Superpose all states of an object to one of the states.
print cmd.intra_fit("my-traj////CA", 1)Do the same, but this time the
target/reference is a different object.
for s in range(cmd.count_states()): print(cmd.align('my-traj', 'ref',
mobile_state=s + 1, target_state=1, cycles=0, transform=0))On Mon, Aug 19, 2019 at 9:25 AM Mateusz Bieniek <bieniek...@gmail.com> wrote: > There is also intra_rms and instra_fit commands: > https://pymol.org/pymol-command-ref.html#intra_rms > https://pymol.org/pymol-command-ref.html#intra_fit > > For example: > intra_fit name CA and resid 1326-1350, 0 > > Maybe they will be useful. > > Best, Mat > > On Mon, 19 Aug 2019 at 13:54, sunyeping <sunyep...@aliyun.com> wrote: > >> Hello Mateusz, >> >> Thank you very much for your reply to my inquiry. Before I try the PyMOL >> extension you mentioned, I want to try scripting language in pymol. I >> wrote a attemptive one (align.py): >> >> cmd.load("A.gro") >> cmd.load("A.xtc") >> cmd.load("ref.pdb") >> for i in range(1, 5001): >> cmd.align(ref, A,target_state=i) >> >> I ran it in pymol command line, but it doesn't work. I am new to pymol >> scripting. Could you write a correct one for me? Thank you very much. >> >> Best regards, >> >> Yeping >> >> >> ------------------------------------------------------------------ >> From:Mateusz Bieniek <bieniek...@gmail.com> >> Sent At:2019 Aug. 19 (Mon.) 20:32 >> To:孙业平 <sunyep...@aliyun.com> >> Cc:pymol-users <pymol-users@lists.sourceforge.net> >> Subject:Re: [PyMOL] How to calculate rmsd between each state of a MD >> simulation trajectory and a reference structure? >> >> Hi Sunyeping, >> >> Besides using the scripting language in pymol, you might want to consider >> the experimental PyMOL extension created by the PyMOL Fellows (me and Paul >> Smith, https://pymol.org/fellowship/). The extension relies on the >> MDAnalysis package and so far includes RMSD as an example. Here is the link >> to the right github branch >> https://github.com/bieniekmateusz/pymol-open-source/tree/fellows_mp_2018 >> >> If you compile it, you can use the RMSD this way: >> mda_load systemX.gro >> mda_load_traj systemX.xtc >> mda_rmsd >> >> >> Kind Regards, >> Mateusz >> >> >> On Mon, 19 Aug 2019 at 12:53, sunyeping via PyMOL-users < >> pymol-users@lists.sourceforge.net> wrote: >> Dear everyall, >> >> I loaded a molecular dynamics simulation trajectory (A.xtc) of 5000 >> frames and a reference structure (B.pdb) into pymol. I wish to get the rmsd >> value between each state of the MD simulation trajectory and the >> reference structure, but I don't know how. I can use the align command as: >> "align A, B", but this only gives one rmsd value. Could you tell me how to >> get the rmsd value between each state of the >> MD simulation trajectory and the reference structure? >> _______________________________________________ >> PyMOL-users mailing list >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> Unsubscribe: >> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe >> >> >> _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
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