diff --git a/image_analysis/CMakeLists.txt b/image_analysis/CMakeLists.txt
index 517305c58..098307e75 100644
--- a/image_analysis/CMakeLists.txt
+++ b/image_analysis/CMakeLists.txt
@@ -129,5 +129,6 @@ ADD_SUBDIRECTORY(scale_merge)
 ADD_SUBDIRECTORY(image_preprocessing)
 ADD_SUBDIRECTORY(azint)
 ADD_SUBDIRECTORY(roi)
+ADD_SUBDIRECTORY(structure_refinement)
 
-TARGET_LINK_LIBRARIES(JFJochImageAnalysis JFJochAzIntEngine JFJochROIIntegration JFJochImagePreprocessing JFJochBraggPrediction JFJochBraggIntegration JFJochLatticeSearch JFJochIndexing JFJochSpotFinding JFJochCommon JFJochGeomRefinement JFJochScaleMerge gemmi)
+TARGET_LINK_LIBRARIES(JFJochImageAnalysis JFJochAzIntEngine JFJochROIIntegration JFJochImagePreprocessing JFJochBraggPrediction JFJochBraggIntegration JFJochLatticeSearch JFJochIndexing JFJochSpotFinding JFJochCommon JFJochGeomRefinement JFJochScaleMerge JFJochStructureRefinement gemmi)
diff --git a/image_analysis/structure_refinement/CMakeLists.txt b/image_analysis/structure_refinement/CMakeLists.txt
new file mode 100644
index 000000000..34c5ac3e1
--- /dev/null
+++ b/image_analysis/structure_refinement/CMakeLists.txt
@@ -0,0 +1,16 @@
+ADD_LIBRARY(JFJochStructureRefinement STATIC
+        ModelFFT.cpp ModelFFT.h
+        ModelGrid.cpp ModelGrid.h
+        ModelScaling.cpp ModelScaling.h
+        ModelValidation.cpp ModelValidation.h
+        RigidBodyRefine.cpp RigidBodyRefine.h
+        $<$<BOOL:${JFJOCH_CUDA_AVAILABLE}>:RigidBodyGPU.cpp>
+        $<$<BOOL:${JFJOCH_CUDA_AVAILABLE}>:RigidBodyGPU.cu>
+        RigidBodyGPU.h RigidBodyGPUEngine.h
+        $<$<BOOL:${JFJOCH_CUDA_AVAILABLE}>:ModelMaskGPU.cu> ModelMaskGPU.h
+        $<$<BOOL:${JFJOCH_CUDA_AVAILABLE}>:ModelScaleGPU.cu> ModelScaleGPU.h
+        SigmaA.cpp SigmaA.h)
+
+# JFJochIndexing for CUDAMemHelpers.h and, under CUDA, to put cuFFT (RigidBodyGPU.cu) after these
+# objects on the link line.
+TARGET_LINK_LIBRARIES(JFJochStructureRefinement JFJochScaleMerge JFJochIndexing JFJochCommon gemmi fftw3f)
diff --git a/rugnux/ModelFFT.cpp b/image_analysis/structure_refinement/ModelFFT.cpp
similarity index 99%
rename from rugnux/ModelFFT.cpp
rename to image_analysis/structure_refinement/ModelFFT.cpp
index a70c4fb88..ff5c43ef6 100644
--- a/rugnux/ModelFFT.cpp
+++ b/image_analysis/structure_refinement/ModelFFT.cpp
@@ -14,7 +14,7 @@
 
 #include "gemmi/fail.hpp"
 
