From 118adc93fd92ac6e65eab9bea42711f2a8e5cf36 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Tue, 18 Jun 2024 18:26:30 +0000 Subject: [PATCH] Upload documentation from latest commit --- _sources/cli.md | 10 +- _static/documentation_options.js | 2 +- about.html | 2 +- cli.html | 312 +++++++++++++++---------------- genindex.html | 2 +- index.html | 2 +- quickstart.html | 2 +- search.html | 2 +- searchindex.js | 2 +- troubleshooting.html | 2 +- visualization.html | 2 +- 11 files changed, 170 insertions(+), 170 deletions(-) diff --git a/_sources/cli.md b/_sources/cli.md index 3ccc7a4..80d7d14 100644 --- a/_sources/cli.md +++ b/_sources/cli.md @@ -3,12 +3,12 @@ `matchmaps` is built to be used from the command-line. See the following utilities below. You can also print these messages in the command-line via the `--help` option. ```{eval-rst} -.. autoprogram:: matchmaps._compute_realspace_diff:parse_arguments() +.. autoprogram:: matchmaps._parsers:matchmaps_parser :prog: matchmaps -.. autoprogram:: matchmaps._compute_ncs_diff:parse_arguments() - :prog: matchmaps.ncs - -.. autoprogram:: matchmaps._compute_mr_diff:parse_arguments() +.. autoprogram:: matchmaps._parsers:matchmaps_mr_parser :prog: matchmaps.mr + +.. autoprogram:: matchmaps._parsers:matchmaps_ncs_parser + :prog: matchmaps.ncs ``` diff --git a/_static/documentation_options.js b/_static/documentation_options.js index 4b77377..718e8cc 100644 --- a/_static/documentation_options.js +++ b/_static/documentation_options.js @@ -1,5 +1,5 @@ const DOCUMENTATION_OPTIONS = { - VERSION: '0.1.dev1+gbe8c2f2', + VERSION: '0.1.dev1+g4256ad9', LANGUAGE: 'en', COLLAPSE_INDEX: false, BUILDER: 'html', diff --git a/about.html b/about.html index ac0c8c2..ed920a1 100644 --- a/about.html +++ b/about.html @@ -17,7 +17,7 @@ - + diff --git a/cli.html b/cli.html index fd6e390..e5ee9dd 100644 --- a/cli.html +++ b/cli.html @@ -17,7 +17,7 @@ - + @@ -53,8 +53,8 @@
  • About the algorithm
  • Full command-line API
    • @@ -90,12 +90,12 @@

    matchmapsmatchmaps

    Compute a real-space difference map. You will need two MTZ files, which will be referred to throughout as ‘on’ and ‘off’, though they could also be light/dark, bound/apo, mutant/WT, hot/cold, etc. Each mtz will need to contain structure factor amplitudes and uncertainties; you will not need any phases. You will, however, need an input model (assumed to correspond with the ‘off’ state) which will be used to determine phases. The input file may be in .pdb or .cif format. Please note that both ccp4 and phenix must be installed and active in your environment for this function to run. More information can be found online at https://rs-station.github.io/matchmaps/index.html

    usage: matchmaps [-h] --mtzoff mtzfileoff Foff SigFoff --mtzon mtzfileon Fon
-                 SigFon --pdboff PDBOFF [--ligands [LIGANDS ...]]
-                 [--input-dir INPUT_DIR] [--output-dir OUTPUT_DIR]
-                 [--on-as-stationary] [--no-bss] [--spacing SPACING]
-                 [--dmin DMIN] [--alpha ALPHA]
-                 [--unmasked-radius UNMASKED_RADIUS] [--verbose]
-                 [--rbr-selections [RBR_SELECTIONS ...]] [--eff EFF]
+                 SigFon --pdboff PDBOFF [--on-as-stationary] [--alpha ALPHA]
+                 [--unmasked-radius UNMASKED_RADIUS]
+                 [--rbr-selections [RBR_SELECTIONS ...]]
+                 [--ligands [LIGANDS ...]] [--input-dir INPUT_DIR]
+                 [--output-dir OUTPUT_DIR] [--spacing SPACING] [--dmin DMIN]
+                 [--no-bss] [--verbose] [--eff EFF]
                  [--keep-temp-files KEEP_TEMP_FILES] [--script SCRIPT]
                  [--phenix-version PHENIX_VERSION]
    @@ -124,6 +124,30 @@

    matchmaps +
    +--on-as-stationary
    +

    Include this flag to align ‘off’ data onto ‘on’ data. By default, ‘off’ data is stationary and ‘on’ data is moved.

    +
    + +
    +
    +--alpha <alpha>
    +

    Alpha to use for error weighting of F-obs prior to Fourier Transform. Weights are computed as: 1 / ((1+(alpha*(SigF^2)) / <SigF>^2). Default value is alpha=0, e.g., no weighting is performed.

    +
    + +
    +
    +--unmasked-radius <unmasked_radius>
    +

    Maximum distance (in Anstroms) away from protein model to include voxels. Only applies to the ‘unmasked’ difference map output. Defaults to 5. Note that the regular difference map (e.g. the ‘masked’ version) is not affected by this parameter and maintains a solvent mask radius of 2 Angstroms.

    +
    + +
    +
    +--rbr-selections <rbr_selections>, -r <rbr_selections>
    +

    Specification of multiple rigid-body groups for refinement. By default, everything is refined as one rigid-body group.

    +
    +
    --ligands <ligands>, -l <ligands>
    @@ -142,18 +166,6 @@

    matchmaps -
    ---on-as-stationary
    -

    Include this flag to align ‘off’ data onto ‘on’ data. By default, ‘off’ data is stationary and ‘on’ data is moved.

    -

    - -
    -
    ---no-bss
    -

    Include this flag to skip bulk solvent scaling in phenix.refine. By default, BSS is included.

    -
    -
    --spacing <spacing>, -s <spacing>
    @@ -167,15 +179,9 @@

    matchmaps -
    ---alpha <alpha>
    -

    Alpha to use for error weighting of F-obs prior to Fourier Transform. Weights are computed as: 1 / ((1+(alpha*(SigF^2)) / <SigF>^2). Default value is alpha=0, e.g., no weighting is performed.

    -

    - -
    -
    ---unmasked-radius <unmasked_radius>
    -

    Maximum distance (in Anstroms) away from protein model to include voxels. Only applies to the ‘unmasked’ difference map output. Defaults to 5. Note that the regular difference map (e.g. the ‘masked’ version) is not affected by this parameter and maintains a solvent mask radius of 2 Angstroms.

    +
    +--no-bss
    +

    Include this flag to skip bulk solvent scaling in phenix.refine. By default, BSS is included.

    @@ -184,12 +190,6 @@

    matchmaps -
    ---rbr-selections <rbr_selections>, -r <rbr_selections>
    -

    Specification of multiple rigid-body groups for refinement. By default, everything is refined as one rigid-body group.

    -

    -
    --eff <eff>
    @@ -215,246 +215,246 @@

    matchmaps -

    matchmaps.ncs

    -

    Compute an ‘internal’ real-space difference map between NCS-related molecules. You will need an MTZ file with structure factor amplitudes and optionally containing phases, and a PDB/CIF file.Please note that phenix must be installed and active in your environment for this function to run. More information can be found online at https://rs-station.github.io/matchmaps/index.html

    -
    usage: matchmaps.ncs [-h] --mtz [MTZ ...] [--phases PHASES] --pdb PDB
-                     --ncs-chains fixed_chain moving_chain [--mapname MAPNAME]
-                     [--ligands [LIGANDS ...]] [--input-dir INPUT_DIR]
-                     [--output-dir OUTPUT_DIR] [--no-bss] [--spacing SPACING]
-                     [--dmin DMIN] [--verbose] [--eff EFF]
-                     [--keep-temp-files KEEP_TEMP_FILES] [--script SCRIPT]
-                     [--phenix-version PHENIX_VERSION]
+
    
+
    matchmaps.mr
    
+
    Compute a real-space difference map between inputs in different space groups / crystal packings. You will need two MTZ files, which will be referred to throughout as ‘on’ and ‘off’, though they could also be light/dark, bound/apo, mutant/WT, hot/cold, etc. Each mtz will need to contain structure factor amplitudes and uncertainties; you will not need any phases. You will, however, need an input model (assumed to correspond with the ‘off’ state) which will be used to determine phases. The input file may be in .pdb or .cif format. Please note that phenix must be installed and active in your environment for this function to run. If your mtzoff and mtzon are in the same spacegroup and crystal packing, see the basic matchmaps utility. More information can be found online at https://rs-station.github.io/matchmaps/index.html
    
