Chimera

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The UCSF Chimera program displaying the PDB code 1VRT as a ribbon diagram.

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.

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)