-#include "../common/FFTWPlannerLock.h"
+#include "../../common/FFTWPlannerLock.h"
 
 namespace {
 
diff --git a/rugnux/ModelFFT.h b/image_analysis/structure_refinement/ModelFFT.h
similarity index 100%
rename from rugnux/ModelFFT.h
rename to image_analysis/structure_refinement/ModelFFT.h
diff --git a/rugnux/ModelGrid.cpp b/image_analysis/structure_refinement/ModelGrid.cpp
similarity index 99%
rename from rugnux/ModelGrid.cpp
rename to image_analysis/structure_refinement/ModelGrid.cpp
index 65eb64c39..9323a2cfe 100644
--- a/rugnux/ModelGrid.cpp
+++ b/image_analysis/structure_refinement/ModelGrid.cpp
@@ -10,7 +10,7 @@
 
 #include "gemmi/solmask.hpp"   // SolventMasker
 
-#include "../common/ParallelFor.h"
+#include "../../common/ParallelFor.h"
 
 namespace {
 
diff --git a/rugnux/ModelGrid.h b/image_analysis/structure_refinement/ModelGrid.h
similarity index 100%
rename from rugnux/ModelGrid.h
rename to image_analysis/structure_refinement/ModelGrid.h
diff --git a/rugnux/ModelMaskGPU.cu b/image_analysis/structure_refinement/ModelMaskGPU.cu
similarity index 99%
rename from rugnux/ModelMaskGPU.cu
rename to image_analysis/structure_refinement/ModelMaskGPU.cu
index e1cf91466..5a2db4b21 100644
--- a/rugnux/ModelMaskGPU.cu
+++ b/image_analysis/structure_refinement/ModelMaskGPU.cu
@@ -7,7 +7,7 @@
 #include <cstdint>
 #include <string>
 
-#include "../common/JFJochException.h"
+#include "../../common/JFJochException.h"
 
 namespace {
 
diff --git a/rugnux/ModelMaskGPU.h b/image_analysis/structure_refinement/ModelMaskGPU.h
similarity index 98%
rename from rugnux/ModelMaskGPU.h
rename to image_analysis/structure_refinement/ModelMaskGPU.h
index c7210d9a8..9f821bfb5 100644
--- a/rugnux/ModelMaskGPU.h
+++ b/image_analysis/structure_refinement/ModelMaskGPU.h
@@ -8,7 +8,7 @@
 
 #include <cuda_runtime.h>
 
-#include "../image_analysis/indexing/CUDAMemHelpers.h"
+#include "../indexing/CUDAMemHelpers.h"
 
 // The bulk-solvent mask of PutMaskOnGrid() (ModelGrid.h), i.e. gemmi's
 // SolventMasker(AtomicRadiiSet::Refmac).put_mask_on_grid(), on the GPU. gemmi masks the atoms and then
diff --git a/rugnux/ModelScaleGPU.cu b/image_analysis/structure_refinement/ModelScaleGPU.cu
similarity index 99%
rename from rugnux/ModelScaleGPU.cu
rename to image_analysis/structure_refinement/ModelScaleGPU.cu
index 13ba604ec..c5f7d054b 100644
--- a/rugnux/ModelScaleGPU.cu
+++ b/image_analysis/structure_refinement/ModelScaleGPU.cu
@@ -9,7 +9,7 @@
 #include <string>
 #include <utility>
 
-#include "../common/JFJochException.h"
+#include "../../common/JFJochException.h"
 #include "RigidBodyGPUEngine.h"   // ModelScaleGPUTooFewReflections
 
 namespace {
diff --git a/rugnux/ModelScaleGPU.h b/image_analysis/structure_refinement/ModelScaleGPU.h
similarity index 98%
rename from rugnux/ModelScaleGPU.h
rename to image_analysis/structure_refinement/ModelScaleGPU.h
index a850e7e06..f0f4bd7bc 100644
--- a/rugnux/ModelScaleGPU.h
+++ b/image_analysis/structure_refinement/ModelScaleGPU.h
@@ -9,7 +9,7 @@
 
 #include <cuda_runtime.h>
 
-#include "../image_analysis/indexing/CUDAMemHelpers.h"
+#include "../indexing/CUDAMemHelpers.h"
 
