[Chimera-users] How to "Align" two atoms

[Thomas Goddard]

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 at ca #1:2 at 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 at ca #1:1 at 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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>