diff --git a/science/gemmi/Makefile b/science/gemmi/Makefile
index 6a74bf21a478..18f0c34d2ae4 100644
--- a/science/gemmi/Makefile
+++ b/science/gemmi/Makefile
@@ -1,6 +1,6 @@
 PORTNAME=	gemmi
 DISTVERSIONPREFIX=	v
-DISTVERSION=	0.5.7
+DISTVERSION=	0.5.8
 CATEGORIES=	science # chemistry
 
 MAINTAINER=	yuri@FreeBSD.org
diff --git a/science/gemmi/distinfo b/science/gemmi/distinfo
index dc0844f594ee..ac2fb5d3d8f5 100644
--- a/science/gemmi/distinfo
+++ b/science/gemmi/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1664834213
-SHA256 (project-gemmi-gemmi-v0.5.7_GH0.tar.gz) = dede98c52920dac4a86dd77f38daa20bc8a1449ce16833815f5b563f4e8384a0
-SIZE (project-gemmi-gemmi-v0.5.7_GH0.tar.gz) = 1677695
+TIMESTAMP = 1671963605
+SHA256 (project-gemmi-gemmi-v0.5.8_GH0.tar.gz) = b67c8f79d85c4fd6766ce5b0418c79f4cb54a62d9091de6d0a7c20bb6060070e
+SIZE (project-gemmi-gemmi-v0.5.8_GH0.tar.gz) = 1695293
diff --git a/science/gemmi/pkg-plist b/science/gemmi/pkg-plist
index df1ef9df2ca2..369eb6e118c3 100644
--- a/science/gemmi/pkg-plist
+++ b/science/gemmi/pkg-plist
@@ -46,6 +46,7 @@ include/gemmi/merge.hpp
 include/gemmi/metadata.hpp
 include/gemmi/mmcif.hpp
 include/gemmi/mmcif_impl.hpp
+include/gemmi/mmdb.hpp
 include/gemmi/mmread.hpp
 include/gemmi/model.hpp
 include/gemmi/modify.hpp
@@ -220,7 +221,6 @@ include/gemmi/to_chemcomp.hpp
 include/gemmi/to_cif.hpp
 include/gemmi/to_json.hpp
 include/gemmi/to_mmcif.hpp
-include/gemmi/to_mmdb.hpp
 include/gemmi/to_pdb.hpp
 include/gemmi/topo.hpp
 include/gemmi/twin.hpp
diff --git a/science/py-gemmi/Makefile b/science/py-gemmi/Makefile
index 0e82aca8092b..3c1a4fb91ca0 100644
--- a/science/py-gemmi/Makefile
+++ b/science/py-gemmi/Makefile
@@ -1,6 +1,6 @@
 PORTNAME=	gemmi
 DISTVERSIONPREFIX=	v
-DISTVERSION=	0.5.7
+DISTVERSION=	0.5.8
 CATEGORIES=	science python
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
@@ -15,6 +15,7 @@ BUILD_DEPENDS=	${PYTHON_PKGNAMEPREFIX}pip>0:devel/py-pip@${PY_FLAVOR} \
 		pybind11>=2.6:devel/pybind11
 
 USES=		cmake compiler:c++17-lang python
+USE_PYTHON=	flavors
 
 USE_GITHUB=	yes
 GH_ACCOUNT=	project-gemmi
@@ -23,7 +24,10 @@ CMAKE_ON=	USE_PYTHON
 
 PLIST_FILES=	${PYTHON_SITELIBDIR}/gemmi${PYTHON_EXT_SUFFIX}.so
 
+TEST_ENV=	${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}
+TEST_WRKSRC=	${BUILD_WRKSRC}/tests
+
 do-test:
-	@cd ${WRKSRC} && ${PYTHON_CMD} -m unittest discover -v tests/
+	@cd ${WRKSRC} && ${SETENV} ${TEST_ENV} ${PYTHON_CMD} -m unittest discover -v tests/
 
 .include <bsd.port.mk>
diff --git a/science/py-gemmi/distinfo b/science/py-gemmi/distinfo
index dc0844f594ee..4a694c3cbfd2 100644
--- a/science/py-gemmi/distinfo
+++ b/science/py-gemmi/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1664834213
-SHA256 (project-gemmi-gemmi-v0.5.7_GH0.tar.gz) = dede98c52920dac4a86dd77f38daa20bc8a1449ce16833815f5b563f4e8384a0
-SIZE (project-gemmi-gemmi-v0.5.7_GH0.tar.gz) = 1677695
+TIMESTAMP = 1671964416
+SHA256 (project-gemmi-gemmi-v0.5.8_GH0.tar.gz) = b67c8f79d85c4fd6766ce5b0418c79f4cb54a62d9091de6d0a7c20bb6060070e
+SIZE (project-gemmi-gemmi-v0.5.8_GH0.tar.gz) = 1695293