Start from current slide in Impress

I use LibreOffice and sometimes, when I go through a presentation I want to enter full screen mode from the current slide. This can be done by pressing SHIFT + F5, but I decided to put a button in the toolbar. To do this, right click on the toolbar you want to edit and select Customize Toolbar. Go to Toolbars > Add. From Category select “View” and from Command select “Start From Current Slide”:

Screenshot - 02182015 - 05:05:56 PM

Click the Add button. To specify an icon, go to Modify > Change Icon:

Screenshot - 02182015 - 05:12:09 PM

That’s it!

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Protein MSA secondary structure

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.

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Setting date and time

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 “HH:MM:SS“.


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Sound in Skype via apulse

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:

apulse skype

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:

[Desktop Entry]
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 (17.02.2015): you can find additional information at adioe3.

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


Filed under desktop, media, network, system

LyX icon

Although I do not often use it, I like to have the LyX Document processor available. It can be easily installed from SBo and works very well. A little inconvenience is the absence of a menu entry. Therefore, I just created a file ~/.local/share/applications/lyx.desktop with the following contents:

[Desktop Entry]
Comment=LyX Document Processor

I have been doing this for years, but I usually forget to save the .desktop file when I upgrade Slackware and have to make it again. So, there it is…

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SeaMonkey Composer

From time to time I need to create or maintain a simple web-page. For the purpose I have used KompoZer, which is available at SBo, but as a 32bit application. Although it runs fine on a Slackware64 -multilib system, I have experienced occasional hang ups and crashes. Of course, I can create a SlackBuild that would compile it from source. I actually did a similar thing at the time I used CRUX and I may even still have the port somewhere… However, it is too much work at the moment, also the last update of the program was in 2010.

The SeaMonkey suite comes with a very similar program — the component is called Composer. It is stable, 64bit, comes with Slackware out-of-the-box and gets the job done. It can be started from the Window menu of the browser or independently:

seamonkey -editor

I like to have a separate menu entry for it, so I created the file ~/.local/share/applications/seamonkey-composer.desktop with the following contents:

[Desktop Entry]
Name=SeaMonkey Composer
Comment=Read Mail with SeaMonkey
Exec=/usr/bin/seamonkey -editor

Works very well. Of course I knew about that program before, but I somehow never really gave it a try till now.

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Customizing SeaMonkey

With the latest Firefox update (31.2.0) I decided to migrate to something more traditional, like SeaMonkey. I am not going to list all the reasons for my decision to abandon Firefox, as it will turn into a rant (and who cares?). I do not exactly like the path the browser has taken and I am tired of doing so many tweaks (including installing addons) in order to make it look like it used to. All that being said, I do respect the developers behind the project and wish Firefox all the best. If an addon appears that can restore the previous look and feel, I will come back to it. There’s this discussion at Slashdot.

Now SeaMonkey. At the moment it is version 2.30, installed on Slackware 14.1 by slackpkg. I went to the browser’s Extensions collection and went through the Interface Customizations category. The following caught my attention:

  • Menu Wizard: Removing, moving and renaming of menus.
  • Tab Wheel Scroll: Switch tabs by scrolling with the mouse wheel.
  • CuteButtons — Cystal SVG: Add icons to buttons/menus/anywhere.
  • Sea Fox: Transform SeaMonkey into Firefox 3..
  • SeaTab-X: Adds Firefox-style tab closers into SeaMonkey.
  • MonkeyFix: Fixes up numerous SeaMonkey browser interface issues (eg. adding support for popup ALT attributes), as well as adding some handy features for developers and power users (eg. configure source viewer, work online/offline).

I played with them and in the end I left only Tab Wheel Scroll, SeaTab-X and MonkeyFix. The last one is great, adding a lot of functionality to the interface, including additional buttons. I also rearranged some of the buttons, added the search fields, etc. In the end I got something very much to my liking.


Screenshot - 11072014 - 07:16:47 PM

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GTK1 engine and theme

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:

Screenshot - 11012014 - 01:00:27 PM

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…

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Convert mp3 tags encoding

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.

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Batch resize of pictures

I had generated graphics from the Simple Modular Architecture Research Tool (S.M.A.R.T.) in the highest possible resolution. However, later on I needed to scale down the graphics.

How to do that? I searched a bit and I found these explanations about the convert command, part of Imagemagic. Very useful tips there, however I needed something that will batch process a bunch of picture files. The command mogrify, also part of Imagemagic, is what I needed.

Just go to the folder with the pictures and do:

mogrify -resize 50% *

This will resize in half everything in the current folder, overwriting the original files. In case, you may need the original files later, better back them up. Also, Imagemagic comes with the standard Slackware installation.

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Filed under Academic, media