Hi Yeping, The return value of cmd.align() is documented here:
https://pymolwiki.org/index.php/Align#PyMOL_API Cheers, Thomas > On Aug 20, 2019, at 5:15 AM, sunyeping via PyMOL-users > <pymol-users@lists.sourceforge.net> wrote: > > Hello Mat, > > Thank you for your reply. > I followed your codes in the second line and get a series of output, which > look like: > > (9.949092864990234, 267, 0, 9.949092864990234, 267, 420.0, 226) > > I guess the first and the fourth float numbers are the rmsd, but what are > other numbers in the line? > > Best regards. > > Yeping > ------------------------------------------------------------------ > From:Istvan Kolossvary <ikolos...@gmail.com> > Sent At:2019 Aug. 20 (Tue.) 00:29 > To:Mateusz Bieniek <bieniek...@gmail.com> > Cc:孙业平 <sunyep...@aliyun.com>; 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? > > 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 > > _______________________________________________ > 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 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. _______________________________________________ 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
