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 <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
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users