VMD-L Mailing List

From: Evelyn Maizels (evelyn.maizels_at_gmail.com)
Date: Fri Feb 18 2022 - 10:14:25 CST

Looks like the software for handling the listserve converts the links -
suggest that readers interested in the announcement go directly to the RSCB
PDB web page and look for announcement - it is listed under "features and
announcements"

here is the text of the announcement
Distributing PDBx/mmCIF-Formatted Assembly Files02/08

Starting May 3, 2022, the PDB archive will distribute assembly files in
PDBx/mmCIF format, allowing direct access and visualization of the curated
assemblies for all PDB entries.

Currently, PDBx/mmCIF formatted assembly files are provided for structures
that are non-PDB compliant, however the coordinates use model numbers to
differentiate alternate symmetry copies of PDB chain IDs. This method is
not ideal, nor necessary, for the current archive PDBx/mmCIF format and has
lead to limited use of these files in community software tools. In response
to this issue and recommendations by the wwPDB advisory committee, we are
implementing updated, standardized practices for generation of assembly
files for all PDB entries.

These updated PDBx/mmCIF format assembly files will have improved
organization of assembly data to support usage by the community. These
files will include all symmetry generated copies of each chain within a
single model, with distinct chain IDs (_atom_site.auth_asym_id and
_atom_site.label_asym_id) assigned to each. Generation of distinct chain
IDs in assembly files are based upon the following rules:

   - The applied index of the symmetry operator [link removed - see
   original at RSCB] will be appended to the original chain ID separated by a
   dash (e.g., A-2, A-3, etc.)
   - If there are more than one type of symmetry operators applied to
   generate symmetry copy, a dash sign will be used between two operators
   (e.g., A-12-60, A-60-88, etc.)

In addition, entity ID and chain ID mapping categories will be provided:
_pdbx_entity_remapping and _pdbx_chain_remapping.

A new directory [link removed- see original at RSCB] will be created for
the distribution of these updated assembly files. The directory containing
the existing assembly mmCIF files for large entries will be removed [link
removed- see original at RSCB]

wwPDB asks all PDB users and software developers to review code and address
any limitations related to PDB assemblies. Sample files are made available
for testing purposes and to support community adoption at [link removed-
see original at RSCB]

If you plan to use these assembly files for graphical viewing, check if
your visualization software (e.g., PyMol, ChimeraX, etc.) supports
instantiation of assemblies directly from atomic coordinate files
(_struct_assembly related categories), you do so for improved efficiency.

For any further information please email [email address removed- see
original at RSCB]

   - Chain IDs of the original chains from the atomic coordinate file will
   be retained (e.g., A)
   - Assign unique chain ID (atom_site.label_asym_id and
   atom_site.auth_asym_id) for each symmetry copy within a single model. Rules
   of chain ID assignments:

Evelyn Maizels

Evelyn Maizels MD PhD MS Biomedical Visualization
Adjunct Clinical Associate Professor, Biomedical Visualization Program,
BHIS Dept, College of Applied Health Sciences, University of Illinois at
Chicago

On Thu, Feb 17, 2022 at 7:54 PM Evelyn Maizels <evelyn.maizels_at_gmail.com>
wrote:

> RSCB PDB announced an upcoming formatting change for assembly files in
> PdbX/mmCIF format
> https://urldefense.com/v3/__https://www.rcsb.org/news/feature/61f839908f40f9265109d399__;!!DZ3fjg!vEPkHRpSxpY9V231mLlWxVrdGWGUDYnDdeL_EpyZ3LzGtR3Q7idYPR3k6WPp8R81YQ$
> <https://urldefense.com/v3/__https://www.rcsb.org/news/feature/61f839908f40f9265109d399__;!!DZ3fjg!qjy8zGxOSzvltbAdeAAJ0pLX-GY9MfBzmseNUzoKUugGDMun4bdqaGzTwiyUnnpS5g$>
> f
> iles for testing are made available through github
> https://urldefense.com/v3/__https://github.com/wwpdb/assembly-mmcif-examples__;!!DZ3fjg!vEPkHRpSxpY9V231mLlWxVrdGWGUDYnDdeL_EpyZ3LzGtR3Q7idYPR3k6WOo33ZciQ$
> <https://urldefense.com/v3/__https://github.com/wwpdb/assembly-mmcif-examples__;!!DZ3fjg!qjy8zGxOSzvltbAdeAAJ0pLX-GY9MfBzmseNUzoKUugGDMun4bdqaGzTwizr2Zcq0g$>
>
> I tested one of the files (7lv2) and got 'unable to parse' error for
> selection method for chain with the new-style chain naming format that RSCB
> PDB is putting forward. The new-style chain naming includes hyphens and
> numbers in the chain names.
> Will these assembly files be usable in VMD?
>
> Evelyn Maizels MD PhD MS Biomedical Visualization
> Adjunct Clinical Associate Professor, Biomedical Visualization Program,
> BHIS Dept, College of Applied Health Sciences, University of Illinois at
> Chicago
>