[chimerax-users] PDB upload TER card error

[Eric Pettersen]

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