+
    usage: matchmaps.mr [-h] --mtzoff mtzfileoff Foff SigFoff --mtzon mtzfileon
+                    Fon SigFon --pdboff PDBOFF [--on-as-stationary]
+                    [--alpha ALPHA] [--unmasked-radius UNMASKED_RADIUS]
+                    [--rbr-selections [RBR_SELECTIONS ...]]
+                    [--ligands [LIGANDS ...]] [--input-dir INPUT_DIR]
+                    [--output-dir OUTPUT_DIR] [--spacing SPACING]
+                    [--dmin DMIN] [--no-bss] [--verbose] [--eff EFF]
+                    [--keep-temp-files KEEP_TEMP_FILES] [--script SCRIPT]
+                    [--phenix-version PHENIX_VERSION]
 
    
 
    
 
    
-
    
--h, --help
    
+
    
+-h, --help
    
 
    show this help message and exit
    
 
    
 
 
    
-
    
---mtz <mtz>, -m <mtz>
    
-
    MTZ or sfCIF file containing structure factor amplitudes. Specified as [filename F SigF] or [filename F]. SigF is not necessary if phases are also provided
    
+
    
+--mtzoff <mtzfileoff> <foff> <sigfoff>, -f <mtzfileoff> <foff> <sigfoff>
    
+
    MTZ or sfCIF containing off/apo/ground/dark state data. Specified as [filename F SigF]
    
 
    
 
 
    
-
    
---phases <phases>
    
-
    Optional. Column in MTZ/sfCIF file containing phases. If phases are not provided, phases will be computed via rigid-body refinement of the provided model and structure factor amplitudes.
    
+
    
+--mtzon <mtzfileon> <fon> <sigfon>, -n <mtzfileon> <fon> <sigfon>
    
+
    MTZ or sfCIF containing on/bound/excited/bright state data. Specified as [filename F SigF]
    
 
    
 
 
    
-
    
---pdb <pdb>, -p <pdb>
    
-
    Reference PDB or mmCIF. If phases are not provided, used for rigid-body refinement of input MTZ/sfCIF to generate phases.
    
+
    
+--pdboff <pdboff>, -p <pdboff>
    
+
    Reference PDB or mmCIF corresponding to the off/apo/ground/dark state. Used for rigid-body refinement of both input MTZs to generate phases.
    
 
    
 
 
    
-
    
---ncs-chains <fixed_chain> <moving_chain>, -n <fixed_chain> <moving_chain>
    
-
    NCS chains to overlay and subtract, specified as [fixed_chain, moving_chain].E.g. to overlay chain C onto chain B, specify: –ncs-chains B C
    
+
    
+--on-as-stationary
    
+
    Include this flag to align ‘off’ data onto ‘on’ data. By default, ‘off’ data is stationary and ‘on’ data is moved.
    
 
    
 
 
    
-
    
---mapname <mapname>
    
-
    Base filename for the output map files.
    
+
    
+--alpha <alpha>
    
+
    Alpha to use for error weighting of F-obs prior to Fourier Transform. Weights are computed as: 1 / ((1+(alpha*(SigF^2)) / <SigF>^2). Default value is alpha=0, e.g., no weighting is performed.
    
 
    
 
 
    
-
    
---ligands <ligands>, -l <ligands>
    
+
    
+--unmasked-radius <unmasked_radius>
    
+
    Maximum distance (in Anstroms) away from protein model to include voxels. Only applies to the ‘unmasked’ difference map output. Defaults to 5. Note that the regular difference map (e.g. the ‘masked’ version) is not affected by this parameter and maintains a solvent mask radius of 2 Angstroms.
    
+
    
+
+
    
+
    
+--rbr-selections <rbr_selections>, -r <rbr_selections>
    
+
    Specification of multiple rigid-body groups for refinement. By default, everything is refined as one rigid-body group.
    
+
    
+
+
    
+
    
+--ligands <ligands>, -l <ligands>
    
 
    Any .cif restraint files needed for refinement
    
 
    
 
 
    
-
    
---input-dir <input_dir>, -i <input_dir>
    
+
    
+--input-dir <input_dir>, -i <input_dir>
    
 
    Path to input files. Optional, defaults to ‘./’ (current directory)
    
 
    
 
 
    
-
    
---output-dir <output_dir>, -o <output_dir>
    
+
    
+--output-dir <output_dir>, -o <output_dir>
    
 
    Path to which output files should be written. Optional, defaults to ‘./’ (current directory)
    
 
    
 
 
    
-
    
---no-bss
    
-
    Include this flag to skip bulk solvent scaling in phenix.refine. By default, BSS is included.
    
+
    
+--spacing <spacing>, -s <spacing>
    
+
    Approximate voxel size in Angstroms for real-space maps. Defaults to 0.5 A. Value is approximate because there must be an integer number of voxels along each unit cell dimension
    
 
    
 
 
    
-
    
---spacing <spacing>, -s <spacing>
    
-
    Approximate voxel size in Angstroms for real-space maps. Defaults to 0.5 A. Value is approximate because there must be an integer number of voxels along each unit cell dimension
    
+
    
+--dmin <dmin>
    
+
    Highest-resolution (in Angstroms) reflections to include in Fourier transform for FloatGrid creation. By default, cutoff is the resolution limit of the lower-resolution input MTZ.
    
 
    
 
 
    
-
    
---dmin <dmin>
    
-
    Highest-resolution (in Angstroms) reflections to include in Fourier transform for FloatGrid creation. By default, cutoff is the resolution limit of the input MTZ.
    
+
    
+--no-bss
    
+
    Include this flag to skip bulk solvent scaling in phenix.refine. By default, BSS is included.
    
 
    
 
 
    
-
    
---verbose, -v
    
-
    Include this flag to print out phenix.refine outputs to the terminal. Useful for troubleshooting, but annoying; defaults to False.
    
+
    
+--verbose, -v
    
+
    Include this flag to print out scaleit and phenix.refine outputs to the terminal. Useful for troubleshooting, but annoying; defaults to False.
    
 
    
 
 
    
-
    
---eff <eff>
    
+
    
+--eff <eff>
    
 
    Custom .eff template for running phenix.refine.
    
 
    
 
 
    
-
    
---keep-temp-files <keep_temp_files>, -k <keep_temp_files>
    
+
    
+--keep-temp-files <keep_temp_files>, -k <keep_temp_files>
    
 
    Do not delete intermediate matchmaps files, but rather place them in the supplied directory. This directory is created as a subdirectory of the supplied output-dir.
    
 
    
 
 
    
-
    
---script <script>
    
+
    
+--script <script>
    
 
    Name for a file {script}.sh which can be run to repeat this command. By default, this file is called run_matchmaps.sh. Note that this file is written out in the current working directory, NOT the input or output directories
    
 
    
 
 
    
-
    
---phenix-version <phenix_version>
    
+
    
+--phenix-version <phenix_version>
    
 
    Specify phenix version as a string, e.g. ‘1.20’. If omitted, matchmaps will attempt to automatically detect the version in use by analyzing the output of phenix.version
    
 
    
 
 
    
-
    
-
    matchmaps.mr
    
-
    Compute a real-space difference map between inputs in different space groups / crystal packings. You will need two MTZ files, which will be referred to throughout as ‘on’ and ‘off’, though they could also be light/dark, bound/apo, mutant/WT, hot/cold, etc. Each mtz will need to contain structure factor amplitudes and uncertainties; you will not need any phases. You will, however, need an input model (assumed to correspond with the ‘off’ state) which will be used to determine phases. The input file may be in .pdb or .cif format. Please note that phenix must be installed and active in your environment for this function to run. If your mtzoff and mtzon are in the same spacegroup and crystal packing, see the basic matchmaps utility. More information can be found online at https://rs-station.github.io/matchmaps/index.html
    
-
    usage: matchmaps.mr [-h] --mtzoff mtzfileoff Foff SigFoff --mtzon mtzfileon
-                    Fon SigFon --pdboff PDBOFF [--ligands [LIGANDS ...]]
-                    [--input-dir INPUT_DIR] [--output-dir OUTPUT_DIR]
-                    [--on-as-stationary] [--no-bss] [--spacing SPACING]
-                    [--dmin DMIN] [--unmasked-radius UNMASKED_RADIUS]
-                    [--alpha ALPHA] [--verbose]
-                    [--rbr-selections [RBR_SELECTIONS ...]] [--eff EFF]
-                    [--keep-temp-files KEEP_TEMP_FILES] [--script SCRIPT]
-                    [--phenix-version PHENIX_VERSION]
+
    
