22 Jan 2015

Introduction to Mercury

In-Class Activity

Submitted by Anthony L. Fernandez, Merrimack College
Categories
Description: 

In this exercise, students are introduced to Mercury, a program for visualizing and analyzing crystal structure data.  Students are guided through opening the program for the first time and viewing a structure from the Teaching Subset, a selection of structures from the Cambridge Crystallographic Database (CSD). Activites include changing the representation of the complex, moving the structure around the window, accessing information about the structure, and measuring bond lengths and angles within the structure.

A recent update of the Cambridge Crystallogaphic Data Centre's website has provided free access to the Teaching Subset through a web-based interface. This is ideal for students who use iPads or other tablets. An alternate set of instructions has been added to this learning object. 

Learning Goals: 

After completing this activity, students should be able to:

  • open the teaching subset in Mercury;
  • view a structure included in the teaching subset;
  • manipulate the structure;
  • access basic information about the structure that is included in the datafile;
  • measure bond distances and angles in a structure.
Equipment needs: 

Students can access the structures in two ways.

  • They may use the desktop version of Mercury on a computer that has the software package installed. Mercury is freely available for Mac, Windows, and Linux operating systems. Computers with the Mac OS may also need to install XQuartz, which is also a free download, to run Mecury. 
  • They may also access the structures on an iPad or any computer that has a web browser.

Instructions for both methods of access are included linked to this learning object.

Related activities: 
Implementation Notes: 

At Merrimack, it is common practice to not run lab sections the first week of the semester. For a number of years, I have used the lab period in this first week with my sophomore- and junior-level inorganic students to inform them of lab procedures and have them install required software (Mercury) on their laptops. After students install Mercury on their computers, they complete this exercise individually to familiarize themselves with the program.

I usually have the students download and install Mercury while they are in the room with me so I can troubleshoot any downloading or installation issues. The downloads are not that large [MacOS ~ 150 MB; Windows ~ 120 MB], but having a number of students all connecting to the internet through the same access point could slow the download speed. If you are pressed for time or are using it during a 50 minute lecture, it might be better to either ask students to download the installer before coming to class or to have copies on USB drives for those who have trouble downloading the installation file.

More recently, I have had the students use their iPads to access the strucutres and no software must be installed for them to complete this exercise. New instructions for accessing the structures using an iPad have been added to this learning object.

 

Time Required: 
20 minutes to complete exercise; 20 minutes to download and install software
Evaluation
Evaluation Methods: 

As the students work through this exercise, I walk through the classroom and look "over their shoulder" to see how they are doing. Once they complete the exercise, I choose another metal-containing structure and ask them to follow the same process with that structure.

Evaluation Results: 

In looking at the responses from my 13 students, all 13 were able to provide correct answers for all of the questions in the exercise. They had very little trouble following the instructions or interacting with the software. Students were also able to open other structures and perform a similar analysis on their own, with no input or guidance from me.

Creative Commons License: 
Creative Commons Licence

Comments

Terrific! I'll be devoting an empty lab space in my schedule to Mercury and 3D visualization. I'm going to walk through examples with them showing packing and other neat features, so I won't need to hand out instructions, but Would you be ok with me posting your instruction sheet on my Moodle page so the students can go back to it if they forget something? No problem if not!

Hi Mitchell, Not sure how i missed your post so long ago... You can feel free to use anything I have here on VIPEr. If you need anything else, let me know. I have other items that are not quite ready for primetime but I would be happy to share with you. 

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