Chimera
Chimera is a good program for visualization of proteins and small molecules and is freely available for downloading at the UCSF Chimera website.
It also includes plugins for interfacing with the DOCK program. The DOCK Prep module prepares a protein complex for redocking, while the DOCK View module allows the convenient browsing of docked results. To start learning how to use chimera, go to Help > Tutorials, or the Chimera Tutorial.
Additionally, these two short videos provided by the protein databank will give a brief introduction to the software and walk through several basic, yet important structure analysis tools available within Chimera:
Contents
ViewDock Tool
Useful for reading mol2 files produced by dock. Access from Tools > Surface/Binding Analysis > ViewDock. Can read the energy, rmsd and cluster size of each pose reported by dock and sort by these columns.
MD MOVIE
MD trajectories can be visualized with chimera.
loading trajectories with the GUI.
Tools > MD/Ensemble Analysis > MD Movie load in parm and then crd, rst, mdcrd, etc.
command line option:
write a meta file
cat << EOF > meta_file.txt amber active_15rewcastle.com.wat.leap.parm active_15rewcastle.com.wat.leap.crd EOF
In command line issue the following command:
open md:C:\Documents and Settings\trent\Desktop\meta_file.txt
Useful Command line
calculating distance between 2 atoms
distance #1.1@N2 #0:71@HG2
picking a selection
sel #0:47-50,67,71,80-82,92-110,146,149,159-162
color by atoms by charge
rangecol charge -1 red 0 white 1 blue
Enabling the Toolbar
Favorites > Preferences > Tools and select the features you want. Viewdock can be placed here. Click Save to make these changes permanent.
Aligning proteins
First, you can run chimera "scripts". These are text files with the extension .com.
chimera --nogui chimera.com
To align two proteins, we use mmkaer to align them and matrixcopy to apply the transformation to the ligand as well.
open zzz.master/$ref_system.rec.mol2
open zzz.master/system.rec.mol2
open zzz.master/system.lig.chelpg.mol2
mmaker #0 #1 ss false iter 2.0
matrixcopy #1 #2
write format mol2 1 zzz.matched/${system}_matched.rec.mol2
write format mol2 2 zzz.matched/${system}_matched.lig.mol2
The following mmaker command works better for gp41
mmaker #0 #1 pair ss ss false iter 2.0
To write pdb files instead of mol2 files use
write format pdb 1 matched_frame/${file}.matched.pdb
Running Python Scripts
Chimera will run Python scripts directly using the built-in python distribution.
chimera --nogui test.py
Example script that opens a pdb file and prints out list of residues.
import chimera
model = chimera.openModels.open('file.pdb')
mol = model[0]
print 'Molecule Name %s\n' % mol.name
for res in mol.residues:
print "%s%s " % (res.type, res.id)