 // The rigid body's scale fit on the GPU: what RigidBodyTarget::Residuals does with a gemmi
 // Scaling<float> (use_solvent, k_sol and b_sol fixed) - fit_isotropic_b_approximately() followed by
diff --git a/rugnux/ModelScaling.cpp b/image_analysis/structure_refinement/ModelScaling.cpp
similarity index 99%
rename from rugnux/ModelScaling.cpp
rename to image_analysis/structure_refinement/ModelScaling.cpp
index e0c64e626..4fa5aee59 100644
--- a/rugnux/ModelScaling.cpp
+++ b/image_analysis/structure_refinement/ModelScaling.cpp
@@ -7,7 +7,7 @@
 #include <cmath>
 #include <vector>
 
-#include "../common/ParallelFor.h"
+#include "../../common/ParallelFor.h"
 
 namespace {
 
diff --git a/rugnux/ModelScaling.h b/image_analysis/structure_refinement/ModelScaling.h
similarity index 100%
rename from rugnux/ModelScaling.h
rename to image_analysis/structure_refinement/ModelScaling.h
diff --git a/rugnux/ModelValidation.cpp b/image_analysis/structure_refinement/ModelValidation.cpp
similarity index 99%
rename from rugnux/ModelValidation.cpp
rename to image_analysis/structure_refinement/ModelValidation.cpp
index c5b370888..f7cf29601 100644
--- a/rugnux/ModelValidation.cpp
+++ b/image_analysis/structure_refinement/ModelValidation.cpp
@@ -29,17 +29,17 @@
 #include <gemmi/ccp4.hpp>      // Ccp4 map I/O
 #include <gemmi/mtz.hpp>       // Mtz (map-coefficient output)
 
-#include "../common/CorrelationCoefficient.h"
-#include "../common/JFJochMath.h"   // PI (M_PI is not standard, and MSVC does not define it)
-#include "../common/Logger.h"
-#include "../image_analysis/scale_merge/ReindexAmbiguity.h"   // ReindexReflections
-#include "../image_analysis/scale_merge/CrystalSetting.h"     // CellMappingOperators
+#include "../../common/CorrelationCoefficient.h"
+#include "../../common/JFJochMath.h"   // PI (M_PI is not standard, and MSVC does not define it)
+#include "../../common/Logger.h"
+#include "../scale_merge/ReindexAmbiguity.h"   // ReindexReflections
+#include "../scale_merge/CrystalSetting.h"     // CellMappingOperators
 #include "ModelFFT.h"
 #include "RigidBodyRefine.h"
 #include "SigmaA.h"
 #ifdef JFJOCH_USE_CUDA
 #include "RigidBodyGPU.h"
-#include "../common/CUDAWrapper.h"
+#include "../../common/CUDAWrapper.h"
 #endif
 
 namespace {
diff --git a/rugnux/ModelValidation.h b/image_analysis/structure_refinement/ModelValidation.h
similarity index 99%
rename from rugnux/ModelValidation.h
rename to image_analysis/structure_refinement/ModelValidation.h
index 1198ccaa2..47bffdd26 100644
--- a/rugnux/ModelValidation.h
+++ b/image_analysis/structure_refinement/ModelValidation.h
@@ -11,8 +11,8 @@
 
 #include "gemmi/symmetry.hpp"
 
-#include "../common/Reflection.h"   // MergedReflection
-#include "../common/UnitCell.h"
+#include "../../common/Reflection.h"   // MergedReflection
+#include "../../common/UnitCell.h"
 
 class Logger;
 namespace gemmi { struct Structure; }
@@ -185,7 +185,7 @@ struct ModelValidationResult {
     // The model as it was scored: re-fractionalized into the data cell and moved by the rigid-body
     // step, everything else exactly as it was read. Null where the validation did not run. The frame
     // it is written in is only settled by AdoptModelFrame below, so it is the caller that puts it on
-    // disk, with WritePlacedModel (WriteModel.h).
+    // disk, with WritePlacedModel (writer/WriteModel.h).
     std::shared_ptr<gemmi::Structure> placed_model;
 };
 
