servalcat 0.4.72__tar.gz → 0.4.99__tar.gz

{servalcat-0.4.72 → servalcat-0.4.99}/CMakeLists.txt

@@ -8,11 +8,14 @@ string(REGEX REPLACE "__version__ = '(.+)'" "\\1" serval_version_str ${serval_ve
 project(servalcat LANGUAGES C CXX VERSION ${serval_version_str})
 message(STATUS "Servalcat version ${PROJECT_VERSION}")
 
+option(SEARCH_INSTALLED_GEMMI "Search for gemmi-config.cmake and use it if found" ON)
+option(INSTALL_GEMMI_IF_BUILT "Install also Python module gemmi, if it was built" OFF)
+
 include(GNUInstallDirs)
 
 if (DEFINED SKBUILD)  # building with scikit-build-core (pip install)
   set(PYTHON_INSTALL_DIR "${SKBUILD_PLATLIB_DIR}")
-  set(CMAKE_INSTALL_BINDIR "${SKBUILD_SCRIPTS_DIR}")
+  #set(CMAKE_INSTALL_BINDIR "${SKBUILD_SCRIPTS_DIR}")
 endif()
 
 set(CMAKE_CXX_EXTENSIONS OFF)
@@ -28,6 +31,7 @@ if (NOT CMAKE_BUILD_TYPE AND NOT USING_ENV_CXXFLAGS)
       FORCE)
 endif()
 
+
 # CMake >=3.18 has subcomponent Development.Module, scikit-build-core also has it
 if (${CMAKE_VERSION} VERSION_LESS 3.18 AND NOT SKBUILD)
   find_package(Python ${PYTHON_VERSION} REQUIRED COMPONENTS Interpreter Development)
@@ -35,13 +39,14 @@ else()
   find_package(Python ${PYTHON_VERSION} REQUIRED COMPONENTS Interpreter Development.Module)
 endif()
 
-# use pybind11-config (if available) to determine pybind11_DIR
-execute_process(COMMAND pybind11-config --cmakedir OUTPUT_VARIABLE pybind11_DIR)
-string(STRIP "${pybind11_DIR}" pybind11_DIR)
-find_package(pybind11 2.6 CONFIG REQUIRED)
-message(STATUS "Found pybind11 ${pybind11_VERSION}: ${pybind11_INCLUDE_DIRS}")
+execute_process(
+  COMMAND "${Python_EXECUTABLE}" -m nanobind --cmake_dir
+  OUTPUT_STRIP_TRAILING_WHITESPACE OUTPUT_VARIABLE NB_DIR)
+list(APPEND CMAKE_PREFIX_PATH "${NB_DIR}")
+find_package(nanobind 2.2.0 CONFIG REQUIRED)
+message(STATUS "Found nanobind ${nanobind_VERSION}: ${NB_DIR}")
 
-pybind11_add_module(ext src/ext.cpp src/intensity.cpp src/amplitude.cpp src/refine.cpp)
+nanobind_add_module(ext src/ext.cpp src/intensity.cpp src/amplitude.cpp src/refine.cpp src/twin.cpp)
 
 if (EXISTS "${CMAKE_HOME_DIRECTORY}/eigen/Eigen")
   include_directories("${CMAKE_CURRENT_SOURCE_DIR}/eigen")
@@ -52,31 +57,46 @@ else()
   target_link_libraries(ext PRIVATE Eigen3::Eigen)
 endif()
 
