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Difference between revisions of "Biochemistry student intro"
| Line 12: | Line 12: | ||
=== Find a suitable protein data file === | === Find a suitable protein data file === | ||
We need to find a Protein Databank File (PDB), which describe the x,y,z coordinates of your enzyme.<br> | We need to find a Protein Databank File (PDB), which describe the x,y,z coordinates of your enzyme.<br> | ||
| − | These are stored at the homepage: http://www.rcsb.org | + | These are stored at the homepage: http://www.rcsb.org <br> |
| − | Find a suitable file by searching for: '''porcine kidney fructose 1,6-bisphosphatase''' | + | Find a suitable file by searching for: '''porcine kidney fructose 1,6-bisphosphatase''' <br> |
| + | The PDB file "1lev", seems suitable. | ||
| + | |||
| + | === Read more about your protein === | ||
| + | There exist homepages, to get more info about your protein.<br> | ||
| + | These homepages collect material from several sources, and present them in easy format. | ||
| + | |||
| + | http://www.proteopedia.org/wiki/index.php/1lev <br> | ||
| + | http://www.proteopedia.org/wiki/index.php/1lev | ||
Revision as of 13:02, 2 June 2012
Biochemistry course
This tutorial was written directly for biochemistry students at Copenhagen University, 2012.
This is the very first introduction to the powerful molecular visualizer PyMOL.
We will only cover the very basic steps to get a image of your enzyme and put in your written student article.
Install PyMOL to your windows computer
You first want to install PyMOL.
Do this, by following this guide Pre-compiled_PyMOL
You don't have to follow the steps of extending PyMOL, but if you are a little technical, and want to become friends with PyMOL over time, then consider it.
Find a suitable protein data file
We need to find a Protein Databank File (PDB), which describe the x,y,z coordinates of your enzyme.
These are stored at the homepage: http://www.rcsb.org
Find a suitable file by searching for: porcine kidney fructose 1,6-bisphosphatase
The PDB file "1lev", seems suitable.
Read more about your protein
There exist homepages, to get more info about your protein.
These homepages collect material from several sources, and present them in easy format.
http://www.proteopedia.org/wiki/index.php/1lev
http://www.proteopedia.org/wiki/index.php/1lev