Hansol Choi

Hi Petr. Thanks for the response. I visualized the structure with cogli. Thanks! Best, Hansol

Dear oxDNA team, I’m having trouble while visualizing the structure with chimera. pdb file and chiemra.com file are generated by running traj2chimera.py. But whenever I try to run chimera.com with command line in chimera program to see nicer view, error occurs saying ‘Choose only 2 atoms to bond(10 chosen)’. Visualizing the structure with VMD with both pdb or xyz format has no problem so I think this problem is not coming from the simulation process. Please let me know if there is any way to fix...

Hi Petr Thank you for the immediate response. I was using chimera 1.12 and same error occurs even though I tried with chimera 1.9 I attached topology, configuration, json files and chimera.com file. Best, Hansol

Dear oxDNA team, I’m having trouble while visualizing the structure with chimera. pdb file and chiemra.com file are generated by running traj2chimera.py. But whenever I try to run chimera.com with command line in chimera program to see nicer view, error occurs saying ‘Choose only 2 atoms to bond(10 chosen)’. Visualizing the structure with VMD with both pdb or xyz format has no problem so I think this problem is not coming from the simulation process. Please let me know if there is any way to fix...

Hi, Lorenzo Thanks a lot for immediate response. Tetrahedron structure you gave me as an example seems that it came from json file which is designed by caDNAno. Is that structure relaxed by changing UTILS/cadnano_interface.py? I would really appreciate it if you could give me example code. Thanks. Best, Hansol

Dear oxDNA team. I’m trying to simulate polyhedral structures or wireframe DNA origami with oxDNA. I designed the structures with caDNAno. Wireframe DNA origami was generated by just connecting beams using 'pencil tool' in caDNAno. Configuration file and topology file are successfully generated from json file however, I failed to generated trajectory file whenever I tried to run oxDNA. It seems that oxDNA program doesn’t allow abnormal connection (crossovers in wrong position). Error coded is stated...

Dear oxDNA team. I’m trying to simulate polyhedral structures or wireframe DNA origami with oxDNA. I designed the structures with caDNAno. Wireframe DNA origami was generated by just connecting beams using 'pencil tool' in caDNAno. Configuration file and topology file are successfully generated from json file however, I failed to generated trajectory file whenever I tried to run oxDNA. It seems that oxDNA program doesn’t allow abnormal connection (crossovers in wrong position). Error coded is stated...