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• Problem with executing dssp (secondary structure assignment)

  - by Mana

  I followed a previous post to install dssp on ubuntu How to install dssp (secondary structure assignments) under 12.04? After the installation I tried to execute dssp which was in /usr/local/bin/dssp But it gave me the following error bash: /usr/local/bin/dssp: cannot execute binary file Also I tried to analyse some trajectory files from a simulation using the code do_dssp -s md.tpr -f traj.xtc But it also failed giving me the error below Reading file md.tpr, VERSION 4.5.5 (single precision) Reading file md.tpr, VERSION 4.5.5 (single precision) Segmentation fault (core dumped) Please post me a solution for this problem. Thank you!

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• How to install Revolution R Enterprise?

  - by Abe

  Revolution R Enterprise is available as a red-hat rpm file. Normally I would use alien to install an rpm file, but the instructions for installing this package have an install.py file that I am supposed to execute. When I ./install.py, I get the following instructions: rpm: please use alien to install rpm packages on Debian, if you are really sure use --force-debian switch. See README.Debian for more details. There is no README.Debian file in the directory, and although I am not proficient in python, I can tell that there are at least four different directories with *rpm files in them. Has anyone had success with this? If possible, I'd prefer to install the Enterprise version instead of community version in the Ubuntu repository so that I can test it out.

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• Exadata Storage Server software upgrade is a new era in Patching

  - by Luis Moreno Campos

  Since it was first released, Exadata Storage Server software has been releasing patch releases like every software on the planet. Storage administrators would have to do this, but by some weird tradition, no matter what level of technology, if it says "Oracle" in it, IT Managers will immediately associate this with a task for the DBA. Not the case, but if it falls onto a DBA lap, fear no evil.The last patch released for Exadata Cells, is a true master piece in patching technology. This sentence is not mine, it's from both the customer and the partner that witnessed how 3 Exadata Cells where patch in less than 4 hours, after 12 months of without a single upgrade.The patch manager that takes care of everything will patch not only the software but also the firmware and the operating system. And you know it will all work out because back in the lab everything was already tested.All you have to do is stare at the 3 Sun ILOM Windows from the 3 cells and watch as they boot and reboot, patch and fix to the latest versions all layers of the storage machines. It's a new era in Patching technology!LMC

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• Rhythmbox not saving the album art permanently

  - by Nik

  I run ubuntu 10.10 and use rhythmbox (version 0.13.1) regularly with the albumartsearch plugin installed. However when I change the album art it is only temporary. On moving to the next song it automatically removes the previous song's album art cover. (I do know about banshee but would like to use rhythmbox). The cover art plugin is also installed by default however it cannot display some of the album covers since the songs are in my local language (tamil) hence it cannot retrieve the album cover from the internet. However the albumartsearch plugin seems to do the job although only temporarily. Any reason why it might be? I have tried looking for other rhythmbox plugins which might be similar to albumartsearch but in vain. Any help would be appreciated. I have filed a bug in the albumartsearch plugin's website. Waiting for the reply.

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• Brightness keys adjust brightness too many times

  - by erjiang

  Every time I hit a brightness key on my laptop's keyboard, it adjusts the brightness by three steps instead of one. How can I fix it so that it only adjusts one step at a time? I am using an Acer Aspire D250 with the newest firmware. It was working better when I was using Ubuntu 10.10 with older firmware (although the scale was off). Any tips on debugging this would be appreciated. Edit: My graphics: 00:02.0 VGA compatible controller: Intel Corporation Mobile 945GME Express Integrated Graphics Controller (rev 03) /sys/class/backlight$ ls acpi_video0 intel_backlight

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• Why is mysql unable to configure?

  - by Tijs

  I try to install mysql-server on my Ubuntu vps server, and it's able to install, but not to configure. If it tries to configure I get this: ...fail! invoke-rc.d: initscript mysql, action "start" failed. dpkg: error processing mysql-server-5.0 (--configure): subprocess post-installation script returned error exit status 1 dpkg: dependency problems prevent configuration of mysql-server: mysql-server depends on mysql-server-5.0; however: Package mysql-server-5.0 is not configured yet. dpkg: error processing mysql-server (--configure): dependency problems - leaving unconfigured Errors were encountered while processing: mysql-server-5.0 mysql-server E: Sub-process /usr/bin/dpkg returned an error code (1) Does someone know a solution to this? Btw, my other question can be closed, it's solved, but I cant comment on it anymore.