-if (DEFINED SKBUILD)
-  if (WIN32)
-    # Gemmi is installed in an overlay directory in virtualenv.
-    # For now, locate it relatively to pybind11.
-    get_filename_component(gemmi_ROOT "${pybind11_INCLUDE_DIR}/../../../.." ABSOLUTE)
+# We need either gemmi C++ development files (headers, library, cmake config)
+# or gemmi sources. If we have the former with a shared library, it may require
+# extra effort to make sure that the shared library is found at runtime.
+if (SEARCH_INSTALLED_GEMMI)
+  find_package(gemmi 0.7.0 CONFIG)
+endif()
+if (gemmi_FOUND)
+  message(STATUS "  based on config from ${gemmi_DIR}")
+  get_target_property(gemmi_TYPE gemmi::gemmi_cpp TYPE)
+  if (${gemmi_TYPE} STREQUAL "SHARED_LIBRARY")
+    message(STATUS "** Servalcat Python module will be linked with gemmi shared library.  **")
+    message(STATUS "** The module may require 'repairing' to find the library at runtime. **")
   endif()
-  find_package(gemmi 0.6.6 CONFIG REQUIRED)
 else()
   set(USE_PYTHON ON CACHE BOOL "" FORCE)
+  set(BUILD_GEMMI_PROGRAM OFF CACHE BOOL "" FORCE)
+  set(INSTALL_DEV_FILES OFF CACHE BOOL "" FORCE)
+  set(BUILD_SHARED_LIBS OFF CACHE BOOL "" FORCE)
   message(STATUS "")
   message(STATUS "Configuring GEMMI...")
+  if (INSTALL_GEMMI_IF_BUILT AND NOT gemmi_FOUND)
+    set(exclude_or_not)
+  else()
+    set(exclude_or_not EXCLUDE_FROM_ALL)
+  endif()
   if (EXISTS "${CMAKE_HOME_DIRECTORY}/gemmi/include/gemmi")
     message(STATUS "Using ${CMAKE_HOME_DIRECTORY}/gemmi (internal copy).")
-    add_subdirectory(gemmi EXCLUDE_FROM_ALL)
+    add_subdirectory(gemmi ${exclude_or_not})
   else()
+    message(STATUS "Using FetchContent...")
     include(FetchContent)
     FetchContent_Declare(
       gemmi
       GIT_REPOSITORY https://github.com/project-gemmi/gemmi.git
-      GIT_TAG        v0.6.6
+      GIT_TAG        v0.7.0
     )
     FetchContent_GetProperties(gemmi)
     if (NOT gemmi_POPULATED)
       FetchContent_Populate(gemmi)
-      add_subdirectory(${gemmi_SOURCE_DIR} ${gemmi_BINARY_DIR} EXCLUDE_FROM_ALL)
+      add_subdirectory(${gemmi_SOURCE_DIR} ${gemmi_BINARY_DIR} ${exclude_or_not})
     endif()
   endif()
   add_dependencies(ext gemmi_py)

{servalcat-0.4.72 → servalcat-0.4.99}/PKG-INFO

@@ -1,16 +1,16 @@
 Metadata-Version: 2.1
 Name: servalcat
-Version: 0.4.72
+Version: 0.4.99
 Summary: Structure refinement and validation for crystallography and single particle analysis
 Author: Keitaro Yamashita, Garib N. Murshudov
 License: MPL-2.0
 Project-URL: Repository, https://github.com/keitaroyam/servalcat
-Requires-Python: >=3.7
+Requires-Python: >=3.8
 Requires-Dist: packaging
 Requires-Dist: numpy>=1.15
 Requires-Dist: scipy
 Requires-Dist: pandas>=1.1.0
-Requires-Dist: gemmi==0.6.6
+Requires-Dist: gemmi==0.7.0
 Description-Content-Type: text/markdown
 
 # Servalcat
@@ -40,7 +40,7 @@ pip install servalcat
 ```
 will install the stable version.
 
-The required GEMMI version is now [v0.6.6](https://github.com/project-gemmi/gemmi/releases/tag/v0.6.6). It may not work with the latest gemmi code from the github. The policy is in the main branch I only push the code that works with the latest package of GEMMI.
+The required GEMMI version is now [v0.7.0](https://github.com/project-gemmi/gemmi/releases/tag/v0.7.0). It may not work with the latest gemmi code from the github. The policy is in the main branch I only push the code that works with the latest package of GEMMI.
 
 To use the Refmac5 related commands, you also need to install [CCP4](https://www.ccp4.ac.uk/). For "No Refmac5" commands, you may just need [the monomer library](https://github.com/MonomerLibrary/monomers) if CCP4 is not installed.
 

{servalcat-0.4.72 → servalcat-0.4.99}/README.md

@@ -25,7 +25,7 @@ pip install servalcat
 ```
 will install the stable version.
 