+
    matchmaps.ncs
    
+
    Compute an ‘internal’ real-space difference map between NCS-related molecules. You will need an MTZ file with structure factor amplitudes and optionally containing phases, and a PDB/CIF file.Please note that phenix must be installed and active in your environment for this function to run. More information can be found online at https://rs-station.github.io/matchmaps/index.html
    
+
    usage: matchmaps.ncs [-h] --mtz [MTZ ...] [--phases PHASES] --pdb PDB
+                     --ncs-chains fixed_chain moving_chain [--mapname MAPNAME]
+                     [--ligands [LIGANDS ...]] [--input-dir INPUT_DIR]
+                     [--output-dir OUTPUT_DIR] [--spacing SPACING]
+                     [--dmin DMIN] [--no-bss] [--verbose] [--eff EFF]
+                     [--keep-temp-files KEEP_TEMP_FILES] [--script SCRIPT]
+                     [--phenix-version PHENIX_VERSION]
 
    
 
    
 
    
-
    
--h, --help
    
+
    
+-h, --help
    
 
    show this help message and exit
    
 
    
 
 
    
-
    
---mtzoff <mtzfileoff> <foff> <sigfoff>, -f <mtzfileoff> <foff> <sigfoff>
    
-
    MTZ or sfCIF containing off/apo/ground/dark state data. Specified as [filename F SigF]
    
+
    
+--mtz <mtz>, -m <mtz>
    
+
    MTZ or sfCIF file containing structure factor amplitudes. Specified as [filename F SigF] or [filename F]. SigF is not necessary if phases are also provided
    
 
    
 
 
    
-
    
---mtzon <mtzfileon> <fon> <sigfon>, -n <mtzfileon> <fon> <sigfon>
    
-
    MTZ or SFCIF containing on/bound/excited/bright state data. Specified as [filename F SigF]This file may be in a different spacegroup / crystal packing than mtzoff
    
+
    
+--phases <phases>
    
+
    Optional. Column in MTZ/sfCIF file containing phases. If phases are not provided, phases will be computed via rigid-body refinement of the provided model and structure factor amplitudes.
    
 
    
 
 
    
-
    
---pdboff <pdboff>, -p <pdboff>
    
-
    Reference PDB or mmCIF corresponding to the off/apo/ground/dark state. Used as a molecular replacement solution for mtzon and for rigid-body refinement of both input MTZs to generate phases.Should match mtzoff well enough that molecular replacement is not necessary.
    
+
    
+--pdb <pdb>, -p <pdb>
    
+
    Reference PDB or mmCIF. If phases are not provided, used for rigid-body refinement of input MTZ/sfCIF to generate phases.
    
 
    
 
 
    
-
    
---ligands <ligands>, -l <ligands>
    
-
    Any .cif restraint files needed for refinement
    
+
    
+--ncs-chains <fixed_chain> <moving_chain>, -n <fixed_chain> <moving_chain>
    
+
    NCS chains to overlay and subtract, specified as [fixed_chain, moving_chain].E.g. to overlay chain C onto chain B, specify: –ncs-chains B C
    
 
    
 
 
    
-
    
---input-dir <input_dir>, -i <input_dir>
    
-
    Path to input files. Optional, defaults to ‘./’ (current directory)
    
+
    
+--mapname <mapname>
    
+
    Base filename for the output map files.
    
 
    
 
 
    
-
    
---output-dir <output_dir>, -o <output_dir>
    
-
    Path to which output files should be written. Optional, defaults to ‘./’ (current directory)
    
+
    
+--ligands <ligands>, -l <ligands>
    
+
    Any .cif restraint files needed for refinement
    
 
    
 
 
    
-
    
---on-as-stationary
    
-
    Include this flag to align ‘off’ data onto ‘on’ data. By default, ‘off’ data is stationary and ‘on’ data is moved.For matchmaps.mr, this only applies to the post-molecular-replacement alignment; all maps will be placed in the spacegroup of mtzoff.
    
+
    
+--input-dir <input_dir>, -i <input_dir>
    
+
    Path to input files. Optional, defaults to ‘./’ (current directory)
    
 
    
 
 
    
-
    
---no-bss
    
-
    Include this flag to skip bulk solvent scaling in phenix.refine. By default, BSS is included.
    
+
    
+--output-dir <output_dir>, -o <output_dir>
    
+
    Path to which output files should be written. Optional, defaults to ‘./’ (current directory)
    
 
    
 
 
    
-
    
---spacing <spacing>, -s <spacing>
    
+
    
+--spacing <spacing>, -s <spacing>
    
 
    Approximate voxel size in Angstroms for real-space maps. Defaults to 0.5 A. Value is approximate because there must be an integer number of voxels along each unit cell dimension
    
 
    
 
 
    
-
    
---dmin <dmin>
    
+
    
+--dmin <dmin>
    
 
    Highest-resolution (in Angstroms) reflections to include in Fourier transform for FloatGrid creation. By default, cutoff is the resolution limit of the lower-resolution input MTZ.
    
 
    
 
 
    
-
    
---unmasked-radius <unmasked_radius>
    
-
    Maximum distance (in Anstroms) away from protein model to include voxels. Only applies to the ‘unmasked’ difference map output. Defaults to 5. Note that the regular difference map (e.g. the ‘masked’ version) is not affected by this parameter and maintains a solvent mask radius of 2 Angstroms.
    
-
    
-
-
    
-
    
---alpha <alpha>
    
-
    Alpha to use for error weighting of F-obs prior to Fourier Transform. Weights are computed as: 1 / ((1+(alpha*(SigF^2)) / <SigF>^2). Default value is alpha=0, e.g., no weighting is performed.
    
-
    
-
-
    
-
    
---verbose, -v
    
-
    Include this flag to print out phenix.phaser and phenix.refine outputs to the terminal. Useful for troubleshooting, but annoying; defaults to False.
    
+
    
+--no-bss
    
+
    Include this flag to skip bulk solvent scaling in phenix.refine. By default, BSS is included.
    
 
    
 
 
    
-
    
---rbr-selections <rbr_selections>, -r <rbr_selections>
    
-
    Specification of multiple rigid-body groups for refinement. By default, everything is refined as one rigid-body group. For matchmaps.mr, everything will always be molecular replaced as a single rigid-body, but may then be refined as multiple rigid bodies.
    
+
    
+--verbose, -v
    
+
    Include this flag to print out scaleit and phenix.refine outputs to the terminal. Useful for troubleshooting, but annoying; defaults to False.
    
 
    
 
 
    
-
    
---eff <eff>
    
+
    
+--eff <eff>
    
 
    Custom .eff template for running phenix.refine.
    
 
    
 
 
    
-
    
---keep-temp-files <keep_temp_files>, -k <keep_temp_files>
    
+
    
+--keep-temp-files <keep_temp_files>, -k <keep_temp_files>
    
 
    Do not delete intermediate matchmaps files, but rather place them in the supplied directory. This directory is created as a subdirectory of the supplied output-dir.
    
