Difference between revisions of "Chimera"

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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 [http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/frametut.html Chimera Tutorial].  
 
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 [http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/frametut.html Chimera Tutorial].  
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 +
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:
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*[https://www.youtube.com/watch?v=hQxKYSUdiD8 Chimera Basics - Video]
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*[https://www.youtube.com/watch?v=eLxhKc7Ljjk Chimera Structure Analysis - Video]
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== ViewDock Tool ==
 
== 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.
 
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.
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== MD MOVIE ==
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MD trajectories can be visualized with chimera.
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 +
loading trajectories with the GUI.
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Tools > MD/Ensemble Analysis > MD Movie
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load in parm and then crd, rst, mdcrd, etc.
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command line option:
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write a meta file
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cat << EOF > meta_file.txt
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amber
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active_15rewcastle.com.wat.leap.parm
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active_15rewcastle.com.wat.leap.crd
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EOF
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In command line issue the following command:
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open md:C:\Documents and Settings\trent\Desktop\meta_file.txt
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== Useful Command line ==
 
== Useful Command line ==
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   sel #0:47-50,67,71,80-82,92-110,146,149,159-162
 
   sel #0:47-50,67,71,80-82,92-110,146,149,159-162
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color by atoms by charge
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  rangecol charge -1 red 0 white 1 blue
  
 
== Enabling the Toolbar ==
 
== Enabling the Toolbar ==
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To write pdb files instead of mol2 files use  
 
To write pdb files instead of mol2 files use  
 
  write format pdb 1 matched_frame/${file}.matched.pdb
 
  write format pdb 1 matched_frame/${file}.matched.pdb
−
== Command line ==
 
−
=== color atoms by charge ===
 
  
−
   rangecol  charge -1 red 0 white 1 blue
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== Running Python Scripts ==
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Chimera will run Python scripts directly using the built-in python distribution.
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   chimera --nogui test.py
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Example script that opens a pdb file and prints out list of residues.
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  import chimera
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  model = chimera.openModels.open('file.pdb')
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  mol = model[0]
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  print 'Molecule Name %s\n' % mol.name
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  for res in mol.residues:
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        print "%s%s " % (res.type, res.id)

Latest revision as of 09:48, 6 February 2019

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.

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:


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)
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