-The required GEMMI version is now [v0.6.6](https://github.com/project-gemmi/gemmi/releases/tag/v0.6.6). It may not work with the latest gemmi code from the github. The policy is in the main branch I only push the code that works with the latest package of GEMMI.
+The required GEMMI version is now [v0.7.0](https://github.com/project-gemmi/gemmi/releases/tag/v0.7.0). It may not work with the latest gemmi code from the github. The policy is in the main branch I only push the code that works with the latest package of GEMMI.
 
 To use the Refmac5 related commands, you also need to install [CCP4](https://www.ccp4.ac.uk/). For "No Refmac5" commands, you may just need [the monomer library](https://github.com/MonomerLibrary/monomers) if CCP4 is not installed.
 

{servalcat-0.4.72 → servalcat-0.4.99}/docs/commands.rst

@@ -4,10 +4,10 @@ Servalcat commands
 SPA
 ---
 
-refine_spa
-~~~~~~~~~~
+refine_spa_norefmac
+~~~~~~~~~~~~~~~~~~~
 
-REFMAC5 pipeline for SPA. The weighted and sharpened Fo-Fc map is calculated after the refinement. For details please see the reference.
+Refinement pipeline for SPA. The weighted and sharpened Fo-Fc map is calculated after the refinement. For details please see the reference.
 
 .. literalinclude:: help/refine_spa.txt
    :language: console

{servalcat-0.4.72 → servalcat-0.4.99}/docs/conf.py

@@ -19,7 +19,7 @@ import os
 # -- Project information -----------------------------------------------------
 
 project = 'Servalcat'
-copyright = '2021-2022, MRC Laboratory of Molecular Biology'
+copyright = '2021-2024, Keitaro Yamashita'
 author = 'Keitaro Yamashita, Garib Murshudov'
 
 

{servalcat-0.4.72 → servalcat-0.4.99}/docs/help/fofc.txt

@@ -1,15 +1,16 @@
 $ servalcat fofc -h
 usage: servalcat fofc [-h] [--halfmaps HALFMAPS HALFMAPS | --map MAP]
                       [--pixel_size PIXEL_SIZE] --model MODEL -d RESOLUTION
-                      [-m MASK] [-r MASK_RADIUS] [-B B] [--half1_only]
-                      [--normalized_map] [--no_fsc_weights]
-                      [--sharpening_b SHARPENING_B] [--trim] [--trim_mtz]
-                      [--monlib MONLIB] [--omit_proton] [--omit_h_electron]
-                      [-o OUTPUT_PREFIX]
+                      [-m MASK] [-r MASK_RADIUS] [--no_check_mask_with_model]
+                      [-B B] [--half1_only] [--normalized_map]
+                      [--no_fsc_weights] [--sharpening_b SHARPENING_B]
+                      [--trim] [--trim_mtz] [--monlib MONLIB] [--omit_proton]
+                      [--omit_h_electron] [--source {electron,xray,neutron}]
+                      [-o OUTPUT_PREFIX] [--keep_charges]
 
