[Chimera-users] writing multiple chains from Modeller to one PDB

Khải Trần Gia trangiakhai97 at gmail.com
Thu Feb 28 20:17:57 PST 2019

Dear Meng,
Your guiding is very helpful to me. It unties the knot for me. Thank you
very much!!
Best regards,

Vào Th 5, 28 thg 2, 2019 vào lúc 00:28 Elaine Meng <meng at cgl.ucsf.edu> đã

> Dear Khai,
> (I changed the Subject line because the original one was not useful for
> other people on the mailing list)
> The problem may be because the chains that come back from Modeller do not
> have any chain IDs.  After you get more models back from Modeller with the
> missing residues added, you would combine them and assign chain IDs, then
> save the PDB file.  I give a detailed example below:
> I opened a structure 1www that has two chains with missing residues (V and
> W) and I made 5 models of V with missing residues added and 5 models of W
> with missing residues added.
> I looked in the Model Panel (open from Favorites menu) and I can see that
> there is
> #0   the original model
> #1.1-5 the models of chain V
> #2.1-5 the models of chain W
> Model Panel:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html>
> I decided to use #1.1 and #2.4 as the chain models to combine into a new
> model, so in Model Panel I chose just those two (click the name of one,
> Ctrl-click the name of the other one) and clicked the “copy/combine…”
> function on the right.
> Then in the Copy/Combine dialog I chose “rename them uniquely” for
> assigning two different chain IDs.  You can enter a name for new model that
> will be shown in the Model Panel, or else it will just be the default name
> “combination”.
> Now I see there is a new model #3 named combination, so in Model Panel you
> can just choose that one and then click the “write PDB” function on the
> right to save it as a PDB file.  Now when I close everything and then
> reopen the PDB file I saved, it shows both chains and they are A and B (not
> V and W because Modeller lost that information).
> If you don’t like which chain is A and which is B, or you want to assign
> other different IDs like V and W, you could change chain IDs (menu: Tools…
> Structure Editing… Change Chain IDs) and then write another PDB.
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/changechains.html
> >
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Feb 26, 2019, at 10:23 PM, Khải Trần Gia <trangiakhai97 at gmail.com>
> wrote:
> >
> > Dear Mr/Mrs,
> > I am a person using Chimera to adding missing residues to a protein from
> Protein Data Bank. My protein has 2 chains: A and B which both have missing
> residues. I have used Chimera tools compliment with Modeller to adding
> missing residues in both chain. The problem is I want to save the whole
> protein which consists of 2 fixed chains, however when I saved with PDB it
> only show 1 chain. How can I do that?
> > I am looking forward for your replying.
> > Thank you.
> > Best regards,
> > Khai.
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