I have an ATI Radeon HD 6450 card. Sometimes upon boot, just when the console should switch to the screen native resolution, it apparently fails to do so. The screen goes black and the computer restarts.
I suspect there is some problem with loading the radeon driver. Therefore I decided to include it in my
initrd image, together with the filesystem driver. Like this:
mkinitrd -c -k 3.10.17 -m ext4:radeon -o /boot/initrd-radeon.gz
The firmware got included automatically and the size of the generated
initrd-radeon.gz is 6.8 MB. The screen switches to its native resolution a little bit earlier when booting. The problem does not occur anymore and I have not observed any issues, except that once X crashed over a period of 3 months.
However, I do not know if it is safe to do this and I have never seen anyone use this approach! I put it here solely for my future reference.
Therefore, I asked in the LQ forum three months ago how safe this is. People actually suggested that I better check my RAM and or to upgrade the kernel. When I have more time I will do that, but for now this fix seems to work.
If someone knows better, please let me know.
Filed under desktop, system
I needed to predict the secondary structure of amino acid sequences, already in a multiple sequence alignment (MSA). This means that the sequences had gaps, which could be a problem. I searched the net for a suitable, easy-to-use application or online server.
Somehow, none of the tools I found seemed to be suitable for me. I needed a program that can load the MSA (no need to generate it by itself), predict the secondary structure for each sequence independently (not making a consensus secondary structure prediction) and graphically present the result over the sequences (as they are aligned, including gaps).
Turns out, I have had the answer all the time: UCSF Chimera. I have mentioned this powerful program before. It can open a protein MSA (let’s say in FASTA format) in it’s own window. You simply go to
Structure > Secondary Structure > Show predicted. That’s it! You can customise the appearance by
Info > Region Browser.
After, it is very easy to export the result as EPS and later open it with Inkscape, if some polishing of the image is needed.
It is worth mentioning that while searching for the best solution, I found some very nice tools. Among them were: PRALINE, Jpred3, APSSP2, ESPript and CFSSP.
Whenever I need to adjust my computer’s clock, I set the right time in the
BIOS. I am using XFCE, which does not provide a graphical tool for this (unlike KDE). Recently, I searched for a smarter way to do it and came across these nice examples.
Setting the date as the example says is as simple as:
# date +%Y%m%d -s "20150104"
This will reset your clock to 00:00:00. The date format is “
YYYYMMDD“. Following the instructions, I adjusted my clock:
# date +%T -s "12:25:00"
Where the time format is “
Filed under desktop, system
I have been using the 4.3 version of Skype for several months already, with PulseAudio and its compat packages installed. However, I experienced problems with some audio programs. XMMS would crash regularly and Clementine would refuse playing. Very strange, probably I did not configure PulseAudio properly. Anyway, I got rid of it and its dependencies, as well as their compat packages. Of course sound in Skype stopped.
I recently found out about apulse. It provides PulseAudio emulation for ALSA and does not require PulseAudio. Thanks to Ryan, it is now available at SBo. I installed it on a multilib system, and following the instructions, I started skype like this:
Sound works again! I made a skype test call and could hear my voice back. Great. I therefore modified the skype.desktop file like this:
Comment=Skype Internet Telephony
Exec=apulse skype %U
Then, I saved it in
~/.local/share/applications/skype.desktop to make it available for my user.
UPDATE (16.02.2015): to start Skype on a Slackware64 -multilib machine, use
apulse32 in the examples above. At the moment, the version of
apulse is 0.1.5.
UPDATE (28.02.2015): with the newest at the moment version of apulse (20150103), the
apulse binary works on a -multilib system by default. Therefore, use the instructions in the original post
I like to set a theme for GTK1, so the few programs that use the toolkit do not look as ugly. There is the Industrial engine and theme for GTK1, which has not been developed for a long time, but works just fine. It can be installed from SBo and it does not conflict with the gtk-engines package.
Once the engine/theme has been installed, it is time to select it to be used for GTK1 programs. A tiny, little program that can do this is gtk1-theme-switch, also available from SBo. It will list all GTK themes, as well as any XFCE window manager themes. So don’t get confused by the long list and make sure the theme you select “Industrial”.
Why would anyone want to set a theme for GTK1? Well, at least for me there are still some programs that I use that rely on GTK1. XMMS, that comes with the default Slackware install, is an example. Now, its Preferences window looks much better:
Other programs are the various XMMS plug-ins, Grip2, Arka.
I have mentioned about setting a GTK1 theme before, but I decided it needed its own post…
I need to change the language encoding of some mp3 files, because they are not displayed properly in Clementine. The song names and albums are in Cyrillic, so I wanted to convert all tags text to
CP1251. I googled around and found the solution here. I decided to use the
mid3iconv method. I installed mutagen from SBo, and executed the following in the folder with the files:
find . -name "*.mp3" -print0 | xargs -0 mid3iconv -e CP1251 -d
The music in question is Nautilus Pompilius – MP3 КОЛЛЕКЦИЯ. The disc contains several albums and is sold as an mp3 collection.