 Fo-Fc map calculation based on model and data errors
 
-optional arguments:
+options:
   -h, --help            show this help message and exit
   --halfmaps HALFMAPS HALFMAPS
   --map MAP             Use only if you really do not have half maps.
@@ -20,10 +21,13 @@ optional arguments:
   -m MASK, --mask MASK  mask file
   -r MASK_RADIUS, --mask_radius MASK_RADIUS
                         mask radius (not used if --mask is given)
+  --no_check_mask_with_model
+                        Disable mask test using model
   -B B                  Estimated blurring
   --half1_only          Only use half 1 for map calculation (use half 2 only
                         for noise estimation)
-  --normalized_map      Write normalized map in the masked region
+  --normalized_map      Write normalized map in the masked region. Now this is
+                        on by default.
   --no_fsc_weights      Just for debugging purpose: turn off FSC-based
                         weighting
   --sharpening_b SHARPENING_B
@@ -34,4 +38,8 @@ optional arguments:
   --monlib MONLIB       Monomer library path. Default: $CLIBD_MON
   --omit_proton         Omit proton from model in map calculation
   --omit_h_electron     Omit hydrogen electrons from model in map calculation
+  --source {electron,xray,neutron}
   -o OUTPUT_PREFIX, --output_prefix OUTPUT_PREFIX
+                        output file name prefix (default: diffmap)
+  --keep_charges        Use scattering factor for charged atoms. Use it with
+                        care.