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• My Message to the Software Craftsmanship Group

  - by Liam McLennan

  This is a message I posted to the software craftsmanship group, looking for a week-long, pairing / skill sharing opportunity in the USA. I am a journeyman software craftsman, currenlty living and working in Brisbane Australia. In April I am going to travel to the US to attend Alt.Net Seattle and Seattle codecamp. In between the two conferences I have five days in which I would like to undertake a craftsmanship mini-apprenticeship, pairing and skill sharing with your company. I do not require any compensation other than the opportunity to assist you and learn from you. Although my conferences are in Seattle I am happy to travel anywhere in the USA and Canada (excluding Hawaii :) ). Things I am good at: .NET web development, javascript, creating software that solves problems Things I am learning: Ruby, Rails, javascript If you are interested in having me as visiting craftsman from the 12th to the 16th of April please reply on this mailing list or contact me directly. Liam McLennan Now I wait…

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• How to get Spotify running?

  - by Dante Ashton

  A while ago Spotify (the streaming music service) came out with a preview for Linux of their client. I had succesfully run it throughout 10.04. Now I'm on 10.10, I can't seem to find it in the package manager, let alone install it. Software Sources gives me this; Failed to fetch http://repository.spotify.com/dists/stable/Release Unable to find expected entry non-free/source/Sources in Meta-index file (malformed Release file?) Some index files failed to download, they have been ignored, or old ones used instead. So...as I'm paying for Spotify what...umm...do I do? :P

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• Sword and Sworcery - seg fault

  - by Synesso

  I've just bought, installed Sword and Sworcery via the Software Centre. When I run it, the screen goes black, the cursor changes and then all reverts back to normal. I found the executable that matches the menu item. /bin/sh /opt/swordandsworcery/run.sh When I run it from the console: Segmentation fault (core dumped) My setup: Linux jem-doxie 3.2.0-24-generic #39-Ubuntu SMP Mon May 21 16:52:17 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux Where to from here? Refund? Or can I do something?

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• how to get the application listed on open with menu?

  - by user17182377182122092121021929

  I have installed the sublime text 2 in sublime text by http://www.technoreply.com/how-to-install-sublime-text-2-on-ubuntu-12-04-unity/ way. now I can see them on when I click Win button and search for it. Same time I want to see them in open with context. I means when I right click on file and choose. open with other application how I can choose the sublime text. I can't see the option their to do this. Thanks for help in advance.

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• apache2 tomcat6 virtual hosting

  - by user3215

  I've apache2 and tomcat6 running on port 80 on ubuntu server 9.10. I've a registered domain name and I'll access the jsp index page navigating to http://abc.mydomain.com. The page is under tomcat_home/webapps/myapp and the below are tomcat virtual hosting in server.xml file: <Host name="abc.mydomain.com" debug="0" appBase="webapps" unpackWARs="true"> <Logger className="org.apache.catalina.logger.FileLogger" directory="logs" prefix="virtual_log1." suffix=".log" timestamp="true"/> <Context path="" docBase="/usr/share/tomcat/webapps/myapps" debug="0" reloadable="true"/> </Host> Recently a new domain has been bought(xyz.mydomain.com) and I'm asked to do the virtual hosting so that the new domain name directly points the page "admin.jsp" which is located under 'tomcat_home/webapps/myapps/WE-INF/js/'. How could I do this? If I type http://abc.mydomain.com/admin I'll get the page what I wanted. I should access the page just by typing http://xyz.mydomain.com.

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• No wireless and display issues on Dell Inspiron 1210 (Mini 12)

  - by Bryan M.

