Arking:JCAOligoTutoria24

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
(Download a File)
Line 7: Line 7:
===Download a File===
===Download a File===
-
There are several ways to get
+
There are several ways to get structure files (.pdb files) for viewing in DeepView.  DeepView can access pdb files from the Protein Data Bank directly, but I'll show you how to get to things via pubmed.  For this tutorial, we want to work with Hen Egg-White Lysozyme in complex with the trisaccharide inhibitor tri-(N-acetylglucosamine).  The ID code for the file we want is 1HEW.
 +
 
 +
Go to www.pubmed.gov, type "Hen Egg-White Lysozyme" into the search box, put the search pulldown menu on "Structure" and hit GO.  This will pull up a lot of hits of different structures of Lysozyme.  Each entry is a distinct crystal structure.  Often the different hits are mutants of the original, different inhibitors bound to the protein, or maybe just another author's structure of the same protein.  Unless you know specifically what ID file you want, you usually use keyword searches and browsing through the list to find what you are looking for.  For this example, we know exactly what we want:  1HEW.pdb.  So, type "1HEW" in the search box and hit GO.  You should get this:<br>
 +
[[Image:JCA_DeepView1.jpg]]<br>
 +
Click on the image, and that should take you to a screen that looks like this:<br>
 +
[[Image:JCA_DeepView2.jpg]]<br>
 +
I've circled the link you should now follow to get to the Protein Data Bank where you can download the file.  Click it.<br>
 +
[[Image:JCA_DeepView3.jpg]]<br>
 +
I've circled the link to click to download the pdb file.  Click it and save the file to your desktop.  Now you can open it into DeepView.  Double-clicking the desktop icon might do the job.  If not, do file > open within DeepView to open the file.  There might be some error messages that pop up.  If you really want it not to give you these error messages, you can turn them off in the DeepView preferences.  Just say ok to get rid of them for now.  You should have something that looks like this:<br>
 +
[[Image:JCA_DeepView4.jpg]]<br>
 +
If you don't have that rightmost window, the "Control Panel", you should open it up from the Window menu.

Revision as of 21:27, 27 March 2009

This tutorial was adapted from the "Basic Tutorial For DeepView" available at http://spdbv.vital-it.ch/TheMolecularLevel/SPVTut/. I've simplified it somewhat to illustrate the basic operation of the program. For the full glory of DeepView, I recommend following the complete tutorial available at the above URL.


Download DeepView

Go to http://spdbv.vital-it.ch/disclaim.html, accept the disclaimer, and then download the file. On a windows machine, it will come down as a zip file. You should unzip the file, and then double click on spdbv.exe to launch the program. (There is no "installer" for DeepView, and you can launch it from anywhere).

DeepView is often referred to by different names including spdbv, Swiss view, and Swiss-PdbViewer...it's all the same program, just different names.

Download a File

There are several ways to get structure files (.pdb files) for viewing in DeepView. DeepView can access pdb files from the Protein Data Bank directly, but I'll show you how to get to things via pubmed. For this tutorial, we want to work with Hen Egg-White Lysozyme in complex with the trisaccharide inhibitor tri-(N-acetylglucosamine). The ID code for the file we want is 1HEW.

Go to www.pubmed.gov, type "Hen Egg-White Lysozyme" into the search box, put the search pulldown menu on "Structure" and hit GO. This will pull up a lot of hits of different structures of Lysozyme. Each entry is a distinct crystal structure. Often the different hits are mutants of the original, different inhibitors bound to the protein, or maybe just another author's structure of the same protein. Unless you know specifically what ID file you want, you usually use keyword searches and browsing through the list to find what you are looking for. For this example, we know exactly what we want: 1HEW.pdb. So, type "1HEW" in the search box and hit GO. You should get this:
Image:JCA_DeepView1.jpg
Click on the image, and that should take you to a screen that looks like this:
Image:JCA_DeepView2.jpg
I've circled the link you should now follow to get to the Protein Data Bank where you can download the file. Click it.
Image:JCA_DeepView3.jpg
I've circled the link to click to download the pdb file. Click it and save the file to your desktop. Now you can open it into DeepView. Double-clicking the desktop icon might do the job. If not, do file > open within DeepView to open the file. There might be some error messages that pop up. If you really want it not to give you these error messages, you can turn them off in the DeepView preferences. Just say ok to get rid of them for now. You should have something that looks like this:
Image:JCA_DeepView4.jpg
If you don't have that rightmost window, the "Control Panel", you should open it up from the Window menu.

Personal tools