diff --git a/rugnux/RigidBodyGPU.cpp b/image_analysis/structure_refinement/RigidBodyGPU.cpp
similarity index 99%
rename from rugnux/RigidBodyGPU.cpp
rename to image_analysis/structure_refinement/RigidBodyGPU.cpp
index b961107c7..e6d4cddcc 100644
--- a/rugnux/RigidBodyGPU.cpp
+++ b/image_analysis/structure_refinement/RigidBodyGPU.cpp
@@ -16,9 +16,9 @@
 
 #include "ModelScaling.h"           // FitModelScale
 #include "RigidBodyGPUEngine.h"
-#include "../common/CUDAWrapper.h"
-#include "../common/JFJochException.h"
-#include "../common/Logger.h"
+#include "../../common/CUDAWrapper.h"
+#include "../../common/JFJochException.h"
+#include "../../common/Logger.h"
 
 namespace {
 
diff --git a/rugnux/RigidBodyGPU.cu b/image_analysis/structure_refinement/RigidBodyGPU.cu
similarity index 99%
rename from rugnux/RigidBodyGPU.cu
rename to image_analysis/structure_refinement/RigidBodyGPU.cu
index 695231527..60ee20193 100644
--- a/rugnux/RigidBodyGPU.cu
+++ b/image_analysis/structure_refinement/RigidBodyGPU.cu
@@ -13,8 +13,8 @@
 
 #include "ModelMaskGPU.h"
 #include "ModelScaleGPU.h"
-#include "../common/JFJochException.h"
-#include "../image_analysis/indexing/CUDAMemHelpers.h"
+#include "../../common/JFJochException.h"
+#include "../indexing/CUDAMemHelpers.h"
 
 // Every kernel below is deterministic: nothing is summed with a floating-point atomic, each grid point
 // adds its atoms in model order, and every reduction runs in a fixed order. The same placement gives the
diff --git a/rugnux/RigidBodyGPU.h b/image_analysis/structure_refinement/RigidBodyGPU.h
similarity index 100%
rename from rugnux/RigidBodyGPU.h
rename to image_analysis/structure_refinement/RigidBodyGPU.h
diff --git a/rugnux/RigidBodyGPUEngine.h b/image_analysis/structure_refinement/RigidBodyGPUEngine.h
similarity index 100%
rename from rugnux/RigidBodyGPUEngine.h
rename to image_analysis/structure_refinement/RigidBodyGPUEngine.h
diff --git a/rugnux/RigidBodyRefine.cpp b/image_analysis/structure_refinement/RigidBodyRefine.cpp
similarity index 99%
rename from rugnux/RigidBodyRefine.cpp
rename to image_analysis/structure_refinement/RigidBodyRefine.cpp
index 16535e169..dc9e71b2d 100644
--- a/rugnux/RigidBodyRefine.cpp
+++ b/image_analysis/structure_refinement/RigidBodyRefine.cpp
@@ -26,9 +26,9 @@
 #ifdef JFJOCH_USE_CUDA
 #include "RigidBodyGPU.h"           // RigidBodyTargetGPU
 #endif
-#include "../common/JFJochMath.h"   // PI
-#include "../common/ParallelFor.h"
-#include "../common/Logger.h"
+#include "../../common/JFJochMath.h"   // PI
+#include "../../common/ParallelFor.h"
+#include "../../common/Logger.h"
 