 
    
 
 
    
-
    
---script <script>
    
+
    
+--script <script>
    
 
    Name for a file {script}.sh which can be run to repeat this command. By default, this file is called run_matchmaps.sh. Note that this file is written out in the current working directory, NOT the input or output directories
    
 
    
 
 
    
-
    
---phenix-version <phenix_version>
    
+
    
+--phenix-version <phenix_version>
    
 
    Specify phenix version as a string, e.g. ‘1.20’. If omitted, matchmaps will attempt to automatically detect the version in use by analyzing the output of phenix.version
    
 
    
 
diff --git a/genindex.html b/genindex.html
index 49c0370..238727a 100644
--- a/genindex.html
+++ b/genindex.html
@@ -16,7 +16,7 @@
   
         
         
-        
+        
         
         
     
diff --git a/index.html b/index.html
index 4cda28c..cca4265 100644
--- a/index.html
+++ b/index.html
@@ -17,7 +17,7 @@
   
         
         
-        
+        
         
         
         
diff --git a/quickstart.html b/quickstart.html
index d9c7a53..ca6dc85 100644
--- a/quickstart.html
+++ b/quickstart.html
@@ -17,7 +17,7 @@
   
         
         
-        
+        
         
         
     
diff --git a/search.html b/search.html
index 7568691..1860c7e 100644
--- a/search.html
+++ b/search.html
@@ -17,7 +17,7 @@
   
         
         
-        
+        
         
         
     
