[Chimera-users] Chimera/Modeller to add missing residues

Elaine Meng meng at cgl.ucsf.edu
Tue Nov 14 09:47:25 PST 2017

Dear Daipayan,
I do not know what your three models are, because each time you make a model with this tool there is a “number of models” choice.  If you chose to only make 1 model for chain A and 1 model for chain B, maybe your three models are:

(1) original structure (1yph chains A-F)
(2) one model of chain A with missing residues added, now without chain ID
(3) one model of chain B with missing residues added, now without chain ID

You can see a list of what the current models are by opening the Model Panel (from Favorites menu).

I tried opening 1yph (model #0) and making those other models (#1.1 and #2.1) When I hid the original model 1yph (unchecking “S” box in Model Panel) I could see that the new models include not just the peptides, but a bunch of water and sulfate residues (command “display” displays all atoms)

If my guess about your three models is correct, I would recommend:

(A) deleting the nonprotein parts of the two new models, e.g. command something like: delete #1-2 & ~ protein
… meaning delete models #1-2 AND NOT protein (PS be very very careful entering these delete commands because they are irreversible… maybe save session beforehand, just in case)
(B) deleting chains A and B from the original structure because you are going to replace them with the new models, e.g. something like: delete #0 & protein & :.a-b
(C) merge the 3 models into one, e.g. in Model Panel choose/highlight all three models (rows on the left side) and then use the “copy/combine” button on the right side of the dialog, create new merged model with “rename them uniquely” for any chains that have overlapping IDs
… in my test it made the two newly modeled chains G and H instead of A and B … if that bothers you, you can change chain ID (Tools… Structure Editing… Change Chain IDs)
(D) then save only the single new merged model, in my case #3,  to PDB file

An important point is that the Chimera-Modeller interface will only model one chain at a time.  It does not care that other chains are there, so any added residues/loops might end up clashing with the other chains.  In this case it didn’t seem

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 14, 2017, at 2:53 AM, Daipayan Sarkar <sdaipayan at gmail.com> wrote:
> Hello Elaine, 
> I am using Chmiera-Modeller GUI to add the missing residues for my PDB file:
> (https://files.rcsb.org/view/1YPH.pdb). 
> From the mailing list, I am following the procedure listed in:
> http://www.cgl.ucsf.edu/pipermail/chimera-users/2013-September/009174.html
> However, once the missing residues for chains A and B are included, I save the new PDB file using File > Save PDB... > under save models selection "selected all three files" and clicked OK. The resulting PDB file includes the original header with additional 'MODEL 1', 'MODEL 2' and 'MODEL 3'. How to save the atom coordinates as a single PDB file after adding the missing residues? Any comments/suggestions is appreciated. 
> Regards, 
> Daipayan
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