Reading Coarse Grained Trajectories into UCSF ChimeraX
Hello, I have a quick question regarding loading of coarse-grained molecular simulation trajectories generated using the HPS force-field . I have a PSF and DCD generated out of 2 systems, one that contains only protein beads and another of both protein and DNA. I find that the protein only system is read by UCSF ChimeraX and reads both the PSF and DCD of that system, while the protein and DNA system doesn't. I get this error: IndexError: Cannot create Element with atomic number 119 File "atomic_cpp/cymol.pyx", line 967, in chimerax.atomic.cymol.Element._int_to_cpp_element See log for complete Python traceback. I do want to emphasize that since the HPS model is a single bead coarse-grained model, the actual mass of the nucleic acid beads encompass the mass of the sugar and nucleobase and might not reflect any 'elemental mass', (that is what I understood of the error anyway as there were residues which are having greater mass than recorded elements.) However, despite the protein beads also having masses of entire amino acid residues, not elements, the protein only simulation rendered fine. I was wondering whether there is a work around for this? To prevent ChimeraX from seeking element/atom and just utilizing the PSF file and then reading the DCD file as is? Thank you for your time, Best, Sunera
Hi Sunera, It would be useful if when this error occurs you could use the bug-reporting dialog to submit a bug report, so that I can see where in the DCD-reading code this error occurs and modify the code to allow these non-physical element numbers for coarse-grained simulations. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Feb 10, 2026, at 11:46 PM, Wijeratne, Arambewela A via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I have a quick question regarding loading of coarse-grained molecular simulation trajectories generated using the HPS force-field . I have a PSF and DCD generated out of 2 systems, one that contains only protein beads and another of both protein and DNA. I find that the protein only system is read by UCSF ChimeraX and reads both the PSF and DCD of that system, while the protein and DNA system doesn't. I get this error:
IndexError: Cannot create Element with atomic number 119
File "atomic_cpp/cymol.pyx", line 967, in chimerax.atomic.cymol.Element._int_to_cpp_element
See log for complete Python traceback.
I do want to emphasize that since the HPS model is a single bead coarse-grained model, the actual mass of the nucleic acid beads encompass the mass of the sugar and nucleobase and might not reflect any 'elemental mass', (that is what I understood of the error anyway as there were residues which are having greater mass than recorded elements.) However, despite the protein beads also having masses of entire amino acid residues, not elements, the protein only simulation rendered fine.
I was wondering whether there is a work around for this? To prevent ChimeraX from seeking element/atom and just utilizing the PSF file and then reading the DCD file as is?
Thank you for your time, Best, Sunera _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Hello Eric, Yes, sure I can do that. For the moment, I managed to resolve it by just loading the PDB and then the trajectory. But loading the PSF would definitely be useful. Also, I was kind of hoping that UCSF ChimeraX had the capability of visualizing the simulation box utilizing the PSF file, since the dimensions are stored within it. Best, Sunera ________________________________ From: Eric Pettersen <pett@cgl.ucsf.edu> Sent: Wednesday, February 11, 2026 11:34 AM To: Wijeratne, Arambewela A <sunera@iastate.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Reading Coarse Grained Trajectories into UCSF ChimeraX Hi Sunera, It would be useful if when this error occurs you could use the bug-reporting dialog to submit a bug report, so that I can see where in the DCD-reading code this error occurs and modify the code to allow these non-physical element numbers for coarse-grained simulations. --Eric Eric Pettersen UCSF Computer Graphics Lab On Feb 10, 2026, at 11:46 PM, Wijeratne, Arambewela A via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Hello, I have a quick question regarding loading of coarse-grained molecular simulation trajectories generated using the HPS force-field . I have a PSF and DCD generated out of 2 systems, one that contains only protein beads and another of both protein and DNA. I find that the protein only system is read by UCSF ChimeraX and reads both the PSF and DCD of that system, while the protein and DNA system doesn't. I get this error: IndexError: Cannot create Element with atomic number 119 File "atomic_cpp/cymol.pyx", line 967, in chimerax.atomic.cymol.Element._int_to_cpp_element See log for complete Python traceback. I do want to emphasize that since the HPS model is a single bead coarse-grained model, the actual mass of the nucleic acid beads encompass the mass of the sugar and nucleobase and might not reflect any 'elemental mass', (that is what I understood of the error anyway as there were residues which are having greater mass than recorded elements.) However, despite the protein beads also having masses of entire amino acid residues, not elements, the protein only simulation rendered fine. I was wondering whether there is a work around for this? To prevent ChimeraX from seeking element/atom and just utilizing the PSF file and then reading the DCD file as is? Thank you for your time, Best, Sunera _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (2)
-
Eric Pettersen -
Wijeratne, Arambewela A