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How can I do to extract a single frame as a pdb file from a trajectory traj.xtc file, by using MDAnalysis?

I've got a universe u=mda.Universe('confout.gro','traj.xtc')

Then I selected a residue by doing select_atoms, and I would like to extract a single frame as a pdb file

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  • $\begingroup$ Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking. $\endgroup$
    – Community Bot
    Jul 22, 2022 at 12:57
  • $\begingroup$ Q to more involved folk in admin: why was Community bot was invoked for this, as it was a case of nobody bothering to answer because it is a boring 'please link me to command X in the documentation' request. I.e. docs.mdanalysis.org/stable/documentation_pages/coordinates/… $\endgroup$ Aug 1, 2022 at 10:24

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Check out gmx_trjconv - this command is in GROMACS and accepts several options where you can specify the specific single frame that you want to output/write - out to the new pdb/gro/xtc file. https://manual.gromacs.org/current/onlinehelp/gmx-trjconv.html

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