Hi Elaine, You're right. I forgot about this easy way of running Chimera commands from Python. I think the preferred Python call has changed to: from chimera import runCommand runCommand('align #1:1@ca #1:2@ca') Tom Elaine Meng wrote:

Hello, I thought the EZ way to translate Chimera->python was simply to use makeCommand and enclose the command, for example:

import Midas from Midas.midas_text import makeCommand makeCommand('align #0:1.b@ca #1:1@ca')

Maybe this doesn't always work, or is less efficient? Elaine

On Oct 4, 2007, at 2:37 PM, Thomas Goddard wrote:

...

Hi Matt,

Many Chimera commands are defined in

chimera/share/Midas/__init__.py

They are sometimes a pain to call from Python. Here is some code for the align command.

Tom

from chimera import openModels, selection m = openModels.list()[0] sel = selection.ItemizedSelection() sel.add(m.atoms[0:2]) from Midas import align align(sel)

Matthew Baker wrote:

...

I'm writing a module. I've created a model and added it to the open models. How can I reproduce the command-line function

align #1:1 #1:2

The variable names for my two atoms are newModel.atoms[0] and newModel.atoms[1].

Thanks, Matt

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