diff --git a/src/mol-io/writer/cif/encoder.ts b/src/mol-io/writer/cif/encoder.ts
index 670a8c78fe611c2ad582a62ddadb842c1cd27f91..9c0b8a743f3377edd90527b13977b95165fbfe03 100644
--- a/src/mol-io/writer/cif/encoder.ts
+++ b/src/mol-io/writer/cif/encoder.ts
@@ -139,6 +139,7 @@ export namespace Category {
         const field_blacklist: string[] = [];
 
         for (let d of directives.split(/[\r\n]+/)) {
+            d = d.trim();
             // allow for empty lines in config
             if (d.length === 0) continue;
             // let ! denote blacklisted entries