[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
Your guiding is very helpful to me. It unties the knot for me. Thank you
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:
> 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
> 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.
> I hope this helps,
> 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>
> > 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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