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====Visualizing Protein-Ligand Complexes====
 
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In this section, we will explore ways to visualize structures in the Workspace. Object representation can be changed in a number of ways using the Style toolbox. Presets offers the ability to quickly render a structure in a number of styles styles, similar to PyMOL, to facilitate easy visualization. Presets can be used in a variety of ways, from de-cluttering your structure to creating publication-quality images. We will analyze the protein-ligand complex by looking at the interactions that are made and the surface of the binding pocket. Finally, we will save an image of the complex.

Revision as of 01:12, 8 September 2017

(Click for lab website)

Download

To download the Schrödinger software, please visit the Download Center (login required):

  http://www.schrodinger.com/downloadcenter/

As of September 8, 2017, the current release version is 2017-3 (just released yesterday!).


Just in case, I have a copy downloaded already for Windows and MacOS, which will be provided either by USB key or CD.

It may take a while to download given its large size (about 4GB).

  Now take a break (say, 10 min) while downloading ...

Installation on your laptop

Before we start, make sure you are within the Case campus network, either by connecting through

  CaseWireless

If you are using the CaseGuest wireless, you may need to activate

  VPN

Windows-64

Start by

  1. Double-clicking setup.exe 

Wait for several seconds ... follow the instruction by clicking some 'yes' or 'next' buttons.

  2. "Installing software" ... and wait (depending on how old your laptop is) 

... after several minutes (hopefully), then clicking more 'next' using the default (unless you know what you are doing).

    "Installation completed successfully!" ... 

Now stop and click

   Configure

Since we have been issued a license (installed on a server) , choose

   Add Licenses [I can identify my license server]

Enter Host Name:

   hpctest.case.edu

and Port

   XXXXX

NOTE:

   Replace XXXX with the code provided on-site

Then

   click "Save Server". 

Then check the "Current Status" above. If you see

  "Valid licenses found" 

Congratulations! You are ready to play.

Mac -- License Installation Instructions

After installation, use

  Finder, navigate to Applications → SchrodingerSuites2017-3. 

Then

   Open the Configuration application by double-clicking on it.

Since we have been issued a license (installed on a server) , choose

   Add Licenses [I can identify my license server]

Enter Host Name:

   hpctest.case.edu

and Port

   XXXXX

NOTE:

   Replace XXXX with the code provided on-site

Then

   click "Save Server". 


Then check the "Current Status" above. If you see

  "Valid licenses found" 

you are good to move on.

Getting familiar

Introduction to Structure Preparation and Visualization

This gives an introduction to the Maestro interface and basic visualization tasks. You will learn how to prepare ligand and protein structures, an essential first step for modeling projects.

    using a 3-button mouse with a scroll wheel

Creating Projects and Importing Structures

Visualizing Protein-Ligand Complexes

In this section, we will explore ways to visualize structures in the Workspace. Object representation can be changed in a number of ways using the Style toolbox. Presets offers the ability to quickly render a structure in a number of styles styles, similar to PyMOL, to facilitate easy visualization. Presets can be used in a variety of ways, from de-cluttering your structure to creating publication-quality images. We will analyze the protein-ligand complex by looking at the interactions that are made and the surface of the binding pocket. Finally, we will save an image of the complex.