servalcat-0.4.99/docs/help/refine_spa.txt

@@ -0,0 +1,126 @@
+$ servalcat refine_spa_norefmac -h
+usage: servalcat refine_spa_norefmac [-h] (--halfmaps HALFMAPS HALFMAPS | --map MAP | --hklin HKLIN)
+                                     [--pixel_size PIXEL_SIZE] [--labin LABIN] --model MODEL -d
+                                     RESOLUTION [-r MASK_RADIUS] [--padding PADDING] [--no_mask]
+                                     [--no_trim] [--mask_soft_edge MASK_SOFT_EDGE]
+                                     [--no_sharpen_before_mask] [--b_before_mask B_BEFORE_MASK]
+                                     [--blur BLUR] [--monlib MONLIB] [--ligand [LIGAND ...]]
+                                     [--newligand_continue] [--hydrogen {all,yes,no}] [--hout]
+                                     [--jellybody] [--jellybody_params sigma dmax] [--jellyonly]
+                                     [--pg PG] [--twist TWIST] [--rise RISE]
+                                     [--center CENTER CENTER CENTER] [--axis1 AXIS1 AXIS1 AXIS1]
+                                     [--axis2 AXIS2 AXIS2 AXIS2] [--contacting_only]
+                                     [--ignore_symmetry IGNORE_SYMMETRY] [--find_links]
+                                     [--no_check_ncs_overlaps] [--no_check_ncs_map]
+                                     [--no_check_mask_with_model] [--keywords KEYWORDS [KEYWORDS ...]]
+                                     [--keyword_file KEYWORD_FILE [KEYWORD_FILE ...]]
+                                     [--randomize RANDOMIZE] [--ncycle NCYCLE] [--weight WEIGHT]
+                                     [--no_weight_adjust]
+                                     [--target_bond_rmsz_range TARGET_BOND_RMSZ_RANGE TARGET_BOND_RMSZ_RANGE]
+                                     [--adpr_weight ADPR_WEIGHT] [--ncsr] [--bfactor BFACTOR]
+                                     [--fix_xyz] [--adp {fix,iso,aniso}] [--refine_all_occ]
+                                     [--max_dist_for_adp_restraint MAX_DIST_FOR_ADP_RESTRAINT]
+                                     [--adp_restraint_power ADP_RESTRAINT_POWER]
+                                     [--adp_restraint_exp_fac ADP_RESTRAINT_EXP_FAC]
+                                     [--adp_restraint_no_long_range]
+                                     [--adp_restraint_mode {diff,kldiv}] [--refine_h]
+                                     [--source {electron,xray,neutron}] [-o OUTPUT_PREFIX]
+                                     [--cross_validation]
+                                     [--mask_for_fofc MASK_FOR_FOFC | --mask_radius_for_fofc MASK_RADIUS_FOR_FOFC]
+                                     [--fsc_resolution FSC_RESOLUTION] [--keep_charges]
+                                     [--keep_entities] [--write_trajectory]
+
+EXPERIMENTAL program to refine cryo-EM SPA structures
+
+options:
+  -h, --help            show this help message and exit
+  --halfmaps HALFMAPS HALFMAPS
+                        Input half map files
+  --map MAP             Use this only if you really do not have half maps.
+  --hklin HKLIN         Use mtz file. With limited functionality.
+  --pixel_size PIXEL_SIZE
+                        Override pixel size (A)
+  --labin LABIN         F,PHI for hklin
+  --model MODEL         Input atomic model file
+  -d RESOLUTION, --resolution RESOLUTION
+  -r MASK_RADIUS, --mask_radius MASK_RADIUS
+                        mask radius
+  --padding PADDING     Default: 2*mask_radius
+  --no_mask
+  --no_trim             Keep original box (not recommended)
+  --mask_soft_edge MASK_SOFT_EDGE
+                        Add soft edge to model mask. Should use with --no_sharpen_before_mask?
+  --no_sharpen_before_mask
+                        By default half maps are sharpened before masking by std of signal and
+                        unsharpened after masking. This option disables it.
+  --b_before_mask B_BEFORE_MASK
+                        sharpening B value for sharpen-mask-unsharpen procedure. By default it is
+                        determined automatically.
+  --blur BLUR           Sharpening or blurring B
+  --monlib MONLIB       Monomer library path. Default: $CLIBD_MON
+  --ligand [LIGAND ...]
+                        restraint dictionary cif file(s)
+  --newligand_continue  Make ad-hoc restraints for unknown ligands (not recommended)
+  --hydrogen {all,yes,no}
+                        all: (re)generate hydrogen atoms, yes: use hydrogen atoms if present, no:
+                        remove hydrogen atoms in input. Default: all
+  --hout                write hydrogen atoms in the output model
+  --jellybody           Use jelly body restraints
+  --jellybody_params sigma dmax
+                        Jelly body sigma and dmax (default: [0.01, 4.2])
+  --jellyonly           Jelly body only (experimental, may not be useful)
+  --pg PG               Point group symbol
+  --twist TWIST         Helical twist (degree)
+  --rise RISE           Helical rise (Angstrom)
+  --center CENTER CENTER CENTER
+                        Origin of symmetry. Default: center of the box
+  --axis1 AXIS1 AXIS1 AXIS1
+                        Axis1 (if I: 5-fold, O: 4-fold, T: 3-fold)
+  --axis2 AXIS2 AXIS2 AXIS2
+                        Axis2 (if I: 5-fold, O: 4-fold, T: 3-fold, Dn: 2-fold)
+  --contacting_only     Filter out non-contacting strict NCS copies
+  --ignore_symmetry IGNORE_SYMMETRY
+                        Ignore symmetry information (MTRIX/_struct_ncs_oper) in the model file
+  --find_links          Automatically add links
+  --no_check_ncs_overlaps
+                        Disable model overlap test due to strict NCS
+  --no_check_ncs_map    Disable map symmetry test due to strict NCS
+  --no_check_mask_with_model
+                        Disable mask test using model
+  --keywords KEYWORDS [KEYWORDS ...]
+                        refmac keyword(s)
+  --keyword_file KEYWORD_FILE [KEYWORD_FILE ...]
+                        refmac keyword file(s)
+  --randomize RANDOMIZE
+                        Shake coordinates with the specified rmsd value
+  --ncycle NCYCLE       number of CG cycles (default: 10)
+  --weight WEIGHT       refinement weight. default: automatic
+  --no_weight_adjust    Do not adjust weight during refinement
+  --target_bond_rmsz_range TARGET_BOND_RMSZ_RANGE TARGET_BOND_RMSZ_RANGE
+                        Bond rmsz range for weight adjustment (default: [0.5, 1.0])
+  --adpr_weight ADPR_WEIGHT
+                        ADP restraint weight (default: 1.000000)
+  --ncsr                Use local NCS restraints
+  --bfactor BFACTOR     reset all atomic B values to the specified value
+  --fix_xyz             Fix atomic coordinates
+  --adp {fix,iso,aniso}
+                        ADP parameterization
+  --refine_all_occ
+  --max_dist_for_adp_restraint MAX_DIST_FOR_ADP_RESTRAINT
+  --adp_restraint_power ADP_RESTRAINT_POWER
+  --adp_restraint_exp_fac ADP_RESTRAINT_EXP_FAC
+  --adp_restraint_no_long_range
+  --adp_restraint_mode {diff,kldiv}
+  --refine_h            Refine hydrogen against data (default: only restraints apply)
+  --source {electron,xray,neutron}
+  -o OUTPUT_PREFIX, --output_prefix OUTPUT_PREFIX
+  --cross_validation    Run cross validation. Only "throughout" mode is available (no "shake" mode)
+  --mask_for_fofc MASK_FOR_FOFC
+                        Mask file for Fo-Fc map calculation
+  --mask_radius_for_fofc MASK_RADIUS_FOR_FOFC
+                        Mask radius for Fo-Fc map calculation
+  --fsc_resolution FSC_RESOLUTION
+                        High resolution limit for FSC calculation. Default: Nyquist
+  --keep_charges        Use scattering factor for charged atoms. Use it with care.
+  --keep_entities       Do not override entities
+  --write_trajectory    Write all output from cycles

