Difference between revisions of "Chimera"
| Line 21: | Line 21: | ||
Favorites > Preferences > Tools and select the features you want. Viewdock can be placed here. Click Save to make these changes permanent. | 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 | ||
Revision as of 15:27, 30 June 2009
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.
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
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
