558. More options for PDF annotation: Master PDF Editor and I, Librarian

This is an update to my previous posts (here and here) about annotating PDFs on Linux.

Master PDF Editor
 http://code-industry.net/pdfeditor.php
The linux version of this software is free and closed source. It will not run on Debian Wheezy, as it requires glibc >= 2.14, whereas Wheezy has version 2.13. You can either pull in a newer libc from testing, or simply use testing (Jessie). See here for how to use glibc > 2.13 on wheezy: http://verahill.blogspot.com.au/2014/03/562-pulling-in-glibc-214-from-testing.html

So I tried it on Jessie.

While it almost works, I can't prevent the program from screwing up the fonts in the process. Also, the annotations don't show up in acroread for some reason. Saving as PDF/A didn't make any positive difference.

The annotation shows up in evince -- but the font's weird now

Same goes for Xournal

In acrobat reader before editing with Master PDF Editor

in acrobat reader after adding an annotation. The annotation doesn't show up, but the fonts are screwed up.

So we're almost there -- Master PDF Editor does everything I want in terms of PDF annotation, but at least on linux there are issues with the fonts in the resulting PDFs.

I, Librarian
http://www.bioinformatics.org/librarian/
I, Librarian is both free and open source. It claims to be web-based -- which is true but can be misunderstood. What it means is that it is browser-based and runs a server on your computer. My first thought when I see 'web-based' is that I'm handing over my data to someone else, but luckily that's not the case here.

I installed the .deb file meant for ubuntu.

Using I, Librarian is quite straight forward, but I could not see the annotations in any other program that I tried, which makes it of little use for me -- I make annotations in galley drafts for journal editors, and for students to give them feedback on latex documents.

Either way, to start, just go to http://127.0.0.1/librarian

Make sure to edit the settings to make I, Librarian use the internal pdf viewer in order for editing to work.

No matter what I did, I could not export my pinned annotations though. They did not show up in either evince or acroread.

557. Briefly: Drawing Molecules on Linux: ACD/ChemSketch in Wine

This is another post where I'm cheating a bit -- this is a windows program running in wine.

Let me explain. Sometimes you absolutely need to get a task done -- I use linux at work and I can't not do something just because I can't write/find a piece of software that does it for me. Science is the goal, and the route there is immaterial. So sometimes you need to be pragmatic about your software choices.

I much prefer to use free and open source software since it allows me to keep a copy of the source code which I can recompile in case the prebuilt binary suddenly won't work with a future version of debian. Having the source makes me feel more secure in the assertion that it's worth my time learning how to use that piece of software.

Second to that, I prefer native linux software -- although unfortunately 'native' here often means 'written in java', and -- while not knowing too much about java -- from a user point of view java software tends to be comparatively slow to load and run. Certainly it appears slower than a comparable C/C++ program.

As a last resort, I can accept having to run a windows binary in wine. It doesn't make me happy, and often there are small, niggling issues associated with it -- but if it can get the job done, so be it.

Note that I'm unwilling to actually run a native windows program on a native windows installation -- one has to have some standards...

Either way, this is why I look at windows programs as well for drawing structures and processing NMR spectra.

So I recently tested marvinsketch (linux), bkchem (linux), easychem (linux), chemtool (linux), gchempaint (linux), ISISDraw (wine) and ChemSketch (wine). Out of those I prefer MarvinSketch. However, I'm still exploring the alternatives.

ACD/ChemSketch for Linux is really just an older (2006) version of ACD/LABS free ChemSketch (the windows version is from 2013). To get it, go to http://www.acdlabs.com/resources/freeware/index.php and click on Download. I tried the version 'for linux', and not the windows one. I'm making the presumption that the newer binary won't play well with wine.

You don't need to be an academic to qualify for the free version.

wine ~/Downloads/chemsk50.exe

Once it's installed you can explore ChemSketch. Overall it's fairly similar to e.g. ISISDraw.

556. Briefly: Drawing molecules on linux: ghempaint, chemtool and easychem

chemtool, easychem and gchempaint are in the Wheezy repos.
See also the following posts for ISISDraw, MarvinSketch and BKChem.

Chemtool
I didn't get along with this at all. I managed to import a few structures from the templates, but e.g. the clean molecule function didn't actually work, although it's there. Selecting, deleting etc. were all a bit non-intuitive (to me -- this is obviously very subjective)

Easychem
I can't find any templates. Drawing becomes a bit tedious since I didn't find an easy way of converting an existing bond from e.g. single to double.

gChemPaint
It's pretty straightforward to use and I like it the best of the three. However, it's still very sparse even compared to e.g. bkchem. It certainly works if you quickly need to make a simple structure. There's no clean function.