diff --git a/searchindex.js b/searchindex.js
index 1a0667b..946a440 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"alltitles": {"A note on \u201con\u201d and \u201coff\u201d data": [[3, "a-note-on-on-and-off-data"]], "About the matchmaps algorithm": [[0, "about-the-matchmaps-algorithm"]], "Abstract": [[0, "abstract"]], "Additional dependencies": [[3, "additional-dependencies"]], "Algorithm overview": [[0, "algorithm-overview"]], "Algorithmic details": [[0, "algorithmic-details"]], "Basic usage": [[3, "basic-usage"]], "Comparing chains to each other": [[4, "comparing-chains-to-each-other"]], "Examples": [[3, "examples"]], "Getting started with matchmaps": [[3, "getting-started-with-matchmaps"]], "Input files": [[3, "input-files"]], "Installation": [[3, "installation"]], "Miscellaneous useful options": [[4, "miscellaneous-useful-options"]], "Multiple protein chains": [[4, "multiple-protein-chains"]], "Normalization": [[5, "normalization"]], "Output files": [[3, "output-files"]], "Periodic boundary conditions in Coot": [[5, "periodic-boundary-conditions-in-coot"]], "PyMOL Wiki pages for the commands mentioned": [[5, "pymol-wiki-pages-for-the-commands-mentioned"]], "Questions or thoughts?": [[0, "questions-or-thoughts"]], "Real-space alignment": [[0, "real-space-alignment"]], "Refinement": [[0, "refinement"]], "Refining chains individually": [[4, "refining-chains-individually"]], "Resolution cuts and error weighting": [[4, "resolution-cuts-and-error-weighting"]], "Running matchmaps from a script": [[3, "running-matchmaps-from-a-script"]], "Scaling": [[0, "scaling"]], "Solvent masking": [[0, "solvent-masking"]], "Solvent masking and bulk-solvent scaling": [[4, "solvent-masking-and-bulk-solvent-scaling"]], "Symmetry expansion": [[5, "symmetry-expansion"]], "Symmetry-related molecules": [[4, "symmetry-related-molecules"]], "The Fourier transform": [[0, "the-fourier-transform"]], "The matchmaps functions in brief": [[2, "the-matchmaps-functions-in-brief"]], "Troubleshooting and advanced usage": [[4, "troubleshooting-and-advanced-usage"]], "Variants of matchmaps": [[0, "variants-of-matchmaps"]], "Visualizing matchmaps results": [[5, "visualizing-matchmaps-results"]], "Working with .map files in Coot": [[5, "working-with-map-files-in-coot"]], "Working with .map files in PyMOL": [[5, "working-with-map-files-in-pymol"]], "matchmaps": [[1, "matchmaps"]], "matchmaps Documentation": [[2, "matchmaps-documentation"]], "matchmaps command-line interface": [[1, "matchmaps-command-line-interface"]], "matchmaps.mr": [[0, "matchmaps-mr"], [1, "matchmaps-mr"]], "matchmaps.ncs": [[0, "matchmaps-ncs"], [1, "matchmaps-ncs"]]}, "docnames": ["about", "cli", "index", "quickstart", "troubleshooting", "visualization"], "envversion": {"sphinx": 61, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2}, "filenames": ["about.md", "cli.md", "index.md", "quickstart.md", "troubleshooting.md", "visualization.md"], "indexentries": {"--alpha": [[1, "cmdoption-matchmaps-alpha", false], [1, "cmdoption-matchmaps.mr-alpha", false]], "--dmin": [[1, "cmdoption-matchmaps-dmin", false], [1, "cmdoption-matchmaps.mr-dmin", false], [1, "cmdoption-matchmaps.ncs-dmin", false]], "--eff": [[1, "cmdoption-matchmaps-eff", false], [1, "cmdoption-matchmaps.mr-eff", false], [1, "cmdoption-matchmaps.ncs-eff", false]], "--help": [[1, "cmdoption-matchmaps-h", false], [1, "cmdoption-matchmaps.mr-h", false], [1, "cmdoption-matchmaps.ncs-h", false]], "--input-dir": [[1, "cmdoption-matchmaps-input-dir", false], [1, "cmdoption-matchmaps.mr-input-dir", false], [1, "cmdoption-matchmaps.ncs-input-dir", false]], "--keep-temp-files": [[1, "cmdoption-matchmaps-keep-temp-files", false], [1, "cmdoption-matchmaps.mr-keep-temp-files", false], [1, "cmdoption-matchmaps.ncs-keep-temp-files", false]], "--ligands": [[1, "cmdoption-matchmaps-ligands", false], [1, "cmdoption-matchmaps.mr-ligands", false], [1, "cmdoption-matchmaps.ncs-ligands", false]], "--mapname": [[1, "cmdoption-matchmaps.ncs-mapname", false]], "--mtz": [[1, "cmdoption-matchmaps.ncs-mtz", false]], "--mtzoff": [[1, "cmdoption-matchmaps-mtzoff", false], [1, "cmdoption-matchmaps.mr-mtzoff", false]], "--mtzon": [[1, "cmdoption-matchmaps-mtzon", false], [1, "cmdoption-matchmaps.mr-mtzon", false]], "--ncs-chains": [[1, "cmdoption-matchmaps.ncs-ncs-chains", false]], "--no-bss": [[1, "cmdoption-matchmaps-no-bss", false], [1, "cmdoption-matchmaps.mr-no-bss", false], [1, "cmdoption-matchmaps.ncs-no-bss", false]], "--on-as-stationary": [[1, "cmdoption-matchmaps-on-as-stationary", false], [1, "cmdoption-matchmaps.mr-on-as-stationary", false]], "--output-dir": [[1, "cmdoption-matchmaps-output-dir", false], [1, "cmdoption-matchmaps.mr-output-dir", false], [1, "cmdoption-matchmaps.ncs-output-dir", false]], "--pdb": [[1, "cmdoption-matchmaps.ncs-pdb", false]], "--pdboff": [[1, "cmdoption-matchmaps-pdboff", false], [1, "cmdoption-matchmaps.mr-pdboff", false]], "--phases": [[1, "cmdoption-matchmaps.ncs-phases", false]], "--phenix-version": [[1, "cmdoption-matchmaps-phenix-version", false], [1, "cmdoption-matchmaps.mr-phenix-version", false], [1, "cmdoption-matchmaps.ncs-phenix-version", false]], "--rbr-selections": [[1, "cmdoption-matchmaps-rbr-selections", false], [1, "cmdoption-matchmaps.mr-rbr-selections", false]], "--script": [[1, "cmdoption-matchmaps-script", false], [1, "cmdoption-matchmaps.mr-script", false], [1, "cmdoption-matchmaps.ncs-script", false]], "--spacing": [[1, "cmdoption-matchmaps-spacing", false], [1, "cmdoption-matchmaps.mr-spacing", false], [1, "cmdoption-matchmaps.ncs-spacing", false]], "--unmasked-radius": [[1, "cmdoption-matchmaps-unmasked-radius", false], [1, "cmdoption-matchmaps.mr-unmasked-radius", false]], "--verbose": [[1, "cmdoption-matchmaps-verbose", false], [1, "cmdoption-matchmaps.mr-verbose", false], [1, "cmdoption-matchmaps.ncs-verbose", false]], "-f": [[1, "cmdoption-matchmaps-mtzoff", false], [1, "cmdoption-matchmaps.mr-mtzoff", false]], "-h": [[1, "cmdoption-matchmaps-h", false], [1, "cmdoption-matchmaps.mr-h", false], [1, "cmdoption-matchmaps.ncs-h", false]], "-i": [[1, "cmdoption-matchmaps-input-dir", false], [1, "cmdoption-matchmaps.mr-input-dir", false], [1, "cmdoption-matchmaps.ncs-input-dir", false]], "-k": [[1, "cmdoption-matchmaps-keep-temp-files", false], [1, "cmdoption-matchmaps.mr-keep-temp-files", false], [1, "cmdoption-matchmaps.ncs-keep-temp-files", false]], "-l": [[1, "cmdoption-matchmaps-ligands", false], [1, "cmdoption-matchmaps.mr-ligands", false], [1, "cmdoption-matchmaps.ncs-ligands", false]], "-m": [[1, "cmdoption-matchmaps.ncs-mtz", false]], "-n": [[1, "cmdoption-matchmaps-mtzon", false], [1, "cmdoption-matchmaps.mr-mtzon", false], [1, "cmdoption-matchmaps.ncs-ncs-chains", false]], "-o": [[1, "cmdoption-matchmaps-output-dir", false], [1, "cmdoption-matchmaps.mr-output-dir", false], [1, "cmdoption-matchmaps.ncs-output-dir", false]], "-p": [[1, "cmdoption-matchmaps-pdboff", false], [1, "cmdoption-matchmaps.mr-pdboff", false], [1, "cmdoption-matchmaps.ncs-pdb", false]], "-r": [[1, "cmdoption-matchmaps-rbr-selections", false], [1, "cmdoption-matchmaps.mr-rbr-selections", false]], "-s": [[1, "cmdoption-matchmaps-spacing", false], [1, "cmdoption-matchmaps.mr-spacing", false], [1, "cmdoption-matchmaps.ncs-spacing", false]], "-v": [[1, "cmdoption-matchmaps-verbose", false], [1, "cmdoption-matchmaps.mr-verbose", false], [1, "cmdoption-matchmaps.ncs-verbose", false]], "matchmaps