@VanjaAvdic points us to a wonderful resource that focuses on the installation of crystallographic software on OS X. The site was developed by the Scott Research Group and is wiki style, so feel free to make it better!
In addition, off of the Scott Lab page is a compilation of resources for those that want to brush up on their Unix.
The next step in science journals is online. In recent Nature news article, “the American Chemical Society (ACS) is taking steps towards turning most of its academic journals into online-only publications.”
I along with others have been expecting that science journals would move to an online format. I have been following the comments of other blogs that have discussed various aspects of the issue. The comments have been quite fascinating such as those from Farewell to Hard Copies at the blog In the Pipeline. A number of comments, from that post as well as the correspondence to Nature indicates that not everyone is going to happy with the change.
My guess is that the reasons mentioned are not going to convince the ACS to change its mind (assuming the rumor is true). If you are uncomfortable with the idea of having scientific journals online then here are some tools to hopefully make the experience less stressful.
1) How to find scientific articles
If you are simply using Google scholar or PubMed then you are missing out.
-I have already written about hubmed.org
These FireFox plugins are worth looking at Eccellio Science and i-cite
2) Taking Notes
Mac: Skim PDF Reader and Note-taker for OS X
Windows: Adobe Acrobat Full Version (not just the reader)
Another choice: PDFpen you could use the demo until it runs out.
2) Highlighting
Firefox add on: Wired-Marker (for Firefox 3.5 click here)
Highlight text then drag to a folder to display your desired color (tutorial can be found here)
3) How to quickly and easily track multiple websites
RSS feed reader
4) Difficulty reading a Computer Monitor
Firefox add on: NoSquint (version for Firefox 3.5 here)
This add on is helpful because it allows you to hold down the ‘ctrl’ key and then use the mouse to scroll and adjust image and text size.
5) Quickly viewing PDF files
Mac Users: Firefox PDF Plugin for Mac OS X
Window Users: PDF Download
6) Serendipitous discovery
I use Google Alert for certain key words that may relate to your research. For example, crystallography or phosphotransferase.
-If your word appears in any news stories then you will be sent an email with an excerpt and link to the article
Finally, I would like to acknowledge a great post over at Bitesize Bio that discussed the Firefox add-ons mentioned.
If you are a mac user then the program Papers may be worth checking out.
I previously mentioned having trouble downloading the PDB files from the Zhang Server (I-TASSER). I thought it was just me, until I started getting traffic from users searching for “cannot open PDB file I-TASSER”. The problem ended up being how my Firefox browser was set up on one computer verse another. If you are having this problem – here is how to fix it.
When my browser was not set up correctly, I would get the following displayed when clicking on Download Model2 (for example).
Edit–> Preferences –> Applications
Scroll down until you find the file type PDB then change to Save File then click Close
If you are using an older version of Firefox try the following:
Edit–> Preferences –> Content –> File types Manage
First, you need to open a terminal, which can either be done by right clicking on the desktop then selecting open terminal, Applications -> System Tools -> Terminal, or by clicking on the terminal icon (you can hold your cursor over the icons and they will probably tell you what the particular icon represents) that is usually located at the top of screen.
cd
cd is used to change directories hence ‘cd’. If you want to enter a specific directory then follow the command by the name of that directory (folder).
For example: cd Crystallography (press enter after each command) would move into the directory entitled Crystallography
-as a side note the inputs in linux ARE case sensitive
-if you have entered an unique portion of a file or directory you can fill in the rest of name by using the Tab key
For example: cd Crys (enter Tab)
will result in following assuming that name is unique in that particular directory
cd Crystallography
You are always in a directory as soon as you open a terminal (the window that you type/enter commands). You can navigate to directories hierarchically above or below. If you want to move up in directories use the enter the following:
cd ..
If you would like to move up 2 directories then use:
cd ../..
If you like to return to your home directory (the place that you are located when you first open the terminal) then enter the following:
cd ~ (the symbol located at the extreme upper left of most key boards)
If you would like to make a directory use the command:
mkdir XYZ
The XYZ stands for the name would like your directory to be called.
If you would like to list the files and folders in a particular directory type this:
ls
-you may notice that files and directories are color differently.
alias
Will list aliases which are the abbreviations for longer commands
If you need to terminate a program from running (such as simulated annealing in CNS that can take hours) push down the following at the same time (similar to capitalizing a letter with the shift key):
“control” c
You should be able to solve your structures using only the above commands. I don’t want to overwhelm anyone that is new to using linux, but if you have other commands that you feel are critical please leave me a comment.