[Chimera-users] How to model a loop using a template

[Elaine Meng]

Hi Elisa,
I think I understand, but it’s definitely not trivial!

The “model/refine loops” tool is for using the Modeller program to build peptide segments without a template.  It will just make up some reasonable possible conformations.   You could still try it and then after the fact, see if any of the possibilities are similar to the NMR conformation.  When you see how complicated my other ideas are, you might choose this approach!
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#building>

For actually using the NMR conformation in the modeling, I see two main possibilities, but each has difficulties and possible problems.  (First, if the NMR structure is an ensemble of conformations, you’d have to pick which one to use and discard the rest.)

(A) using Modeller for comparative (homology) modeling, that is, using Modeller with a template structure. In that case you’d need to use both structures (Xray and NMR) as templates and model the entire sequence.

For comparative modeling, you need to have a sequence alignment, so this function is only available from the Multalign Viewer (sequence alignment window) menu.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#comparative>

There are various ways to get a sequence alignment, for example:  Favorites… Sequence to show the sequence of the Xray structure (which will generally include the missing loop residues because the whole sequence is in the SEQRES information of the PDB file).  If it does not, you could instead use main menu: Fetch… UniProt using the protein’s UniProt ID to get its whole sequence. Then in the sequence window menu, Edit… Add Sequence to add the same sequence from the Xray structure (or UniProt) again.  Then you will just have  a “sequence alignment” with 2 of the same sequence, and then the sequence window menu item “Structure… Modeller (homology)” will become available.  Before using it, make sure BOTH structures are associated with a sequence, doesn’t matter which (seq window menu: Structure… Associations) because you should use them both as templates.

** I tried this process and I could not get it to work, but it may be because I started with two copies of the same structure and thus confused the process.  In my case, it was only using the “loop” copy as the template and the main part of the protein was then modeled as an unstructured string.  However, in your case if you have two different PDB ids (Xray and NMR) it may successfully use both as templates.  **

(B) not using Modeller at all, just trying to stick the loop from the NMR structure onto the Xray structure.  The biggest problem here besides the manual labor is that the two ends of the loop might not match up very well between the two structures. You could try to fix it afterward with minimization (Tools… Structure Editing… Minimize Structure), but that might not work very well.

Method I, if there are sufficient overlapping atoms between the two structures:

(1) match (overlay) those overlapping atoms or some subset of them with the match command. May require trying different sets of atoms to get the relative orientation you desire.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
(2) write out the NMR structure in that position relative to the Xray structure (File… Save PDB, see “relative to” option)
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>
(3) manually (with text editor) create a new PDB file by adding the coordinates of the loop from that written-out NMR structure into the X-ray structure PDB file.  Requires deciding which copy of the overlapping atoms you want to keep and some familiarity with PDB file format.  May need to renumber residues, which depending on how messed up the numbering is, may be possible within Chimera after you read in the new file (Tools… Structure Editing… Renumber Residues). Although you could delete atoms and combine models in Chimera, it would not put them into the same chain.

Method II, if there are not sufficient overlapping atoms between the two structures (although you could try it even if there were):

(1) delete atoms from both structures so that you only have one of each residue for the final structure
(2) use the Join Models section of the Build Structure tool to connect them at one end.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html>
(3) use the Adjust Bonds section of the Build Structure tool to connect the other end.  This will probably make a very bad bond.  You could try manually rotating some torsions in the loop before bonding the end, and/or attempting to improve it afterwards with minimization.

So, this is a thorny modeling problem that depending on your structures, may require a lot of manual labor without any guarantee of a good result.  Sorry I don’t have an easier/cleaner answer for you!
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 11, 2016, at 1:54 AM, Elisa Pieri <elisa.pieri90 at gmail.com> wrote:

> Dear all,
> I have installed Chimera on my computer, but I am still new to the program, so forgive me if my question is trivial.
> 
> I have a nmr structure (completely defined) and a X-ray structure of the same protein, but this last structure has a missing loop. How can I model this missing loop in the x-ray structure using the nmr structure as template (i.e. freezing the x-ray structure and adding only the nmr loop)?
> 
> I tried opening both structures and using the Tools > Structure Editing > Model/Refine Loop, but if I choose the x-ray structure, then I don't see where to state that I want to use the nmr structure as template.
> 
> I hope that I explained my problems.
> Can you help me?
> Elisa