ISOLDE error: Please remove “TER” card after the single residue
Dear colleagues,
I have an issue with the validation website after working with my model in ISOLDE.
More detailed: When starting the simulation in ISOLDE, I am running into the error: At least one residue in your model does not match any templates in the MD forcefield. This may be due to missing or superfluous atoms, or an unusual residue that has not yet been parametrized. Launching the unparameterized residue widget to help sort this out. So certain ligand info is missing (MYR). Then appears the window that allows me to add the information about this ligand and proceed with the refinement. After finishing refinement in ChimeraX/ISOLDE, I loaded the model and the map on https://validate-rcsb-1.wwpdb.org/. But this website showed me the error: File upload failed. Please review the errors below and try again. Coordinates issues. ERROR: Please remove “TER” card after the single residue “MYR A 1” in line 136 and upload the file again.
Some more observations: Although MYR is the first residue in the ChimeraX sequence, it is not visible. At the same time, COOT can see it.
Please let me know how I can proceed with the https://validate-rcsb-1.wwpdb.org/ after refinement with ISOLDE.
Please let me know if you require a model/map file for the investigation.
Thank you
Kind regards, Dmitry
Hi Dmitry, Did you try deleting the TER line from the PDB file like the message says? You would just open the file in a text editor, go down to the coordinates section (ATOM and HETATM) and delete that line right after the coordinates of the MYR residue. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 21, 2023, at 11:08 AM, Dmitry Semchonok via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear colleagues, I have an issue with the validation website after working with my model in ISOLDE.
More detailed:
When starting the simulation in ISOLDE, I am running into the error:
At least one residue in your model does not match any templates in the MD forcefield. This may be due to missing or superfluous atoms, or an unusual residue that has not yet been parametrized. Launching the unparameterized residue widget to help sort this out.
So certain ligand info is missing (MYR). Then appears the window that allows me to add the information about this ligand and proceed with the refinement. After finishing refinement in ChimeraX/ISOLDE, I loaded the model and the map on https://validate-rcsb-1.wwpdb.org/. But this website showed me the error:
File upload failed. Please review the errors below and try again.
Coordinates issues.
ERROR: Please remove “TER” card after the single residue “MYR A 1” in line 136 and upload the file again.
Some more observations:
Although MYR is the first residue in the ChimeraX sequence, it is not visible.
At the same time, COOT can see it.
Please let me know how I can proceed with the https://validate-rcsb-1.wwpdb.org/ after refinement with ISOLDE.
Please let me know if you require a model/map file for the investigation.
Thank you Kind regards, Dmitry
Dear Elaine,
I did not try. Instead, I deleted this MYR residue and continued. Can it be added back somehow after?
Thank you. Kind regards, Dmitry
________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: 22 October 2023 17:31 To: Dmitry Semchonok semchonok@gmail.com Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] ISOLDE error: Please remove “TER” card after the single residue
Hi Dmitry, Did you try deleting the TER line from the PDB file like the message says? You would just open the file in a text editor, go down to the coordinates section (ATOM and HETATM) and delete that line right after the coordinates of the MYR residue. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 21, 2023, at 11:08 AM, Dmitry Semchonok via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear colleagues, I have an issue with the validation website after working with my model in ISOLDE.
More detailed:
When starting the simulation in ISOLDE, I am running into the error:
At least one residue in your model does not match any templates in the MD forcefield. This may be due to missing or superfluous atoms, or an unusual residue that has not yet been parametrized. Launching the unparameterized residue widget to help sort this out.
So certain ligand info is missing (MYR). Then appears the window that allows me to add the information about this ligand and proceed with the refinement. After finishing refinement in ChimeraX/ISOLDE, I loaded the model and the map on https://validate-rcsb-1.wwpdb.org/. But this website showed me the error:
File upload failed. Please review the errors below and try again.
Coordinates issues.
ERROR: Please remove “TER” card after the single residue “MYR A 1” in line 136 and upload the file again.
Some more observations:
Although MYR is the first residue in the ChimeraX sequence, it is not visible.
At the same time, COOT can see it.
Please let me know how I can proceed with the https://validate-rcsb-1.wwpdb.org/ after refinement with ISOLDE.
Please let me know if you require a model/map file for the investigation.