 namespace {
 
diff --git a/rugnux/RigidBodyRefine.h b/image_analysis/structure_refinement/RigidBodyRefine.h
similarity index 100%
rename from rugnux/RigidBodyRefine.h
rename to image_analysis/structure_refinement/RigidBodyRefine.h
diff --git a/rugnux/SigmaA.cpp b/image_analysis/structure_refinement/SigmaA.cpp
similarity index 100%
rename from rugnux/SigmaA.cpp
rename to image_analysis/structure_refinement/SigmaA.cpp
diff --git a/rugnux/SigmaA.h b/image_analysis/structure_refinement/SigmaA.h
similarity index 100%
rename from rugnux/SigmaA.h
rename to image_analysis/structure_refinement/SigmaA.h
diff --git a/rugnux/CMakeLists.txt b/rugnux/CMakeLists.txt
index 1fe64b8f6..91995c357 100644
--- a/rugnux/CMakeLists.txt
+++ b/rugnux/CMakeLists.txt
@@ -8,22 +8,6 @@ ADD_LIBRARY(JFJochRugnux STATIC
         Rugnux.h
         RugnuxCommandLine.cpp
         RugnuxCommandLine.h
-        ModelFFT.cpp
-        ModelFFT.h
-        ModelGrid.cpp
-        ModelGrid.h
-        ModelScaling.cpp
-        ModelScaling.h
-        ModelValidation.cpp
-        ModelValidation.h
-        RigidBodyRefine.cpp
-        RigidBodyRefine.h
-        $<$<BOOL:${JFJOCH_CUDA_AVAILABLE}>:RigidBodyGPU.cpp>
-        $<$<BOOL:${JFJOCH_CUDA_AVAILABLE}>:RigidBodyGPU.cu>
-        RigidBodyGPU.h
-        RigidBodyGPUEngine.h
-        SigmaA.cpp
-        SigmaA.h
         ResultReport.cpp
         ResultReport.h
         ReportDocument.h
@@ -31,17 +15,13 @@ ADD_LIBRARY(JFJochRugnux STATIC
         LeftoverLattices.h
         SpotWidth.cpp
         SpotWidth.h
-        $<$<BOOL:${JFJOCH_CUDA_AVAILABLE}>:ModelMaskGPU.cu>
-        $<$<BOOL:${JFJOCH_CUDA_AVAILABLE}>:ModelScaleGPU.cu>
         DiagnosticOutput.cpp
         DiagnosticOutput.h
         SpindleCuspLoss.cpp
         SpindleCuspLoss.h
-        WriteModel.cpp
-        WriteModel.h
 )
 
-TARGET_LINK_LIBRARIES(JFJochRugnux JFJochReader JFJochImageAnalysis JFJochWriter JFJochPreview gemmi fftw3f)
+TARGET_LINK_LIBRARIES(JFJochRugnux JFJochReader JFJochImageAnalysis JFJochWriter JFJochModelWriter JFJochPreview gemmi fftw3f)
 
 # rugnux is the single offline analysis CLI; --mode picks what it does: mx (the full pipeline, the
 # default), azint, scale (re-scale/merge stored reflections) or calibration (powder-ring geometry).
diff --git a/rugnux/Rugnux.cpp b/rugnux/Rugnux.cpp
index fdecd2b9b..e85682a8c 100644
--- a/rugnux/Rugnux.cpp
+++ b/rugnux/Rugnux.cpp
@@ -3,8 +3,8 @@
 
