How to make a PDB of the final frame of trajectory/universe

[Jason Held]

I am trying to save a PDB of the final frame of my trajectory/universe. I apologize if this has been asked before, but I don't see it in the tutorials or the Google group.

Try #1 - The tutorial code below saves the first frame, although, notably, the first frame isn't explicitly specified anywhere in the code:

from MDAnalysis.tests.datafiles import PDB, XTC

u = MDAnalysis.Universe(PDB, XTC)
protein = u.select_atoms("protein")

protein.write("test.pdb")

I'd expect that slicing out on the last frame would save the last frame:

# slice out final frame
finalFrame = u.trajectory[:-1]
protein = finalFrame.select_atoms("protein")
protein.write("test.pdb")

But I get the error:

AttributeError: 'FrameIteratorSliced' object has no attribute 'select_atoms'

Try #2A - This tutorial code saves the PDB for every step in the trajectory:

u = MDAnalysis.Universe(PDB, XTC)

protein = u.select_atoms("protein")

with MDAnalysis.Writer("test.pdb", protein.n_atoms) as W:

     for ts in u.trajectory: W.write(protein)

           W.write(protein)

But if I slice out just the final frame (like below) I get the same AttributeError above.

u = MDAnalysis.Universe(PDB, XTC)

#slice out final frame of trajectory
u = u.trajectory[:-1]

protein = u.select_atoms("protein")
with MDAnalysis.Writer("test.pdb", protein.n_atoms) as W:
    for ts in u.trajectory[-1]:
        W.write(protein)

Try # 2B - and if I slice out the final frame later, like below, it takes at least 1000X+ longer than saving every frame as a PDB and never seems to finish.

u = MDAnalysis.Universe(PDB, XTC)
protein = u.select_atoms("protein")
with MDAnalysis.Writer("test.pdb", protein.n_atoms) as W:
    for ts in u.trajectory[-1]:
        W.write(protein)

So, I am still not sure how to save the final frame as a PDB with MDAnalysis. Thanks for your help! -Jason

[Oliver Beckstein]

Hi Jason,

Welcome to the list!

Sorry I’m advance for the short reply. Others can maybe reply in detail and outline better the fundamental ideas.

Think of the trajectory as having a cursor that points to a specific frame (or the readhead on a tape or drive). Position the frame with

u.trajectory[frame]

That’s it to go to frame. Make frame=-1 to go to the last one. 

Then write the atoms with

u.atoms.write(“last.pdb”)

or 

protein.write(“protein_last.pdb”)

This should do it. 

Oliver

Am 10/15/22 um 12:14 schrieb Jason Held <4000...@gmail.com>:



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[Jason Held]

Thanks Oliver, but I think that is exactly what I am doing with

finalFrame = u.trajectory[:-1]

But I keep getting the error:

AttributeError: 'FrameIteratorSliced' object has no attribute 'select_atoms'.

[Jason Held]

And if i leave out the colon and do:

finalFrame = u.trajectory[-1]

I get a different error when I try to write the PDB:

AttributeError: Timestep object has no attribute 'select_atoms'

[Marcelo Depólo Polêto]

Hi Jason,

Try something like this:

import MDAnalysis

from MDAnalysis.tests.datafiles import PDB, XTC

u = MDAnalysis.Universe(PDB, XTC)

# move universe to last frame

u.trajectory[-1]
protein = u.select_atoms("

protein")
protein.write("test.pdb")

Notice that you don't need to slice or loop over the trajectory like you were trying to do, nor assign a new variable. As Oliver said, by doing "u.trajectory[-1]" you are really defining which frame you are at. It does not return a frame for you to select over once again, you are just updating the entire universe to be at the defined frame. If you need to go back to the first frame for some reason, you can do "u.trajectory[0]".

Best,

--

Marcelo D. Polêto, Ph.D.

Postdoctoral Associate

Office: 106B Engel Hall

Department of Biochemistry
Virginia Tech

340 West Campus Dr.

Blacksburg, VA 24061

gender pronouns: he/him/his

[Jason Held]

Thank you very much Marcelo, that works perfectly.

Jason