  I recently upgraded a friend's Dell Mini 12 (Inspiron 1210) from Ubuntu 8.10 to 10.04 netbook edition. After installing, and performing the available updates, I'm unable to detect any wireless networks (it knows it has a wireless card, but won't list any active networks). There also seems to be an issue with the display drivers: when scrolling, resizing, or drawing any windows there is a noticeable lag as I watch the screen redraw. As if there are no compatible display drivers installed. All these problems go away the moment I boot up a version of 8.10. But I'd like to keep 10.04 if possible. Are these common problems? Everything I've read suggest this is laptop should be compatible. Any suggestions? Thanks.

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• Application to display battery info

  - by Nik

  First of all, I am not sure the title of this question is the most appropriate however this is what I meant to say, There are many ways to extend the life of a laptop battery. One way is by not connecting it to the AC adapter all the time which will overcharge it. I read that in this website. Is there an application which automatically prevents the charging of the battery once it has reached 80% charged? I mean that is such a cool feature. Sometimes people tend to forget to remove the AC adapter and this could diminish the capacity and reduce the life time of the battery. Does the battery indicator in ubuntu display info or pop-up when the battery is almost dead (dead not in the sense of usage time) but rather a degraded battery?

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• Does UX matter for enterprise software?

  - by Ryan

  I've come to notice that a lot of software that companies use for managing things like time, expenses, setting up phone systems, etc is very non-intuitive from a user experience point of view. I know personally I waste a lot of time just trying to figure out how to navigate these systems, especially if I don't have a co-worker close by who I can bug to help me out. The help files are usually just as bad as the user interface itself. Are companies that complacent or are there just not any comparable enterprise products out there which do the job for these sorts of tasks? It seems that on the consumer side there is plenty of market opportunity for creating better user experiences, but how about for enterprise software? Obviously a certain level of slickness is not going to matter to a company, but when a better UX design translates to time saved, it's hard to argue against that. Edit: I'm not referring to in-house applications, but rather off the shelf systems from large software companies.

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• How to configure Xchat and IRC server to transfer files?

  - by takeshin

  How do I configure Xchat to send files? My setup: hardware router: xxx.xxx.xxx.xxx example.com | Ubuntu Server with IRC server: 192.168.1.2 Local machines: 192.168.1.x My aim is to allow to send files between the local machines. By now, they are able to talk on the local IRC channel. which ports do I need to open on the router? what do I need to configure on the server? how to configure XChat on the clients? how to troubleshoot/debug the problems?

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• How do I reset my password?

  - by doug

  I inherited a machine with Ubuntu desktop installed. It has a password in place and I have no idea what the password may be. I cannot get to the command line to use the methods I have found online. No matter how many times I press "Shift" during the boot process it still goes all the way to the desktop login. I never see grub. I am not sure which version I have but I think may be 9 or 10. Thanks Doug

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• Good online auction software

  - by Brett

  We are looking for some PHP-based auction software to start off with and I have have been scouring the net many times and am almost ready to purchase phpprobid as this seems to be the best and most feature rich of the lot; only bad things I have read is the lack of after-sales customer service. Others I have also looked at include: AJ Auction Software WeBid GuruScript Auction PHP Auction (enuuk). Many of them turn me off by having unprofessional sites which makes me think their software will be the same and be rubbish. Many also don't go into detail with the feature set like PHP Pro Bid does. So before we purchase PHP Pro Bid I was wondering if I missed something good? Thanks!

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• How to show context menu when right-click released?

  - by Kev

  I'm using Ubuntu 10.04. When I right-click, menu popup too quickly, and the first menu item is clicked. If I right-click in desktop, it create a new folder sometime. If I right-click in terminal, it open a new terminal sometime. ... Is there some way to delay context menu? Or how can I offset context menu a little bit pixels to the right-bottom direction? (like firefox) Or how can I config Gnome to popup menu when right-mouse released? (like windows xp)

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• How to make sudo remember my password and how to add an application to startup

  - by Bragboy

  I guess this should be a simple thing for ubuntu users out there. I have two questions. Whenever I need to run some command that requires permission from root, I run as sudo followed by that command. It would be nice if that does not prompt for password (but I should still be issuing a sudo to make sure that I know what I am doing). How to do this? Every time I start my system, I go to terminal and start my VPN using sudo vpnc. This is almost everytime! How to automate this to a startup script? Help much appreciated! Thanks

