#PYMOL TUTORIAL CHAIN HOW TO#
#PYMOL TUTORIAL CHAIN DOWNLOAD#

Two unique and valuable features of this program over some other visualization program are the use of the powerful programming language ( Python) and an emphasis on high-quality graphics. It can also perform many other valuable tasks (such as editing PDB files) to assist you in your research. Warren DeLano, PyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations. For example, it is not designed for building molecules or performing many types of calculations that commercial programs such as SYBYL do.Īccording to the program's author, Dr. PyMOL is not as capable as SYBYL in some areas. A secondary reason is that PyMOL offers a uniquely powerful way to create remarkably stunning images and animations that help to understand molecules under study.

#PYMOL TUTORIAL CHAIN DOWNLOAD#

The main reasons of using a program such as PyMOL are affordability and accessibility: as a student you can download an educational version for free, and use it with any computer you have, be it Windows, Mac, or Linux. You will continue mastering this skill today with the help of another molecular visualization program, PyMOL.

#PYMOL TUTORIAL CHAIN HOW TO#

But more importantly, you started learning how to think about the properties and functions of biological macromolecules via computer visualization. Welcome back to the molecular visualization tutorial! In the previous session, you became familiar with the Unix operating system, and learned some basic features of the program SYBYL. PyMOL Tutorial: Introduction Chem 110L: Macromolecular Visualization Laboratory Exercise: PyMOL mview ( 'interpolate', object = 'profilin' ) cmd. mview ( 'interpolate', object = 'actin' ) cmd. mview ( 'store', object = 'profilin' ) cmd. mview ( 'store', object = 'actin' ) cmd. mview ( 'reinterpolate' ) # wait 0.5 second cmd. rotate ( 'y', - 90, object = 'profilin' ) cmd. rotate ( 'y', 70, object = 'actin' ) cmd.

rotate ( 'y', 90, object = 'profilin' ) cmd. rotate ( 'y', - 70, object = 'actin' ) cmd. pse session file if we mess something up later on rather than re-creating the entire process. Set_color pastelbeigeC = set_color pastelbeigeN = set_color pastelbeigeO = set_color pastelbeigeS = set_color pastellightgreenC = set_color pastellightgreenH = set_color pastellightgreenN = set_color pastellightgreenO = set_color pastellightgreenS = color pastelbeigeC, elem C and ( not - int - actin ) color pastelbeigeN, elem N and ( not - int - actin ) color pastelbeigeO, elem O and ( not - int - actin ) color pastelbeigeS, elem S and ( not - int - actin ) color pastellightgreenC, elem C and ( not - int - profilin ) color pastellightgreenN, elem N and ( not - int - profilin ) color pastellightgreenO, elem O and ( not - int - profilin ) color pastellightgreenS, elem S and ( not - int - profilin )Īt this point, it is a good idea to save the PyMOL session. When this is done, we can create selections of the residues that are not in the interface so we can color them separately later.

Duplicate each list and use the search and replace feature (selected text only) to make the list of residues to select (resi 1+2+3).

Use TextWrangler’s powerful search and replace feature to quickly remove the unneeded text from your list of residues.

When you are done selecting all residues, copy all the data from the command line window and paste it into TextWrangler.

Each selection will be recorded in the pymol command line window.

In the pymol viewer, click each residue to select it.

In the pymol command line window, type orient int-profilin.

In the pymol viewer, turn off everything but int-profilin.

To quickly make the list of residues in the interaction, do the following: Change int-actin in the path to actin when you select the residues to color grey, or use residue number (resi 1+2+3). Copy the residue path from the command line window. Then select each of the residues using the mouse.

Turn off all the objects except int-actin. To get the YRB script to color just the residues in the interaction surface, you need to identify all the residues by name so you can exclude them from the object that you will color grey.

Create int - actin, ( interface ) in actin create int - profilin, ( interface ) in profilin

Pymol tutorial chain