Re: [PyMOL] How to calculate rmsd between each state of a MD simulation trajectory and a reference structure?

[Mateusz B. <bie...@gm...>]

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 <sun...@al...> 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 <bie...@gm...>
> Sent At:2019 Aug. 19 (Mon.) 20:32
> To:孙业平 <sun...@al...>
> Cc:pymol-users <pym...@li...>
> 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 <
> pym...@li...> 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?
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