command line option": [[1, "cmdoption-matchmaps-alpha", false], [1, "cmdoption-matchmaps-dmin", false], [1, "cmdoption-matchmaps-eff", false], [1, "cmdoption-matchmaps-h", false], [1, "cmdoption-matchmaps-input-dir", false], [1, "cmdoption-matchmaps-keep-temp-files", false], [1, "cmdoption-matchmaps-ligands", false], [1, "cmdoption-matchmaps-mtzoff", false], [1, "cmdoption-matchmaps-mtzon", false], [1, "cmdoption-matchmaps-no-bss", false], [1, "cmdoption-matchmaps-on-as-stationary", false], [1, "cmdoption-matchmaps-output-dir", false], [1, "cmdoption-matchmaps-pdboff", false], [1, "cmdoption-matchmaps-phenix-version", false], [1, "cmdoption-matchmaps-rbr-selections", false], [1, "cmdoption-matchmaps-script", false], [1, "cmdoption-matchmaps-spacing", false], [1, "cmdoption-matchmaps-unmasked-radius", false], [1, "cmdoption-matchmaps-verbose", false]], "matchmaps.mr command line option": [[1, "cmdoption-matchmaps.mr-alpha", false], [1, "cmdoption-matchmaps.mr-dmin", false], [1, "cmdoption-matchmaps.mr-eff", false], [1, "cmdoption-matchmaps.mr-h", false], [1, "cmdoption-matchmaps.mr-input-dir", false], [1, "cmdoption-matchmaps.mr-keep-temp-files", false], [1, "cmdoption-matchmaps.mr-ligands", false], [1, "cmdoption-matchmaps.mr-mtzoff", false], [1, "cmdoption-matchmaps.mr-mtzon", false], [1, "cmdoption-matchmaps.mr-no-bss", false], [1, "cmdoption-matchmaps.mr-on-as-stationary", false], [1, "cmdoption-matchmaps.mr-output-dir", false], [1, "cmdoption-matchmaps.mr-pdboff", false], [1, "cmdoption-matchmaps.mr-phenix-version", false], [1, "cmdoption-matchmaps.mr-rbr-selections", false], [1, "cmdoption-matchmaps.mr-script", false], [1, "cmdoption-matchmaps.mr-spacing", false], [1, "cmdoption-matchmaps.mr-unmasked-radius", false], [1, "cmdoption-matchmaps.mr-verbose", false]], "matchmaps.ncs command line option": [[1, "cmdoption-matchmaps.ncs-dmin", false], [1, "cmdoption-matchmaps.ncs-eff", false], [1, "cmdoption-matchmaps.ncs-h", false], [1, "cmdoption-matchmaps.ncs-input-dir", false], [1, "cmdoption-matchmaps.ncs-keep-temp-files", false], [1, "cmdoption-matchmaps.ncs-ligands", false], [1, "cmdoption-matchmaps.ncs-mapname", false], [1, "cmdoption-matchmaps.ncs-mtz", false], [1, "cmdoption-matchmaps.ncs-ncs-chains", false], [1, "cmdoption-matchmaps.ncs-no-bss", false], [1, "cmdoption-matchmaps.ncs-output-dir", false], [1, "cmdoption-matchmaps.ncs-pdb", false], [1, "cmdoption-matchmaps.ncs-phases", false], [1, "cmdoption-matchmaps.ncs-phenix-version", false], [1, "cmdoption-matchmaps.ncs-script", false], [1, "cmdoption-matchmaps.ncs-spacing", false], [1, "cmdoption-matchmaps.ncs-verbose", false]]}, "objects": {"matchmaps": [[1, 0, 1, "cmdoption-matchmaps-alpha", "--alpha"], [1, 0, 1, "cmdoption-matchmaps-dmin", "--dmin"], [1, 0, 1, "cmdoption-matchmaps-eff", "--eff"], [1, 0, 1, "cmdoption-matchmaps-h", "--help"], [1, 0, 1, "cmdoption-matchmaps-input-dir", "--input-dir"], [1, 0, 1, "cmdoption-matchmaps-keep-temp-files", "--keep-temp-files"], [1, 0, 1, "cmdoption-matchmaps-ligands", "--ligands"], [1, 0, 1, "cmdoption-matchmaps-mtzoff", "--mtzoff"], [1, 0, 1, "cmdoption-matchmaps-mtzon", "--mtzon"], [1, 0, 1, "cmdoption-matchmaps-no-bss", "--no-bss"], [1, 0, 1, "cmdoption-matchmaps-on-as-stationary", "--on-as-stationary"], [1, 0, 1, "cmdoption-matchmaps-output-dir", "--output-dir"], [1, 0, 1, "cmdoption-matchmaps-pdboff", "--pdboff"], [1, 0, 1, "cmdoption-matchmaps-phenix-version", "--phenix-version"], [1, 0, 1, "cmdoption-matchmaps-rbr-selections", "--rbr-selections"], [1, 0, 1, "cmdoption-matchmaps-script", "--script"], [1, 0, 1, "cmdoption-matchmaps-spacing", "--spacing"], [1, 0, 1, "cmdoption-matchmaps-unmasked-radius", "--unmasked-radius"], [1, 0, 1, "cmdoption-matchmaps-verbose", "--verbose"], [1, 0, 1, "cmdoption-matchmaps-mtzoff", "-f"], [1, 0, 1, "cmdoption-matchmaps-h", "-h"], [1, 0, 1, "cmdoption-matchmaps-input-dir", "-i"], [1, 0, 1, "cmdoption-matchmaps-keep-temp-files", "-k"], [1, 0, 1, "cmdoption-matchmaps-ligands", "-l"], [1, 0, 1, "cmdoption-matchmaps-mtzon", "-n"], [1, 0, 1, "cmdoption-matchmaps-output-dir", "-o"], [1, 0, 1, "cmdoption-matchmaps-pdboff", "-p"], [1, 0, 1, "cmdoption-matchmaps-rbr-selections", "-r"], [1, 0, 1, "cmdoption-matchmaps-spacing", "-s"], [1, 0, 1, "cmdoption-matchmaps-verbose", "-v"]], "matchmaps.mr": [[1, 0, 1, "cmdoption-matchmaps.mr-alpha", "--alpha"], [1, 0, 1, "cmdoption-matchmaps.mr-dmin", "--dmin"], [1, 0, 1, "cmdoption-matchmaps.mr-eff", "--eff"], [1, 0, 1, "cmdoption-matchmaps.mr-h", "--help"], [1, 0, 1, "cmdoption-matchmaps.mr-input-dir", "--input-dir"], [1, 0, 1, "cmdoption-matchmaps.mr-keep-temp-files", "--keep-temp-files"], [1, 0, 1, "cmdoption-matchmaps.mr-ligands", "--ligands"], [1, 0, 1, "cmdoption-matchmaps.mr-mtzoff", "--mtzoff"], [1, 0, 1, "cmdoption-matchmaps.mr-mtzon", "--mtzon"], [1, 0, 1, "cmdoption-matchmaps.mr-no-bss", "--no-bss"], [1, 0, 1, "cmdoption-matchmaps.mr-on-as-stationary", "--on-as-stationary"], [1, 0, 1, "cmdoption-matchmaps.mr-output-dir", "--output-dir"], [1, 0, 1, "cmdoption-matchmaps.mr-pdboff", "--pdboff"], [1, 0, 1, "cmdoption-matchmaps.mr-phenix-version", "--phenix-version"], [1, 0, 1, "cmdoption-matchmaps.mr-rbr-selections", "--rbr-selections"], [1, 0, 1, "cmdoption-matchmaps.mr-script", "--script"], [1, 0, 1, "cmdoption-matchmaps.mr-spacing", "--spacing"], [1, 0, 1, "cmdoption-matchmaps.mr-unmasked-radius", "--unmasked-radius"], [1, 0, 1, "cmdoption-matchmaps.mr-verbose", "--verbose"], [1, 0, 1, "cmdoption-matchmaps.mr-mtzoff", "-f"], [1, 0, 1, "cmdoption-matchmaps.mr-h", "-h"], [1, 0, 1, "cmdoption-matchmaps.mr-input-dir", "-i"], [1, 0, 1, "cmdoption-matchmaps.mr-keep-temp-files", "-k"], [1, 0, 1, "cmdoption-matchmaps.mr-ligands", "-l"], [1, 0, 1, "cmdoption-matchmaps.mr-mtzon", "-n"], [1, 0, 1, "cmdoption-matchmaps.mr-output-dir", "-o"], [1, 0, 1, "cmdoption-matchmaps.mr-pdboff", "-p"], [1, 0, 1, "cmdoption-matchmaps.mr-rbr-selections", "-r"], [1, 0, 1, "cmdoption-matchmaps.mr-spacing", "-s"], [1, 0, 1, "cmdoption-matchmaps.mr-verbose", "-v"]], "matchmaps.ncs": [[1, 0, 1, "cmdoption-matchmaps.ncs-dmin", "--dmin"], [1, 0, 1, "cmdoption-matchmaps.ncs-eff", "--eff"], [1, 0, 1, "cmdoption-matchmaps.ncs-h", "--help"], [1, 0, 1, "cmdoption-matchmaps.ncs-input-dir", "--input-dir"], [1, 0, 1, "cmdoption-matchmaps.ncs-keep-temp-files", "--keep-temp-files"], [1, 0, 1, "cmdoption-matchmaps.ncs-ligands", "--ligands"], [1, 0, 1, "cmdoption-matchmaps.ncs-mapname", "--mapname"], [1, 0, 1, "cmdoption-matchmaps.ncs-mtz", "--mtz"], [1, 0, 1, "cmdoption-matchmaps.ncs-ncs-chains", "--ncs-chains"], [1, 0, 1, "cmdoption-matchmaps.ncs-no-bss", "--no-bss"], [1, 0, 1, "cmdoption-matchmaps.ncs-output-dir", "--output-dir"], [1, 0, 1, "cmdoption-matchmaps.ncs-pdb", "--pdb"], [1, 0, 1, "cmdoption-matchmaps.ncs-phases", "--phases"], [1, 0, 1, "cmdoption-matchmaps.ncs-phenix-version", "--phenix-version"], [1, 0, 