Fixed documentation according to comments.

README.md

@@ -174,10 +174,13 @@ where `data` is the same directory as in the previous step. If `jackhmmer`,
 `/usr/bin`, their `binary_path` command-line arguments can be dropped.
 If you've already computed alignments for the query, you have the option to 
 skip the expensive alignment computation here with 
-`--use_precomputed_alignments`. If you wish to use a specific template as input,
+`--use_precomputed_alignments`.
+
+If you wish to use **custom templates** as input,
 you can use the argument `--use_custom_template`, which then will read all .cif
 files in `template_mmcif_dir`. Make sure the chains of interest have the identifier _A_
-and have the same length as the input sequence.  
+and have the same length as the input sequence. The same templates will be read for
+all sequences that are passed for inference.
 
 `--openfold_checkpoint_path` or `--jax_param_path` accept comma-delineated lists
 of .pt/DeepSpeed OpenFold checkpoints and AlphaFold's .npz JAX parameter files, 

openfold/data/templates.py

@@ -962,6 +962,7 @@ def get_custom_template_features(
     else:
         logging.error("Custom template path %s does not exist", mmcif_path)
         raise ValueError(f"Custom template path {mmcif_path} does not exist")
+    
     warnings = []
     template_features = dict()
     for template_path in template_paths:
@@ -973,7 +974,6 @@ def get_custom_template_features(
         mmcif_parse_result = mmcif_parsing.parse(
             file_id=pdb_id, mmcif_string=cif_string
         )
-        # chain_id defaults to A, should be changed?
         template_sequence = mmcif_parse_result.mmcif_object.chain_to_seqres[chain_id]
         mapping = {x: x for x, _ in enumerate(template_sequence)}
 
@@ -1200,7 +1200,7 @@ class HhsearchHitFeaturizer(TemplateHitFeaturizer):
 
 class CustomHitFeaturizer(TemplateHitFeaturizer):
     """Featurizer for templates given in folder.
-     Chain of interest has to be chain A and of same residue size as input sequence."""
+     Chain of interest has to be chain A and of same sequence length as input sequence."""
     def get_templates(
         self,
         query_sequence: str,