{servalcat-0.4.72 → servalcat-0.4.99}/docs/index.rst

@@ -7,15 +7,17 @@ Servalcat - refinement and map calculation
 ==========================================
 
 Servalcat (for **S**\ tructur\ **e** **r**\ efinement and **val**\ idation for **c**\ rystallography and single p\ **a**\ r\ **t**\ icle analysis) is a software package for atomic model refinement and map calculation.
-We currently focus on cryo-EM single particle analysis (SPA).
-
 
 Source code repository: https://github.com/keitaroyam/servalcat
 
-.. note::
+References
+----------
+
+| Cryo-EM SPA refinement:
+| `Yamashita, K., Palmer, C. M., Burnley, T., Murshudov, G. N. (2021) "Cryo-EM single particle structure refinement and map calculation using Servalcat" Acta Cryst. D77, 1282-1291 <https://doi.org/10.1107/S2059798321009475>`_
 
-   If Servalcat is useful for your research, please cite:
-   Yamashita, K., Palmer, C. M., Burnley, T., Murshudov, G. N. (2021) "Cryo-EM single particle structure refinement and map calculation using Servalcat" *Acta Cryst. D*\ **77**, 1282-1291 doi: `10.1107/S2059798321009475 <https://doi.org/10.1107/S2059798321009475>`_
+| Refmacat and restraint generation using GEMMI:
+| `Yamashita, K., Wojdyr, M., Long, F., Nicholls, R. A., Murshudov, G. N. (2023) "GEMMI and Servalcat restrain REFMAC5" Acta Cryst. D79, 368-373 <https://doi.org/10.1107/S2059798323002413>`_
 
