[Chimera-users] Hello I have a question

Teddy Chen j147589 at gmail.com
Thu Apr 5 08:59:21 PDT 2018

Thank you for your answer! That really helps!

On Wed, Apr 4, 2018 at 4:32 PM Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> 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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