Thank you Kind regards, Dmitry
Hi Dmitry, I don't know. It would be better to try just deleting the TER card only (since the message says that is the thing to do), and then you would not need to add the MYR back later. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 25, 2023, at 8:43 AM, Dmitry Semchonok via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear Elaine,
I did not try. Instead, I deleted this MYR residue and continued.
Can it be added back somehow after?
Thank you.
Kind regards,
Dmitry
From: Elaine Meng meng@cgl.ucsf.edu Sent: 22 October 2023 17:31 To: Dmitry Semchonok semchonok@gmail.com Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] ISOLDE error: Please remove “TER” card after the single residue
Hi Dmitry, Did you try deleting the TER line from the PDB file like the message says? You would just open the file in a text editor, go down to the coordinates section (ATOM and HETATM) and delete that line right after the coordinates of the MYR residue. I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 21, 2023, at 11:08 AM, Dmitry Semchonok via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear colleagues, I have an issue with the validation website after working with my model in ISOLDE.
More detailed:
When starting the simulation in ISOLDE, I am running into the error:
At least one residue in your model does not match any templates in the MD forcefield. This may be due to missing or superfluous atoms, or an unusual residue that has not yet been parametrized. Launching the unparameterized residue widget to help sort this out.
So certain ligand info is missing (MYR). Then appears the window that allows me to add the information about this ligand and proceed with the refinement. After finishing refinement in ChimeraX/ISOLDE, I loaded the model and the map on https://validate-rcsb-1.wwpdb.org/. But this website showed me the error:
File upload failed. Please review the errors below and try again.
Coordinates issues.
ERROR: Please remove “TER” card after the single residue “MYR A 1” in line 136 and upload the file again.
Some more observations:
Although MYR is the first residue in the ChimeraX sequence, it is not visible.
At the same time, COOT can see it.
Please let me know how I can proceed with the https://validate-rcsb-1.wwpdb.org/ after refinement with ISOLDE.
Please let me know if you require a model/map file for the investigation.
Thank you Kind regards, Dmitry
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Thank you, Elaine,
I should give it a try.
Sincerely, Dmitry ________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: 25 October 2023 17:23 To: Dmitry Semchonok semchonok@gmail.com Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] ISOLDE error: Please remove “TER” card after the single residue
Hi Dmitry, I don't know. It would be better to try just deleting the TER card only (since the message says that is the thing to do), and then you would not need to add the MYR back later. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 25, 2023, at 8:43 AM, Dmitry Semchonok via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear Elaine,
I did not try. Instead, I deleted this MYR residue and continued.
Can it be added back somehow after?
Thank you.
Kind regards,
Dmitry
From: Elaine Meng meng@cgl.ucsf.edu Sent: 22 October 2023 17:31 To: Dmitry Semchonok semchonok@gmail.com Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] ISOLDE error: Please remove “TER” card after the single residue
Hi Dmitry, Did you try deleting the TER line from the PDB file like the message says? You would just open the file in a text editor, go down to the coordinates section (ATOM and HETATM) and delete that line right after the coordinates of the MYR residue. I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 21, 2023, at 11:08 AM, Dmitry Semchonok via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear colleagues, I have an issue with the validation website after working with my model in ISOLDE.
More detailed:
When starting the simulation in ISOLDE, I am running into the error:
At least one residue in your model does not match any templates in the MD forcefield. This may be due to missing or superfluous atoms, or an unusual residue that has not yet been parametrized. Launching the unparameterized residue widget to help sort this out.
So certain ligand info is missing (MYR). Then appears the window that allows me to add the information about this ligand and proceed with the refinement. After finishing refinement in ChimeraX/ISOLDE, I loaded the model and the map on https://validate-rcsb-1.wwpdb.org/. But this website showed me the error:
File upload failed. Please review the errors below and try again.
Coordinates issues.
ERROR: Please remove “TER” card after the single residue “MYR A 1” in line 136 and upload the file again.
Some more observations:
Although MYR is the first residue in the ChimeraX sequence, it is not visible.
At the same time, COOT can see it.
Please let me know how I can proceed with the https://validate-rcsb-1.wwpdb.org/ after refinement with ISOLDE.
Please let me know if you require a model/map file for the investigation.
Thank you Kind regards, Dmitry
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (2)
-
Dmitry Semchonok -
Elaine Meng