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

Atomic multi-state structures break some of the struct_group categories in the PDBx/mmCIF dictionary #70

Open
brindakv opened this issue Aug 10, 2018 · 4 comments
Assignees

Comments

@brindakv
Copy link
Collaborator

Although the atom_site category has been extended in the IHM-dictionary to accommodate compositionally different multi-state structures, the struct_group categories still assume uniform composition across models (e.g. struct_conf, struct_conn). Data categories that are derived from the coordinates in the atom_site category and assume uniform composition will therefore break in case of atomic multi-state structures. This could be addressed either in the PDBx/mmCIF dictionary or in the IHM-dictionary extension.

@brindakv brindakv self-assigned this Aug 10, 2018
@benmwebb
Copy link
Contributor

Perhaps I don't understand the issue here, but as far as I can see both struct_conf and struct_conn point to one or more pairs of asym_id/seq_id. I haven't seen any multi-state models (atomic or coarse-grained) where for a given asym_id composition is so different that a given seq_id refers to a different part of the structure in two different states. Why would it? If the sequence is different it would have to be a different entity, and thus a distinct asym_id.

@tomgoddard
Copy link
Collaborator

tomgoddard commented Aug 15, 2018 via email

@brindakv
Copy link
Collaborator Author

The problem is that struct-conf, struct_conn and some of the other struct_group categories do not have a data item pointing to the _atom_site.pdbx_PDB_model_num. Therefore, they are only populated for the first model in an ensemble. The assumption of a homogenous ensemble is therefore implicit.

@benmwebb
Copy link
Contributor

They don't need to reference a model number, because a given seq_id/asym_id pair should be valid for all models. I'd assume if you have one model with only chain A in it, and another model with only chain B, your struct_conf would contain entries for both asym_id=A and asym_id=B.

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

3 participants