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• Fan control on Acer Aspire One D255 netbook

  - by AdamB

  I have Ubuntu netbook edition on my Acer Aspire One D255 netbook and I notice that I always hear the fan working at 100% despite the actual temperature. I run the sensors command its only at 13c, theres no reason why the fan needs to be running this hard at that temp. root@adam-netbook:~# sensors acpitz-virtual-0 Adapter: Virtual device temp1: +13.0°C (crit = +100.0°C) I'm guessing I may need some drivers in order to interact with the fan? Does anyone have any experience with this? It also seems that "sensors" may not be all that accurate, the temperature never seems to fluctuate.

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• Ubuntuone fails to sync with 'File Sync starting...' displayed

  - by a different ben

  I am on 12.04 using ubuntuone-client 3.0.1-0ubuntu1.0.1. I actually have two machines that I sync with, having the same Ubuntu version and ubuntuone-client version. One is fine, the other is not. File sync has frozen within a user-defined folder under my home folder. The graphical client reports in the top-right corner: 'File Sync starting...', but this doesn't change. I have two files with changes that show a syncing overlay in Nautilus. They are both very small text files. Here are some details: harb@joan:~$ u1sdtool --status State: READY connection: With User Not Network description: ready to connect is_connected: False is_error: False is_online: False queues: WORKING harb@joan:~$ u1sdtool --current-transfers Current uploads: 0 Current downloads: 0 The status seems to suggest that I am not connected to a network, however I am connected to a network - in fact I am accessing this machine via NX. Is it not working because I am connected via NX? Happy to provide other info, just not sure what would be useful.

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• Packard Bell Easynote NJ65 not saving gamma Setup.

  - by Pablo Gomez

  Hi. There seems to be a issue with the Easynote range of PB laptops. Since Ubuntu 10.10 does not use a Xorg.conf file to save your gamma / resolution /brightness setting, everytime I turn on my laptop I have to open up a terminal window and use the x-gamma command to set it up to my personal preference. Is there a way to create a configuration file which can save that into the system everytime I load up the OS? When I used to have a Compaq Presario (an F564LA with integrated nVIDIA graphics), I could save a config. file into the system which loaded up everything on startup To those who don't know the spec's for a NJ65 laptop, I'll provide them Processor: Intel® Pentium Dual Core @ 2.2 GHZ Video: Integrated Intel® GMA 4500MHD graphics HDD: 320GB SATA RAM: 2GB DDR2

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• File system maintenance error, press ctrl+d to continue

  - by user3215

  In my office I've Ubuntu 8.10 desktop installed and it's running for a long time. When ever the system is started, I'll get a file system maintenance error and something it's prompted for the root password or (press ctrl+d to continue). After pressing Ctrl+D the system normally boots up. I could not resolve this issue for a long time and I think something should be done in the fstab file. I'm not sure to do anything and expecting the experts here to help to perfectly fix this. Any help is appreciated. Thanks!

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• How can I remove the Unity Launcher?

  - by Magnus Hoff

  I'm running Ubuntu Netbook. With the recent upgrade to 10.10 I was excited about the Application Menu/the global menu bar and its implications for screen real estate. Unfortunately, the Unity Launcher on the left hand side of the screen takes more valuable space away than the new menu bar gives. Is there any way to get rid of the Launcher? Alternatives I would be satisfied with include: Not having the Launcher at all Having the Launcher hide automatically Having applications open on top of the Launcher (not next to it) (edit:) Note that I am specifically looking for a way to keep the global menubar, while getting rid of the Launcher.

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• Applications Menu disappeared

  - by Sophie Sperner

  I'm using Ubuntu 12.04, classic desktop without effects. Once the indicator-applet-complete (right part of the top panel) had been disappeared. I found how to fix it: Alt-Win-RightMouseClick on the panel, then "Add to the Panel", where choose "Indicator Applet Complete" to add. Now, the left part of the top panel (Applications Menu) has been disappeared! If I do Alt-Win-RightMouseClick on the panel, I can add only individual Menu sections like Internet, Office, Settings etc. But how to get back the full Menu as it ought to be?

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