[Chimera-users] Very similar structures

Tom Goddard goddard at sonic.net
Thu Apr 11 16:14:30 PDT 2013

Hi Rebecca,

   Here's a crazy trick to see atoms in structure #1 that are not in 
structure #0.

     ~display #0
     display #1
     mcopy #0 #1 set v

This hides all the atoms of #0, displays all the atoms of #1, then 
copies the visibility of atoms in #0 to matching atoms in #1.  In other 
words it undisplays just the atoms of #1 that have mates in #0.

You could abbreviate this command sequence

     alias ^diff ~display $1 ; display $2 ; mcopy $1 $2 set v

then use

     diff #0 #1
     diff #1 #0

Here is the mcopy documentation



> On Apr 11, 2013, at 2:46 PM, Rebecca Swett wrote:
>> Hi guys, I have a question, I have two structures that are different by just a few atoms. Is there any way I could use the selection tools in chimera to find them and display them?
> Hi Rebecca,
> 	In the general case I don't have any good ideas.  If your two structures have consistent residue naming and numbering then it isn't too hard to do in Python.  In case your structures have consistent nomenclature, I have appended a script that will print the differences to the reply log and select the differences on the structures.  You run the script simply by opening it with File->Open.
> --Eric
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