Producing a colored dot surface using mdanalysis hole over a trajectory

[Yogesh Sharma]

Hi everyone

 I was using mdanalysis hole tool for pore analysis and i found out that In tutorial section visualizing a pore over a trajectory is not mentioned.

 I guess it should not be difficult once we have hole.sph  file. I a, not good with python. Can anyone suggest something? why cant we visualize pore throughout the trajectory by writing pdb files for every frame?

[Lily Wang]

There’s not currently a very straightforward solution to this. You could try the code in this branch. For me the following works:

import MDAnalysis as mda

from MDAnalysis.tests.datafiles import MULTIPDB_HOLE

from MDAnalysis.analysis import hole

h = hole.HOLEtraj(u, executable='~/hole2/exe/hole’)

h.run()

h.create_vmd_surface(filename=‘hole.vmd’, dotden=15)

In VMD (the filename is the long version of MULTIPDB_HOLE):

vmd 1grm_elNemo_mode7.pdb

In Extensions > Tk Console

source hole.vmd

At this point nothing will be drawn, but hopefully when you update the frame the pore will appear. It might be very slow.

Cheers,

Lily

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[Yogesh Sharma]

hi,

 thanks fort looking into issue.

 but i am getting an error stating there is  no function create_vmd_surface in holetraj

do i have to add some changes here?

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[Lily Wang]

You need to download the source from that particular branch and compile it. e.g. (if you have git and conda)

git clone https://github.com/lilyminium/mdanalysis.git

cd mdanalysis/

git checkout hole

conda create --name mda-hole

conda activate mda-hole

conda install numpy cython

cd package/

pip install -e .

Alternatively you can import HOLEtraj from the attached (untested) file.

Cheers,

Lily

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[Yogesh Sharma]

hi 

can we get name of residues involved at a particular hole restrictions. iteratively over trajectory?

hole just gives us coordinates but how to trace it back to residue in real time. for instance to observe variation at residue involvement.

[Lily Wang]

Dear Yogesh,

We have now moved to GitHub Discussions — could you please ask your question there? While we are leaving the mailing lists open for the time being to resolve existing discussions, this thread is three years old and it would be best to move discussion to our new forum. Thank you very much and hope you had a happy holidays!

Cheers,

Lily

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