 #include <cstdlib>
 #include "Rugnux.h"
-#include "ModelValidation.h"
-#include "WriteModel.h"
+#include "../image_analysis/structure_refinement/ModelValidation.h"
+#include "../writer/WriteModel.h"
 #include "SpindleCuspLoss.h"
 #include "SpotWidth.h"
 #include "../image_analysis/bragg_integration/SpotFootprint.h"
diff --git a/rugnux/Rugnux.h b/rugnux/Rugnux.h
index 8ef3f2af0..bb3351e05 100644
--- a/rugnux/Rugnux.h
+++ b/rugnux/Rugnux.h
@@ -30,7 +30,7 @@
 #include "../image_analysis/scale_merge/CentreOfSymmetry.h"   // CentreOfSymmetryResult
 #include "../image_analysis/scale_merge/TranslationalNCS.h"   // TranslationalNCSResult
 #include "../image_analysis/indexing/HarmonicContamination.h"  // HarmonicContaminationResult
-#include "ModelValidation.h"                  // ModelValidationResult
+#include "../image_analysis/structure_refinement/ModelValidation.h"                  // ModelValidationResult
 #include "LeftoverLattices.h"                 // LeftoverLatticeCensus
 #include "ReportDocument.h"                   // ReportWarning, PathologyCode
 #include "../image_analysis/scale_merge/SearchSpaceGroup.h"   // SearchSpaceGroupResult
diff --git a/rugnux/rugnux_cli.cpp b/rugnux/rugnux_cli.cpp
index fea02e121..a4d711b96 100644
--- a/rugnux/rugnux_cli.cpp
+++ b/rugnux/rugnux_cli.cpp
@@ -61,8 +61,8 @@
 #include "../image_analysis/scale_merge/SearchSpaceGroup.h"
 #include "Rugnux.h"
 #include "RugnuxDefaults.h"
-#include "ModelValidation.h"
-#include "WriteModel.h"
+#include "../image_analysis/structure_refinement/ModelValidation.h"
+#include "../writer/WriteModel.h"
 #include "ResultReport.h"
 #include "RugnuxConsole.h"
 
diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index d2243ba6c..887fa4221 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -175,7 +175,7 @@ ADD_EXECUTABLE(jfjoch_test
 )
 
 target_link_libraries(jfjoch_test Catch2WithMain JFJochBroker JFJochReceiver JFJochReader JFJochStreamWriter
-                      JFJochRugnux JFJochImageAnalysis JFJochCommon JFJochHLSSimulation JFJochPreview
+                      JFJochRugnux JFJochModelWriter JFJochImageAnalysis JFJochCommon JFJochHLSSimulation JFJochPreview
                       jfjoch_xds_plugin ZLIB::ZLIB httplib::httplib)
 target_include_directories(jfjoch_test PRIVATE .)
 
diff --git a/tests/ModelMaskGPUTest.cpp b/tests/ModelMaskGPUTest.cpp
index d3a313b42..f464ce36c 100644
--- a/tests/ModelMaskGPUTest.cpp
+++ b/tests/ModelMaskGPUTest.cpp
@@ -16,8 +16,8 @@
 #include <gemmi/solmask.hpp>
 #include <gemmi/symmetry.hpp>
 
-#include "../rugnux/ModelGrid.h"
-#include "../rugnux/ModelMaskGPU.h"
+#include "../image_analysis/structure_refinement/ModelGrid.h"
+#include "../image_analysis/structure_refinement/ModelMaskGPU.h"
 
 namespace {
 
diff --git a/tests/ModelScaleGPUTest.cpp b/tests/ModelScaleGPUTest.cpp
index 8dbd576f8..7406565c2 100644
--- a/tests/ModelScaleGPUTest.cpp
+++ b/tests/ModelScaleGPUTest.cpp
@@ -23,12 +23,12 @@
 #include "gemmi/unitcell.hpp"
 
 #include "../common/Logger.h"
-#include "../rugnux/ModelFFT.h"
-#include "../rugnux/ModelGrid.h"
-#include "../rugnux/ModelScaling.h"
-#include "../rugnux/ModelScaleGPU.h"
-#include "../rugnux/ModelValidation.h"
-#include "../rugnux/RigidBodyRefine.h"
+#include "../image_analysis/structure_refinement/ModelFFT.h"
+#include "../image_analysis/structure_refinement/ModelGrid.h"
+#include "../image_analysis/structure_refinement/ModelScaling.h"
+#include "../image_analysis/structure_refinement/ModelScaleGPU.h"
+#include "../image_analysis/structure_refinement/ModelValidation.h"
+#include "../image_analysis/structure_refinement/RigidBodyRefine.h"
 
 namespace {
 
diff --git a/tests/ModelScalingTest.cpp b/tests/ModelScalingTest.cpp
index 28aa20bbc..741f19d39 100644
--- a/tests/ModelScalingTest.cpp
+++ b/tests/ModelScalingTest.cpp
@@ -7,7 +7,7 @@
 #include <algorithm>
 #include <complex>
 