1, "cmdoption-matchmaps.ncs-script", "--script"], [1, 0, 1, "cmdoption-matchmaps.ncs-spacing", "--spacing"], [1, 0, 1, "cmdoption-matchmaps.ncs-verbose", "--verbose"], [1, 0, 1, "cmdoption-matchmaps.ncs-h", "-h"], [1, 0, 1, "cmdoption-matchmaps.ncs-input-dir", "-i"], [1, 0, 1, "cmdoption-matchmaps.ncs-keep-temp-files", "-k"], [1, 0, 1, "cmdoption-matchmaps.ncs-ligands", "-l"], [1, 0, 1, "cmdoption-matchmaps.ncs-mtz", "-m"], [1, 0, 1, "cmdoption-matchmaps.ncs-ncs-chains", "-n"], [1, 0, 1, "cmdoption-matchmaps.ncs-output-dir", "-o"], [1, 0, 1, "cmdoption-matchmaps.ncs-pdb", "-p"], [1, 0, 1, "cmdoption-matchmaps.ncs-spacing", "-s"], [1, 0, 1, "cmdoption-matchmaps.ncs-verbose", "-v"]]}, "objnames": {"0": ["std", "cmdoption", "program option"]}, "objtypes": {"0": "std:cmdoption"}, "terms": {"": [0, 1, 2, 3, 4, 5], "0": [0, 1, 3, 4], "006": 5, "1": [0, 1, 3, 4], "15": 3, "2": [0, 1, 3, 4, 5], "20": [1, 3, 5], "21": 3, "25": [0, 4], "3": 3, "4": 0, "5": [0, 1, 3, 4], "6": 3, "7": 0, "9": 3, "90": 5, "A": [0, 1, 2, 4], "As": [3, 5], "At": 3, "But": [0, 5], "By": [0, 1, 3, 4], "For": [0, 1, 2, 3, 4], "If": [0, 1, 2, 3, 4, 5], "In": [0, 3, 4, 5], "It": 3, "NOT": 1, "No": 3, "ON": [0, 4], "Of": 5, "On": 3, "One": [0, 4], "Such": 0, "The": [1, 3, 4], "Then": [0, 5], "There": [3, 4, 5], "These": [0, 3], "To": [0, 3, 4], "_unmask": [0, 4], "about": [2, 4, 5], "abov": [0, 3, 5], "abruptli": 5, "absolut": 3, "accordingli": 0, "account": 0, "across": [0, 2, 4], "action": 2, "activ": [1, 3], "actual": 3, "ad": [0, 3], "add": 3, "addit": 0, "addition": 3, "address": 4, "admittedli": 4, "affect": 1, "after": [0, 3, 4], "afterward": 0, "again": 3, "against": 4, "aim": 4, "algorithm": [3, 4], "align": [1, 2, 3, 4], "all": [0, 1, 2, 3, 4, 5], "allow": 0, "along": [0, 1, 2, 3, 5], "alpha": [0, 1, 4, 5], "alreadi": 5, "also": [0, 1, 3, 4], "alter": 4, "altern": [3, 4], "altogeth": 0, "alwai": [1, 3, 4, 5], "ambigu": 4, "amplitud": [0, 1, 3], "an": [0, 1, 2, 3, 4, 5], "analysi": [0, 3], "analyz": [1, 4], "angstrom": [0, 1, 3], "ani": [0, 1, 3, 4, 5], "anisotrop": 0, "annoi": [1, 4], "anoth": [4, 5], "anstrom": 1, "anyth": 4, "apo": [1, 3, 4], "apo_data": 3, "appar": 3, "appli": [0, 1, 3, 4, 5], "approach": [0, 4, 5], "appropri": 0, "approxim": [0, 1, 4], "ar": [0, 1, 2, 3, 4, 5], "argument": 3, "aris": 5, "around": [4, 5], "artif": 5, "artifact": 0, "artifactu": 4, "assist": 0, "assum": [1, 3, 4, 5], "asymmetr": 0, "atom": 0, "attempt": [1, 5], "automat": 1, "avail": 0, "averag": 4, "avoid": 0, "awai": [0, 1, 3, 4], "b": [0, 1, 3, 4], "bad": 4, "balanc": 0, "base": 1, "basic": [1, 2], "becaus": [0, 1, 4, 5], "becom": [3, 4], "been": 3, "befor": 3, "behavior": 5, "behind": 0, "being": [3, 4], "believ": 0, "belong": 0, "below": [0, 1, 3, 4, 5], "best": [0, 5], "better": 4, "between": [0, 1, 2], "bia": [0, 3], "big": 4, "biolog": 0, "black": 0, "bodi": [0, 1, 4], "booster": 0, "both": [0, 1, 3], "bottom": 5, "bound": [0, 1, 3, 4], "bound_data": 3, "box": 0, "brief": 5, "briefli": [2, 5], "bright": 1, "brookner": 2, "bss": [1, 4], "bug": [4, 5], "built": 1, "bulk": [0, 1], "c": [0, 1], "calcul": 0, "call": [1, 3], "can": [0, 1, 2, 3, 4, 5], "carri": 0, "case": [0, 4, 5], "catch": 5, "ccp4": [0, 1, 3, 4, 5], "cell": [0, 1, 2, 5], "chain": [0, 1], "chang": [0, 2, 3, 4], "check": [0, 2, 5], "chosen": 0, "cif": [1, 3], "clariti": 3, "close": 5, "code": [0, 4], "coerc": 5, "cold": [1, 3], "column": [0, 1, 3], "com": 3, "combin": 0, "come": 4, "command": [0, 2, 3], "common": 0, "compat": 3, "complet": 3, "complex": 0, "complic": 3, "comput": [0, 1, 2, 3, 4, 5], "conceiv": 2, "conda": 3, "conform": 0, "consid": 4, "consist": 2, "contain": [0, 1, 2, 3, 4], "content": 3, "contour": 5, "conveni": 0, "convers": 0, "convinc": 5, "coordin": 3, "coot": [0, 4], "copi": [0, 5], "core": [0, 2], "corner": 5, "correct": 0, "correspond": [1, 3], "cost": 4, "could": [0, 1, 3, 4], "counterintuit": 5, "cours": [4, 5], "creat": [0, 1, 3], "creation": 1, "critic": 0, "cryo": 5, "crystal": [0, 1, 2], "crystallograph": [0, 2, 4, 5], "crystallographi": [0, 2], "cube": 0, "curiou": 3, "current": [1, 3], "custom": [0, 1, 4], "cut": 0, "cutoff": 1, "d": [2, 3], "dark": [1, 3], "data": [0, 1, 2, 4], "dataset": [0, 2, 3, 4], "deactiv": 0, "deal": 5, "debug": 4, "decid": 4, "default": [0, 1, 3, 4, 5], "defin": [0, 2, 4], "defint": 4, "delet": [1, 3], "denni": 2, "densiti": [0, 4, 5], "depend": [0, 4], "describ": [0, 3], "descript": 5, "design": 5, "desir": [4, 5], "detail": 3, "detect": [0, 1], "determin": 1, "dialog": 5, "differ": [0, 1, 2, 3, 4, 5], "difference_map": 5, "differencemesh_posit": 5, "different_dir_with_input_fil": 3, "dimens": [1, 2], "dir": [1, 3], "direct": 3, "directli": [3, 4, 5], "directori": [1, 3], "disabl": 4, "discard": 0, "discuss": 0, "disregard": 4, "distanc": 1, "dmin": [1, 4], "do": [0, 1, 2, 3, 4, 5], "doc": 2, "docum": 3, "document": [3, 4], "doe": [4, 5], "doek": 2, "doesn": [2, 4], "domin": 4, "don": [0, 3, 4, 5], "downgrad": 3, "downstream": 5, "due": 2, "e": [0, 1, 3, 4], "each": [0, 1, 3], "earlier": 3, "easi": [0, 4, 5], "easiest": 0, "edg": 5, "editor": 5, "eff": [0, 1, 4], "effect": 4, "either": 3, "electron": 0, "elegantli": 4, "em": 5, "encount": 5, "end": [0, 4, 5], "enough": [1, 5], "ensur": 3, "env": 3, "environ": [0, 1, 3], "equal": [3, 4], "equat": 0, "error": [0, 1, 3], "essenti": [0, 4, 5], "estim": 4, "etc": [1, 3], "even": [0, 2, 4, 5], "ever": 5, "everyth": [1, 3, 4], "exactli": [0, 3, 4], "examin": 3, "exampl": 0, "excit": 1, "excitedli": 3, "exclus": 3, "exit": 1, "expand": 5, "expect": [0, 3, 4], "experi": 5, "explicit": 0, "explor": [2, 3], "extend": 0, "extern": 3, "extraordinari": 0, "f": [0, 1, 4], "factor": [0, 1, 3], "fals": 1, "famili": 2, "familiar": 5, "far": [0, 3, 4], "farther": 4, "featur": [0, 3, 4], "figur": [3, 4, 5], "file": [0, 1, 4], "filenam": [1, 3], "filter": 0, "final": [0, 3, 4], "find": [0, 2, 4, 5], "fine": [3, 4, 5], "finer": 4, "finish": 3, "finnicki": 4, "first": 3, "fit": 0, "fixed_chain": 1, "flag": [1, 3, 4], "flatten": 4, "flexibl": 0, "floatgrid": 1, "fly": 5, "fob": 3, "foff": 1, "follow": [1, 3, 4], "fon": 1, "form": 0, "format": 1, "formula": [0, 4], "found": [0, 1, 2, 3], "fourier": [1, 4, 5], "fp": 3, "frac": 4, "free": 3, "fresh": 3, "from": [0, 1, 4, 5], "full": [0, 3, 4], "fulli": 0, "function": [0, 1, 4], "further": 4, "futur": 3, "g": [0, 1, 3, 4], "gemmi": 0, "gener": [0, 1, 3, 4], "get": 0, "git": 3, "github": [0, 1, 3, 4, 5], "given": 5, "global": 4, "go": 3, "goal": 4, "good": [3, 4, 5], "grid": 0, "ground": 1, "group": 1, "guid": [0, 2, 4], "h": 1, "ha": [0, 4], "hand": 3, "handl": 0, "happi": 5, "hard": [4, 5], "harvard": 2, "hasn": 3, "have": [0, 2, 3, 4, 5], "headach": 4, "hear": 0, "hekstra": 2, "help": [0, 1, 3, 4, 5], "here": [0, 2, 3, 4, 5], "hesit": [0, 4], "high": 0, "highest": [1, 4], "homo": 4, "hope": 3, "hopefulli": 5, "hot": 1, "how": [0, 3, 4, 5], "howev": [0, 1, 4, 5], "html": 1, "http": [1, 3], "i": [0, 1, 2, 3, 4, 5], "idea": [0, 3, 4], "ident": 0, "identifi": 4, "ignor": 3, "immedi": 4, "impercept": 5, "implement": [0, 4], "import": [0, 4], "importantli": 3, "includ": [0, 1, 4], "increas": 4, "index": 