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

[sunyeping <sun...@al...>]

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 <iko...@gm...>
Sent At:2019 Aug. 20 (Tue.) 00:29
To:Mateusz Bieniek <bie...@gm...>
Cc:孙业平 <sun...@al...>; pymol-users <pym...@li...>
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 <bie...@gm...> 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 <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 


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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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