon...) >> >> JPK >> >> >> *** >> Jacob Pearson Keller >> Northwestern University >> Medical Scientist Training Program >> cel: <773.608.9185>773.608.9185 >> email: j-kell...@northwestern.edu >> *** >> >> >> >> -- >> Xiaoguang Xue, PhD student >> Utrecht University >> Crystal & Structural Chemistry >> Padualaan 8. Room N807 >> 3584 CH Utrecht >> The Netherlands >> Tel. <%2B31-30-253-2383>+31-30-253-2383 >> >> >> >> -- >> Xiaoguang Xue, PhD student >> Utrecht University >> Crystal & Structural Chemistry >> Padualaan 8. Room N807 >> 3584 CH Utrecht >> The Netherlands >> Tel. <%2B31-30-253-2383>+31-30-253-2383 >> > > Tommi Kajander, Ph.D. > Structural Biology and Biophysics > Institute of Biotechnology > University of Helsinki > Viikinkaari 1 > (P.O. Box 65) > 00014 Helsinki > Finland > p. <%2B358-9-19158903>+358-9-19158903 > tommi.kajan...@helsinki.fi > -- Xiaoguang Xue, PhD student Utrecht University Crystal & Structural Chemistry Padualaan 8. Room N807 3584 CH Utrecht The Netherlands Tel. +31-30-253-2383
Re: [ccp4bb] CCP4 for iphones
But I don't know what will happen if we make a cluster by hundreds and thousands of iphones. On Fri, Feb 25, 2011 at 9:25 PM, Xiaoguang Xue wrote: > Hi, > > Your idea is very cool, but i think it's difficult to run CCP4, Coot or > Phenix on iphone/itouch. Because the CPU of iphone/itouch is very slow and > the graphics engine is also not good enough for these programs. > > But I think we can install an SSH client app on iphone/itouch/ipad, such as > iSSH, then we can control our server or workstation by iphone/itouch, and we > can run these 'big' software remotely. If this can be considered working on > an iphone, I think we can do that. > > Nice weekend! > > Xiaoguang > > > > > On Fri, Feb 25, 2011 at 8:54 PM, Jacob Keller < > j-kell...@fsm.northwestern.edu> wrote: > >> Hello All, >> >> is there a ccp4 app for iphones yet? Has any structure been solved on >> an iphone? I know BR uses an iphone to drive his robots, but what >> about structures? >> >> (A question for Friday afternoon...) >> >> JPK >> >> >> *** >> Jacob Pearson Keller >> Northwestern University >> Medical Scientist Training Program >> cel: <773.608.9185> <773.608.9185>773.608.9185 >> email: j-kell...@northwestern.edu >> *** >> > > > > -- > Xiaoguang Xue, PhD student > Utrecht University > Crystal & Structural Chemistry > Padualaan 8. Room N807 > 3584 CH Utrecht > The Netherlands > Tel. <%2B31-30-253-2383>+31-30-253-2383 > -- Xiaoguang Xue, PhD student Utrecht University Crystal & Structural Chemistry Padualaan 8. Room N807 3584 CH Utrecht The Netherlands Tel. +31-30-253-2383
Re: [ccp4bb] CCP4 for iphones
Hi, Your idea is very cool, but i think it's difficult to run CCP4, Coot or Phenix on iphone/itouch. Because the CPU of iphone/itouch is very slow and the graphics engine is also not good enough for these programs. But I think we can install an SSH client app on iphone/itouch/ipad, such as iSSH, then we can control our server or workstation by iphone/itouch, and we can run these 'big' software remotely. If this can be considered working on an iphone, I think we can do that. Nice weekend! Xiaoguang On Fri, Feb 25, 2011 at 8:54 PM, Jacob Keller < j-kell...@fsm.northwestern.edu> wrote: > Hello All, > > is there a ccp4 app for iphones yet? Has any structure been solved on > an iphone? I know BR uses an iphone to drive his robots, but what > about structures? > > (A question for Friday afternoon...) > > JPK > > > *** > Jacob Pearson Keller > Northwestern University > Medical Scientist Training Program > cel: 773.608.9185 > email: j-kell...@northwestern.edu > *** > -- Xiaoguang Xue, PhD student Utrecht University Crystal & Structural Chemistry Padualaan 8. Room N807 3584 CH Utrecht The Netherlands Tel. +31-30-253-2383
Re: [ccp4bb] linux flavors
Hi, Maybe CentOS 5 or Scientific Linux 5 is another option for you. Because you have experiences of RPM based distributions, I think you can install and maintain software easily. CentOS and Scientific Linux are based on Red Hat Enterprise Linux 5, so actually they are similarly as Fedora Core. You can install the NVIDIA driver from ATrpm (http://atrpms.net/) or http://ftp.scientificlinux.org/linux/scientific/55/i386/contrib/video/ BTW, I think CentOS and Scientific Linux are much more robust than UBUNTU. Xiaoguang On Tue, Feb 22, 2011 at 4:16 PM, David Roberts wrote: > 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 > -- Xiaoguang Xue, PhD student Utrecht University Crystal & Structural Chemistry Padualaan 8. Room N807 3584 CH Utrecht The Netherlands Tel. +31-30-253-2383