 Table of Contents
 -----------------

servalcat-0.4.99/docs/overview.rst

@@ -0,0 +1,94 @@
+Overview
+========
+
+Servalcat offers various functionalities for refinement and map calculations in crystallography and single particle analysis (SPA).
+
+* SPA
+   * refinement (refine_spa_norefmac)
+   * sharpened and weighted map calculation (Fo and Fo-Fc)
+   * map trimming tool
+* crystallography
+   * amplitude or intensity based refinement (refine_xtal_norefmac)
+   * map calculation from ML parameter estimation (sigmaa)
+* others/general
+   * REFMAC5 wrapper ("refmacat")
+   * geometry optimisation 
+
+The basic usage is:
+
+.. code-block:: console
+
+    $ servalcat <command> <args>
+
+The most common commands are listed below. To see all arguments for a specific command, run:
+
+.. code-block:: console
+
+    $ servalcat <command> -h
+
+
+Command examples for cryo-EM SPA
+--------------------------------
+
+refinement
+~~~~~~~~~~
+Servalcat performs reciprocal space refinement for single particle analysis. The weighted and sharpened Fo-Fc map is calculated after the refinement. For details please see the reference.
+Make a new directory and run:
+
+.. code-block:: console
+
+    $ servalcat refine_spa_norefmac \
+     --model input.pdb --resolution 2.5 \
+     --halfmaps ../half_map_1.mrc ../half_map_2.mrc \
+     --ncycle 10 [--pg C2] \
+     [--mask_for_fofc mask.mrc] [-o output_prefix]
+
+Provide unsharpened and unweighted half maps (e.g., from RELION's Refine3D) after ``--halfmaps``.
+
+If map has been symmetrised with a point group, use ``--pg`` to specify the point group symbol along with the asymmetric unit model.
+The centre of the box is assumed to be the origin of symmetry. The axis convention follows `RELION <https://relion.readthedocs.io/en/latest/Reference/Conventions.html#symmetry>`_.
+
+Other useful options:
+   * ``--ligand lig.cif`` : specify restraint dictionary (.cif) file(s)
+   * ``--mask_for_fofc mask.mrc`` : specify mask file for Fo-Fc map calculation
+   * ``--jellybody`` : turn on jelly body refinement
+   * ``--weight value`` : specify the weight. By default Servalcat determines it from resolution and mask/box ratio
+   * ``--keyword_file file`` : specify any refmac keyword file(s) (e.g. prosmart restraint file) Note that not all refmac keywords are supported
+   * ``--pixel_size value`` : override pixel size of map
+
+Output files:
+   * ``prefix.pdb``: refined model
+   * ``prefix_expanded.pdb``: symmetry-expanded version
+   * ``prefix_diffmap.mtz``: can be auto-opened with coot. sharpened and weighted Fo map and Fo-Fc map
+   * ``prefix_diffmap_normalized_fofc.mrc``: Fo-Fc map normalised within a mask. Look at raw values
+
+Fo-Fc map calculation
+~~~~~~~~~~~~~~~~~~~~~
+It is crucial to refine individual atomic B values with electron scattering factors for a meaningful Fo-Fc map.
+While the ``refine_spa_norefmac`` command calculates the Fo-Fc map (explained above), you can use the fofc command to calculate specific maps, like omit maps.
+
+.. code-block:: console
+
+    $ servalcat fofc \
+      --model input.pdb --resolution 2.5 \
+      --halfmaps ../half_map_1.mrc ../half_map_2.mrc \
+      [--mask mask.mrc] [-o output_prefix] [-B B value]
+
+
+``-B`` is to calculate weighted maps based on local B estimate. It may be useful for model building in noisy region.
+
+Map trimming
+~~~~~~~~~~~~
+Maps from single particle analysis are often large due to unnecessary regions outside the molecule. Use trim to save disk space by removing these regions.
+
+.. code-block:: console
+
+    $ servalcat trim \
+      --maps postprocess.mrc halfmap1.mrc halfmap2.mrc \
+      [--mask mask.mrc] [--model model.pdb] [--padding 10]
+
+Maps specified with ``--maps`` are trimmed. The boundary is decided by ``--mask`` or ``--model`` if mask is not available.
+Model(s) are shifted into a new box.
+By default new boundary is centred on the original map and cubic, but they can be turned off with ``--noncentered`` and ``--noncubic``.
+If you do not want to shift maps and models, specify ``--no_shift`` to keep origin.
+