Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Rename ihm_ensemble_info category #105

Open
brindakv opened this issue Jun 19, 2024 · 3 comments
Open

Rename ihm_ensemble_info category #105

brindakv opened this issue Jun 19, 2024 · 3 comments
Assignees

Comments

@brindakv
Copy link
Collaborator

brindakv commented Jun 19, 2024

The term ensemble is used differently by different communities.

In IHMCIF, we want to consider these as a "collection of models" that individually satisfy the input data within a threshold rather than as ensembles.

Consider renaming ihm_ensemble_info accordingly and update category and item descriptions to reflect the change.

List of released entries with ihm_ensemble_info populated (June 19, 2024):

PDBDEV_00000001
PDBDEV_00000002
PDBDEV_00000003
PDBDEV_00000010
PDBDEV_00000011
PDBDEV_00000012
PDBDEV_00000013
PDBDEV_00000017
PDBDEV_00000018
PDBDEV_00000019
PDBDEV_00000020
PDBDEV_00000021
PDBDEV_00000022
PDBDEV_00000023
PDBDEV_00000025
PDBDEV_00000026
PDBDEV_00000034
PDBDEV_00000035
PDBDEV_00000037
PDBDEV_00000038
PDBDEV_00000041
PDBDEV_00000044
PDBDEV_00000049
PDBDEV_00000050
PDBDEV_00000065
PDBDEV_00000071
PDBDEV_00000072
PDBDEV_00000073
PDBDEV_00000074
PDBDEV_00000077
PDBDEV_00000078
PDBDEV_00000079
PDBDEV_00000081
PDBDEV_00000082
PDBDEV_00000088
PDBDEV_00000090
PDBDEV_00000091
PDBDEV_00000097
PDBDEV_00000112
PDBDEV_00000152
PDBDEV_00000154
PDBDEV_00000155
PDBDEV_00000164
PDBDEV_00000211
PDBDEV_00000213
PDBDEV_00000222
PDBDEV_00000223
PDBDEV_00000224
PDBDEV_00000225
PDBDEV_00000226
PDBDEV_00000227
PDBDEV_00000228
PDBDEV_00000229
@brindakv brindakv self-assigned this Jun 19, 2024
@aozalevsky
Copy link
Collaborator

@brindakv

individually satisfy the input data within a threshold rather than as ensembles.

this definition contradicts the current model for crosslinking-MS data. we've discussed and agreed on:

A restraint group is considered satisfied, if the condition was met in at least 
one model of the model group/ensemble. 

if it's simply a group of models, shouldn't they be just left as a model group?

@aozalevsky
Copy link
Collaborator

as Brinda pointed out, in the IHMCIF paper we wrote:

Second, a model can be multi-state. A set of multiple states can be used to describe a system that exists in a mixture of multiple structural and/or compositional states that collectively satisfy the input information. For example, a sample of enzyme molecules in solution is structurally heterogeneous when it exists in an equilibrium between open and closed states; it is compositionally heterogeneous when it contains enzyme molecules both with and without a ligand.

However, multi-state treatment is an explicit choice in the modeling process. One can model the system as a single state and get a collection of structural models that collectively describe the system (like an IDR ensemble).

Also, in the IHMCIF paper we don't mention ensembles at all.

@jaredsagendorf do you have a good definition for the ensemble?

@aozalevsky
Copy link
Collaborator

Also, I just realized that PDBDEV_00000008 is missing from the list. Shouldn't it be a canonical example for the ensemble, where each model has a relatively poor fit to the data but the collection as a whole fits the data well?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants