[Chimera-users] Hello I have a question

[Eric Pettersen]

Hi Teddy,
	Matchmaker does “rigid body” fitting and therefore naturally produces the ‘B’ result.  Perhaps you actually meant to ask if it could produce the ‘A’ result.  If so, it can — but not by using Matchmaker alone.  The general procedure for that would be:

1) Open two copies of the linear form, and match them to opposite sides of the looped form, probably by using Matchmaker while restricting matching to the current selection and selecting one side, then the other.

2) Delete one half of one linear form (select the part to delete and Actions->Atoms/Bond->delete) and the other half of the other form.

3) Use the Model Panel’s “combine” button to combine the two halves into one model.

4) Use the “bond” command to form a (very long) bond connecting the two halves, between atoms that normally are connected.

5) Use Tools->Structure Editing->Minimize Structure to minimize the loop portion while holding the atoms in the matched parts frozen.

—Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Apr 3, 2018, at 6:18 PM, Teddy Chen <j147589 at gmail.com> wrote:
> 
> Hi my name is Teddy, I used UCSF Chimera for my research, and it is a very good software! I appreciate you made it.
> 
> I have a question about structure comparison, I usually use Matchmaker to overlap 2 similar protein fragment to compare the difference. I wonder if the structure is bent or twisted during the matching process, in order to fit the reference structure more?
> 
> For example, the attachment is for demonstration. 
> There is a protein A, and protein A have a short from that miss some amino acid (the green part is missed). So the result produced by the Matchmaker would be A or B?
> If the result is A, can I make result B by UCSF Chimera?
> 
> Thank you!
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