With Hong's assistance I was able to determine that the problem is that the final TER card is missing if the last chain is not followed by other residues (e.g.waters).  I have fixed the problem and the fix will be in tomorrow's daily build.

--Eric

On Dec 21, 2022, at 9:24 AM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:

Hi Hong,
When I open 1WWW and save it as a PDB, there are TER cards after all 4 chains, so it must be something specific to your structure.  So I would need access to the structure to figure out why there is no TER card.  You could use Help→Report A Bug in ChimeraX and attach the file, or, if your want the file to remain private you could email it to me directly.  Without the file I don't know if there's much I can do.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab


On Dec 21, 2022, at 8:30 AM, HONG ZHAN via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

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@cgl.ucsf.edu>
Sent: Wednesday, December 21, 2022 10:27 AM
To: HONG ZHAN <hzhan3@wisc.edu>
Cc: ChimeraX Users Help <chimerax-users@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@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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