diff --git a/projects/dark-matter-metagenomics/translate2modelcif.py b/projects/dark-matter-metagenomics/translate2modelcif.py
index d3d59886c1f4126cfc7eee104336a85a3e0a2833..955df92a8c43e78040f8a2c07e459f7492fba558 100644
--- a/projects/dark-matter-metagenomics/translate2modelcif.py
+++ b/projects/dark-matter-metagenomics/translate2modelcif.py
@@ -1099,10 +1099,15 @@ def _translate2modelcif_single(
     print(f" ({timer()-pstart:.2f}s)")
 
     # save ModelCIF
-    add_aln = (mdl_rank == 1 or opts.all_msa)
     assoc_files = _store_as_modelcif(
-        mdlcf_json, ost_ent, opts.out_dir, mdl_id, opts.compress, add_pae,
-        add_aln, add_files
+        mdlcf_json,
+        ost_ent,
+        opts.out_dir,
+        mdl_id,
+        opts.compress and mdl_rank == 1,
+        add_pae,
+        opts.all_msa or mdl_rank == 1,
+        add_files
     )
 
     # check if result can be read and has expected seq.