Use chimera tool how to#
Use chimera tool manual#
Use chimera tool download#

Give a new unique file name, such as selected_spheres.pdb for the PDB file that will hold the coordinates of selected spheres. You will have one cluster to process and there is no need to generate the surface. Input the filename for the selected spheres file that was generated in the previous step.

Generate the PDB file with binding site sphere coordinates by running the program showsphere in interactive mode.

Notice that a file named selected_spheres.sph was generated.

Select spheres within 10 Angstroms of the active site (OPTION 2) by running the program sphere_selector with receptor spheres file, the prepared ligand file, and the radius as inputs.

Notice that after a successful run, a file with the extension. Generate spheres by running the program sphgen based on the parameters in the INSPH file. Examine this file with a text editor the meaning of each line is explained in the UCSF tutorial.

Use chimera tool download#

Download the text file named INSPH using your browser or the unix command wget link location.

If you are using an older version of Chimera, run the program dms using the prepared receptor without hydrogens as an input and examine the result with UCSF Chimera. Generate the molecular surface of the target ( Actions -> Surface -> Show) and write the molecular surface in the DMS format ( Tools -> Structure Editing -> Write DMS).

Open the prepared receptor structure without hydrogens in UCSF Chimera.

For example, hydroxyl oxygens should be somewhat negative and hydroxyl oxygens somewhat positively charged. Examine this file with a text editor and verify that charges on the ligand are consistent with your chemical intuition. Save the ligand file in MOL2 format after unchecking Sybyl-style hydrogen naming. Prepare ligand by adding hydrogen atoms (use of defaults is OK), and assigning charges using the Chimera Add Charge tool (use of default AMBER force field is OK).

Using UCSF Chimera, re-obtain the structure of the complex (1ABE).

This file will be used in the next part for the generation of the surface and spheres.

Using UCSF chimera, delete hydrogen atoms from the protein and save this receptor structure as a PDB file.

Use chimera tool manual#

Note that if the side-chain with missing atoms is close to the binding site, its replacement with Gly will affect results consider manual replacement with Ala or manual rebuilding of the residue. Thus steps e) and f) in the UCSF tutorial are obsolete and you can directly proceed to write the MOL2 file. UCSF Chimera also check for incomplete residues and automatically change these to glycines. This involves deleting ligand and solvent molecules, elimination alternate locations of residues, change of selenomethionines to methionines, adding hydrogen atoms, and assigning charges to protein atoms.

Using UCSF Chimera, prepare the structure of the receptor for docking.

Using UCSF Chimera, obtain and examine the structure of L-arabinose-binding protein (1ABE).

The list below will serve as a guide to the overall work flow, and suggests which option to follow.

The UCSF tutorial is rather comprehensive and sometimes offers multiple ways of performing a task.

Use chimera tool how to#

You will find details on how to accomplish each of the tasks listed below by carefully reading her tutorial.

Therese Lang, a graduate student at UCSF. The DOCK website has a nice tutorial prepared by P. UCSF Chimera has a nice tutorial for beginners. You can also use Chimera to analyze the results of docking. You will use UCSF Chimera to prepare input files for the program UCSF Dock. This preparation is greatly simplified by molecular modeling programs such as UCSF Chimera that provide a powerful, menu-driven graphical user interface. In reality, meaningful docking calculations require a careful preparation of receptor and ligand structures before the docking programs can do their work. It would be nice if one could just feed the name of the PDB file as stored in the RCSB Protein Databank and a SDF file defining nearly a million of lead-like compounds from a database such as ZINC into a docking program, and sit back while the computer docks every compound to every binding pocket in the protein. In this tutorial, you will learn to use the program DOCK, which was originally developed in Irwin Kuntz group at UCSF. Docking algorithms also generate a score that attempts to distinguish between molecules that bind strongly in their optimal placement from these that bind weakly.

The ligands is typically a small molecule peptide-protein and protein-protein docking algorithms are currently under active development. Docking with DOCK 6 BackgroundДocking is a term that covers a large class of computer algorithms that attempt to find an optimal placement of a rigid or flexible ligand in the receptor binding site. Tutorial: Visualization of MacromoleculesД¬omputer-Aided Drug Design Tutorials: 4.1.