[Chimera-users] Tool:Structure Editing:Model:Refine loops

Elaine Meng meng at cgl.ucsf.edu
Tue Jan 26 10:49:04 PST 2016

Dear Jingchuan,
The modeling that you can do with this interface is only single-chain.  So, using the whole sequence, you can’t just ask to model part of the missing loop and get a free (disconnected) end.  Instead it will always try to connect to the residues before and after the modeled segment even if there are really more residues missing.  I assume you are using the “active region” option and have drawn a box around the sequence of the residues you want to model.


You CAN do it but only by editing the input sequence so that it ends right after the residues you want to model (if you want to model only the first part of a loop and leave its C-term free) or starts with the residues you want to model (if you want to model only the second part of a loop and leave its N-term free).  You can show the original sequence (Favorites… Sequence) and save it to a fasta text file (from the sequence window menu), then use a text-editor outside of Chimera to delete part of the sequence, then main menu File… Open to open the edited sequence.  If it is not automatically associated to your structure, tell it to associate (Structure… Associations in the menu of the edited sequence) and then draw a box around the residues in the sequence and model them (Structure… Modeller (loops/refinement) in the menu of the edited sequence).

I just tried this whole procedure on a test structure to make sure it worked.  I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jan 25, 2016, at 2:14 PM, Jingchuan Sun <jingchuan at gmail.com> wrote:
> Hello,
> When I tried MODEL plugin to model loop, the changes in result model is not just the selected loop to be modelled. It renumbered residues. There are several missing residues outside the selected loop in my old model. They become connected (in not accepting way) in returned models.
> Could I disable this "over-reach"? I only need to model the selected loop, no change to other places or renumbering.
> Best,
> Jingchuan

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