Comments (3)
Dear Tianming,
I recommend featurizing your data first. You can of course flatten it (reshape it to (n_frames, n_atoms * 3)
), this however usually yields poor results in terms of VAMP score. You can think about pairwise distances, VAMPNets, SASA and/or your biochemical intuition to define feature functions. These can be stacked in the second dimension and fed directly into TICA (or implemented using the observable_transform argument).
Cheers
Moritz
from deeptime.
Dear Tianming,
I recommend featurizing your data first. You can of course flatten it (reshape it to
(n_frames, n_atoms * 3)
), this however usually yields poor results in terms of VAMP score. You can think about pairwise distances, VAMPNets, SASA and/or your biochemical intuition to define feature functions. These can be stacked in the second dimension and fed directly into TICA (or implemented using the observable_transform argument).Cheers Moritz
Hi Moritz,
Thanks a lot for your response. I do tried to use dihedral angles as features, but in that way do you know how I can plot the vectors on VMD? To see how the protein will move along each eigenvector?
Best,
Tianming
from deeptime.
Hi, sorry I completely forgot to follow up. I am not sure if this is possible in VMD at all. What you can do is draw representative structures of metastable states and along the transition from your trajectories based on the state assignment in the clustering. That should give you an idea of what the motion that is described by the eigenfunctions looks like.
from deeptime.
Related Issues (20)
- Cannot install deeptime. I have Python 3.10 (Windows 10) and trying to install using Visual Studio 2022 HOT 12
- Error when installing from local repo via pip HOT 4
- TICA fit-once transform-many HOT 6
- Automate generating bdist wheels HOT 1
- Allowing weights for VAMP dimensionality reduction HOT 6
- Error importing deeptime with scikit-learn 1.2.0 HOT 4
- Handling parallel simulations HOT 1
- Implied timescales from deeptime.decomposition.TICA HOT 2
- [Bug] At least one of the given states is not contained in this model HOT 2
- VAMPnet gives highly fluctuating score results HOT 1
- Bayesian Markov models give different MFPT
- How to compute any actual quantity of the coarse-grained kinetics with employing the fuzzy memberships? HOT 7
- Installation without conda and pip HOT 3
- Which version of VAMPNets is there? HOT 1
- deeptime cannot be installed on Mac computers with Apple Silicon and Python 3.12.0. HOT 4
- Does one need identical features to compare between related systems? HOT 4
- Example/tutorial for dealing with MD trajectories HOT 1
- Applying TICA to ragged feature vectors HOT 2
- Cross Validation score for MaximumLikelihoodMSMs and BayesianMSMs HOT 2
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