[chimerax-users] PDB upload TER card error

[Eric Pettersen]

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 at 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 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 <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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