[Chimera-users] [Dock-fans] Help with antechamber

Eric Pettersen pett at cgl.ucsf.edu
Tue Apr 10 12:39:33 PDT 2012

On Apr 9, 2012, at 4:41 PM, Brad Ridder wrote:

> Hi Scott and Eric,

Hi Brad,

> Okay, so I suppose the problem was not using the latest version of Chimera when running dockprep.py. I now correctly get "dp.mol2" written to the working directory.
> Now, I am just confused to where this puts me in the 4-step process. In the tutorial, this .mol2 file should correspond to everything up to and including step 1g in the tutorial.

I think that's correct.

> dp.mol2 has hydrogens in it, which need to be stripped away.
> I have a some new questions then:
> 1. I need to take dp.mol2, and make rec_noH.pdb from it. Is there a quick, easy way to do this with Chimera? e.g. open dp.mol2, strip the hydrogens, and save the results as a .pdb file? I see this commented-out code from ligprep.py could be useful:
> #runCommand('select H')
> #runCommand('delete sel')
> And also this "write" command:
> http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/write.html#options
> But how do I get python to use that "write" command? I don't understand why there is a "write" command here, but there is a totally separate python module "WriteMol2" just for writing .mol2 files. There is no "WritePDB."

You could just add some lines to dockprep.py script to also write out the PDB file, keeping in mind that the runCommand function can be used to run any Chimera command.  So you would probably add lines like these:

from chimera import runCommand
runCommand('select H')
runCommand('delete sel')
runCommand('write 0 rec_noH.pdb')

Alternatively you could write it as a separate script that opened the dp.mol2 file from the previous script if that was better for your workflow.

> 2. I looked at the ligprep.py script, but I don't understand how to run it yet. First, where do you specify the input file? And what format does it have to be in? Also, there is some commented out code up top:
> # $HOME/chimera/1.2470/bin/chimera --nogui ligprep.py
> Is that just the command for running it from the terminal? It has no inputs specified, so the input file appears to be "start.sdf". Am I understanding this correctly? I am just confused because in the original message, the person wanted to loop over many files, but as this ligprep.py script is written, I don't see how any looping could be done since the input file is hard-coded to be "start.sdf".

If you are going to use Scott's ligprep.py script, it looks like you would need to use it in a shell script that copies the input to start.sdf and then copies the output from start.mol2.  In csh syntax, something like this:

foreach sdf in (*.sdf)
	cp $sdf start.sdf
	chimera --nogui ligprep.py
	cp start.mol $sdf:r.mol2

> 3. In the case of 2H4F, I have more than one ligand. I want to keep the large peptide fixed (it has a long lysine pointing into the center of the enzyme), but NAD is what I want to dock. How would I tell Chimera/Python to choose NAD for ligand preparation?

Strip everything but NAD from the system to prep it as a ligand.  Treat the peptide as part of the receptor, not as a ligand.

> 4. The module "chimera" needs to be imported. However, I have three versions of Chimera on my computer: 1.5.3, 1.6, and 1.6.1. How will the Python import command know to go into the 1.6.1 directory to find the correct, up-to-date module files? Just adding the /chimera/share folder to the python path should work, right?

You run a Chimera Python script with "chimera --nogui" not with the system Python.  "chimera --nogui" will have the correct module paths.

> 5. Is there a special procedure for deleting the other Chimera versions, or just trash them?

On Windows there is a de-installer.  On the Mac, just drag them to the Trash.


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