[chimerax-users] PDB upload TER card error

[HONG ZHAN]

Hi Elaine,

I am uploading to the EMDB (wwPDB Deposition) and I am doing a composite deposition.

I saw there are TER XXXX after each chain but lack in the Chain X.

Thanks,

Hong
________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Wednesday, December 21, 2022 10:27 AM
To: HONG ZHAN <hzhan3 at wisc.edu>
Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] PDB upload TER card error

Hi Hong,
Uploaded where?  We try to write correct PDB format, but some websites that use uploaded PDBs may be pickier than others.

Anyway, the solution is exactly what the error message says:
Just use your favorite text-editor to add a line with first 3 characters TER after the X chain coordinates (ATOM lines).

Intro to PDB format:
<https://rbvi.ucsf.edu/chimerax/docs/user/formats/pdbintro.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 Dec 21, 2022, at 6:56 AM, HONG ZHAN via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>
> Dear all,
>
> I saved my protein coordinates in ChimeraX as pdb (it has multiple chains), however, when I was doing upload on the PDB, it shows this error, I am using ChimeraX 1.5rc202211091945 on Linux ubuntu 22.04 LTS.
>
> Coordinates issues:
>
> ERROR: There is no TER card at the end of polymer chain 'X'. All polymer chains should have a TER card at the end of each chain. Please add TER card and restart again.
>
> Many thanks!
> Hong

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