-#include "../rugnux/ModelScaling.h"
+#include "../image_analysis/structure_refinement/ModelScaling.h"
 #include "gemmi/scaling.hpp"
 #include "gemmi/symmetry.hpp"
 #include "gemmi/unitcell.hpp"
diff --git a/tests/ModelValidationTest.cpp b/tests/ModelValidationTest.cpp
index 57fb62860..baf75aff2 100644
--- a/tests/ModelValidationTest.cpp
+++ b/tests/ModelValidationTest.cpp
@@ -18,17 +18,17 @@
 #include <gemmi/solmask.hpp>
 
 #include "../common/Logger.h"
-#include "../rugnux/ModelFFT.h"
-#include "../rugnux/ModelGrid.h"
-#include "../rugnux/ModelValidation.h"
-#include "../rugnux/RigidBodyRefine.h"
+#include "../image_analysis/structure_refinement/ModelFFT.h"
+#include "../image_analysis/structure_refinement/ModelGrid.h"
+#include "../image_analysis/structure_refinement/ModelValidation.h"
+#include "../image_analysis/structure_refinement/RigidBodyRefine.h"
 #ifdef JFJOCH_USE_CUDA
-#include "../rugnux/RigidBodyGPU.h"
-#include "../rugnux/RigidBodyGPUEngine.h"
+#include "../image_analysis/structure_refinement/RigidBodyGPU.h"
+#include "../image_analysis/structure_refinement/RigidBodyGPUEngine.h"
 #include "../common/CUDAWrapper.h"
 #endif
-#include "../rugnux/SigmaA.h"
-#include "../rugnux/WriteModel.h"
+#include "../image_analysis/structure_refinement/SigmaA.h"
+#include "../writer/WriteModel.h"
 #include "../image_analysis/scale_merge/ReindexAmbiguity.h"
 
 namespace {
diff --git a/writer/CMakeLists.txt b/writer/CMakeLists.txt
index a33b967ce..2f6f43738 100644
--- a/writer/CMakeLists.txt
+++ b/writer/CMakeLists.txt
@@ -33,6 +33,13 @@ ADD_LIBRARY(JFJochWriter STATIC
 
 TARGET_LINK_LIBRARIES(JFJochWriter JFJochPreview JFJochLogger JFJochHDF5Wrappers CBORStream2FrameSerialize)
 
+# The placed atomic model (mmCIF/PDB) that rugnux writes beside its merged output. Its own target,
+# because it needs gemmi, which JFJochWriter does not link and a writer-only build does not want.
+IF (NOT JFJOCH_WRITER_ONLY)
+    ADD_LIBRARY(JFJochModelWriter STATIC WriteModel.cpp WriteModel.h)
+    TARGET_LINK_LIBRARIES(JFJochModelWriter JFJochLogger gemmi)
+ENDIF()
+
 # The streaming writer and the jfjoch_writer service belong to the Linux server stack, not the
 # portable viewer subset: JFJochStreamWriter pulls in JFJochImagePuller (not built in a viewer-only
 # tree) and jfjoch_writer uses a fork()/waitpid() multi-process design (<sys/wait.h>, no Windows
diff --git a/rugnux/WriteModel.cpp b/writer/WriteModel.cpp
similarity index 100%
rename from rugnux/WriteModel.cpp
rename to writer/WriteModel.cpp
diff --git a/rugnux/WriteModel.h b/writer/WriteModel.h
similarity index 100%
rename from rugnux/WriteModel.h
rename to writer/WriteModel.h