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Mention unresolved residues in template documentation

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Fixes https://github.com/google-deepmind/alphafold3/issues/373.

PiperOrigin-RevId: 747342015
Change-Id: I09586c5d00cda84db18764cdc735b057f2b4d749
This commit is contained in:
Augustin Zidek
2025-04-14 03:39:37 -07:00
committed by Copybara-Service
parent 5fbae81a9e
commit 7a4a2f7142
1 changed files with 11 additions and 1 deletions
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docs/input.md
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@ -551,7 +551,9 @@ The fields specify the following:
* `queryIndices: list[int]`: O-based indices in the query sequence, defining
the mapping from query residues to template residues.
* `templateIndices: list[int]`: O-based indices in the template sequence,
defining the mapping from query residues to template residues.
specifying the mapping from query residues to template residues defined in
the mmCIF file. Note that unresolved mmCIF residues must be taken into
account when specifying template indices.
A template is specified as an mmCIF string containing a single chain with the
structural template together with a 0-based mapping that maps query residue
@ -564,6 +566,14 @@ you would specify the two indices lists as:
"templateIndices": [0, 2, 5, 6]
```
Note that mmCIFs can have residues with missing atom coordinates (present in
residue tables but missing in the `_atom_site` table) – these must be taken into
account when specifying template indices. E.g. to align residues 4–7 in a
template with unresolved residues 1, 2, 3 and resolved residues 4, 5, 6, 7, you
need to set the template indices to 3, 4, 5, 6 (since 0-based indexing is used).
An example of a protein with unresolved residues 1–20 can be found here:
https://www.rcsb.org/structure/8UXY.
You can provide multiple structural templates. Note that if an mmCIF containing
more than one chain is provided, you will get an error since it is not possible
to determine which of the chains should be used as the template.