1, "indic": 4, "inform": [1, 2, 3, 4], "input": [0, 1, 4, 5], "input_dir": 1, "input_fil": 3, "insid": [3, 5], "inspect": 3, "instal": [1, 2], "instead": 4, "instruct": [0, 2], "instuct": 0, "integ": 1, "interest": [0, 3, 4], "intermedi": 1, "intern": [0, 1, 2], "interpolate_grid_of_aligned_model2": 0, "introduct": 0, "involv": 4, "io": 1, "isn": 4, "isomesh": 5, "isomorph": [0, 2], "issu": [0, 3, 4, 5], "its": [0, 3], "journal": 0, "just": [4, 5], "k": 1, "keep": [0, 1, 3, 5], "keep_temp_fil": 1, "kei": 5, "kept": 3, "know": [0, 3], "l": 1, "lab": 2, "larg": 4, "larger": 4, "later": 5, "latest": 3, "laxli": 4, "learn": [0, 2], "left": 5, "let": [0, 3], "level": 5, "librari": 0, "lie": 5, "ligand": [0, 1, 3, 4], "light": [1, 3], "like": [0, 2, 3, 4, 5], "likelihood": 5, "limit": 1, "line": [0, 2, 3, 4], "lit": 3, "littl": 4, "live": 3, "ll": [3, 5], "load": 5, "log": 4, "long": [3, 4], "look": [0, 3, 4, 5], "lot": 4, "love": 0, "lower": 1, "luck": 5, "m": 1, "macromolecul": 0, "made": 3, "mai": [0, 1, 3, 4], "main": [0, 4], "maintain": 1, "make": [0, 3, 4, 5], "manag": 3, "mani": 5, "manner": 3, "map": [0, 1, 2, 3, 4], "map_auto_expand_sym": 5, "map_from_matchmap": 5, "mapnam": 1, "mask": [1, 3], "match": [0, 1], "matchmap": 4, "mate": 4, "maximum": [0, 1], "me": [0, 4], "mean": [4, 5], "meantim": 3, "measur": 0, "mediat": 0, "medium": 4, "messag": 1, "method": 0, "mi": 0, "might": [3, 4, 5], "mind": 5, "minim": 0, "misalign": 4, "mix": 3, "mmcif": 1, "mmfile": 3, "model": [0, 1, 2, 3, 4, 5], "modest": 0, "modif": 0, "modifi": [0, 4], "molecul": [0, 1], "molecular": [0, 1], "more": [0, 1, 2, 3, 4], "most": [3, 4], "motion": 4, "move": [0, 1, 4], "moving_chain": 1, "mr": [2, 3], "mrc": 5, "mtz": [0, 1, 2, 3, 5], "mtzdump": 3, "mtzfileoff": 1, "mtzfileon": 1, "mtzoff": [1, 3], "mtzon": [1, 3], "much": [0, 3, 4], "multim": 4, "multipl": [0, 1], "must": 1, "mutant": [1, 3], "mutat": 0, "my": 3, "my_new_mesh": 5, "mymtz": 3, "myproject": 3, "n": [1, 3], "name": [0, 1, 3], "nc": [2, 4], "nearest": 0, "nearli": 2, "necessari": [0, 1, 3], "necessarili": 4, "need": [1, 3, 4, 5], "neg": 3, "never": 4, "new": 4, "next": 4, "nicer": 4, "noisi": [0, 4], "nomin": 0, "non": [0, 2, 4], "nonsens": 5, "normal": 0, "normalize_ccp4_map": 5, "note": [0, 1], "number": [0, 1], "o": 1, "ob": [0, 1], "observ": [0, 3], "off": [0, 1, 4, 5], "off_befor": 3, "often": [0, 5], "omit": [0, 1], "on_befor": 3, "on_minus_off": [3, 5], "on_minus_off_unmask": 3, "onc": 5, "one": [0, 1, 3, 4], "onli": [0, 1, 3, 4, 5], "onlin": 1, "onto": 1, "open": [0, 2, 3, 5], "oper": [0, 5], "opportun": 4, "option": [0, 1, 2, 3, 5], "order": 0, "origin": 5, "orthorhomb": 5, "other": [0, 2, 3], "otherwis": 4, "our": 2, "out": [0, 1, 2, 3, 4, 5], "outlin": 5, "output": [0, 1, 4, 5], "output_dir": 1, "outsid": [0, 5], "overal": 0, "overlai": [0, 1], "overwritten": 3, "own": 4, "p": 1, "p1": 5, "pack": [0, 1, 2, 4], "packag": [0, 2, 3], "page": 3, "pair": [2, 3, 4], "paper": 0, "paramet": [0, 1, 3, 4], "part": [2, 5], "particular": 4, "pass": 4, "path": [1, 3], "pdb": [1, 3, 5], "pdb_in_high_symmetry_spacegroup": 5, "pdboff": [1, 3], "peak": 4, "perform": [0, 1, 4], "perhap": 3, "permit": 0, "perturb": [0, 3], "ph2fofcwt": 0, "phase": [0, 1, 2], "phaser": [0, 1], "phenix": [0, 1, 3, 4], "phenix_env": 3, "phenix_vers": 1, "piec": 3, "pip": 3, "pipelin": 3, "place": [0, 1, 3], "plan": 0, "pleas": [0, 1, 2, 3, 4, 5], "plu": 3, "point": [0, 3, 4], "poorli": 0, "popular": 0, "posit": 3, "possibl": [0, 4, 5], "post": 1, "potenti": [4, 5], "pre": 2, "prefer": 5, "preprend": 3, "present": [2, 4], "pretti": [0, 4], "prevent": 0, "previou": 3, "print": [1, 2, 3, 4], "prior": [1, 3, 4], "probabl": [4, 5], "proce": 0, "procedur": 0, "produc": [0, 2, 3, 4, 5], "program": [0, 3], "promin": 3, "properti": 0, "protein": [0, 1, 3, 5], "provid": [0, 1, 3, 4], "pull": 4, "purpos": [4, 5], "pymol": [0, 4], "pypi": 3, "python": [0, 2, 3], "question": [4, 5], "quick": 3, "quickstart": [2, 4], "quirk": 5, "quit": 2, "r": [0, 1, 3], "radiu": [0, 1, 3, 4], "rai": [0, 2], "rang": 0, "rather": [0, 1, 4], "rbr": [1, 4], "rbr_select": 1, "re": [0, 3, 4, 5], "reach": 5, "read": [0, 3, 4], "real": [1, 2, 3, 4, 5], "realli": 4, "reason": [0, 4], "reciproc": 2, "reciprocalspaceship": [0, 3], "recommend": [0, 3, 4], "refer": [0, 1], "refin": [1, 3], "reflect": [0, 1, 2, 4], "regard": 0, "region": [0, 5], "regular": 1, "rel": [0, 3, 4], "relat": [0, 1, 5], "relev": 5, "reli": 3, "remain": [0, 4], "rememb": 3, "remind": 3, "render": [0, 5], "renumb": 0, "reopen": 5, "repeat": 1, "replac": [0, 1], "repres": 3, "reproduc": 3, "request": 4, "requir": [0, 2], "rescu": 0, "resi": 5, "resolut": [0, 1], "resolv": 4, "respect": 3, "restraint": [1, 3], "result": [0, 4], "retain": 0, "revers": 0, "right": 3, "rigid": [0, 1, 4], "rotat": 0, "round": 0, "run": [0, 1, 4, 5], "run_matchmap": [1, 3], "sai": [4, 5], "same": [0, 1, 2, 3], "sampl": 2, "save": 3, "scale": 1, "scaleit": [0, 1], "script": 1, "second": [0, 4], "see": [0, 1, 2, 3, 4], "select": [0, 1, 4, 5], "sens": 0, "sensit": 0, "separ": [0, 4], "seri": 5, "set": [0, 5], "sfcif": 1, "sh": [1, 3], "shift": 0, "short": 3, "shorter": 4, "should": [0, 1, 3, 4, 5], "show": [0, 1], "side": 4, "sigf": [0, 1], "sigfob": 3, "sigfoff": 1, "sigfon": 1, "sigfp": 3, "sigma": 4, "signal": [0, 3, 4], "similar": [2, 3], "simpli": 4, "singl": [1, 2], "situat": 0, "size": [1, 4], "skip": [0, 1], "slightli": [0, 3], "slow": 4, "small": 0, "so": [0, 2, 3, 4], "softwar": [0, 2, 3, 5], "solut": [0, 1], "solvent": [1, 3], "some": [0, 3, 4, 5], "someth": [3, 4], "sometim": 5, "somewher": 3, "sort": 4, "sort_hetatm": 0, "sourc": [0, 2, 3, 4], "space": [1, 2, 3, 4, 5], "spacegroup": [0, 1, 2, 5], "specif": [1, 3, 4, 5], "specifi": [0, 1, 3], "spuriou": 5, "start": [0, 2, 4], "state": [0, 1], "station": [1, 2, 3], "stationari": [1, 4], "statist": 4, "step": 0, "still": 4, "strict": 4, "stricter": 4, "strictli": 4, "string": 1, "strong": 4, "strongli": 4, "structur": [0, 1, 3, 4, 5], "subdirectori": 1, "subtract": [0, 1, 2, 3], "success": 5, "successfulli": 3, "suffix": 4, "suggest": 0, "summari": 3, "suppli": [1, 3, 4], "support": [0, 3], "sure": 3, "symmetri": [0, 2], "t": [0, 2, 3, 4, 5], "take": 2, "tell": 4, "temp": [1, 3], "templat": [0, 1, 4], "temporari": 3, "term": 4, "termin": [1, 4], "text": 5, "than": [0, 1, 3, 4, 5], "thei": [0, 1, 2, 3, 5], "them": [1, 2, 3, 5], "thi": [0, 1, 2, 3, 4, 5], "those": [0, 3], "though": [1, 3, 5], "three": [2, 3], "through": [0, 4], "throughout": [1, 3, 4], "thrown": 3, "thu": [4, 5], "tight": 0, "time": [0, 3], "tip": 2, "togeth": 4, "touch": 0, "tour": 3, "transform": [1, 4, 5], "translat": 0, "trick": 4, "troubl": [3, 4], "troubleshoot": [1, 3], "truncat": [0, 4], "try": [4, 5], "turn": [0, 5], "two": [0, 1, 2, 3, 4, 5], "type": [2, 3], "typic": [4, 5], "unbias": [0, 2], "uncertainti": [0, 1, 3], "unfortun": [4, 5], "uniqu": 3, "unit": [0, 1, 2, 5], "unless": 3, "unlik": 5, "unmask": [1, 3, 4], "unmasked_radiu": 1, "unnecessari": 0, "up": [3, 4], "updat": 3, "us": [0, 1, 2, 3, 5], "usag": [1, 2], "useless": 0, "user": [0, 5], "usual": 5, "util": [0, 1, 2, 3], "utilit": [2, 3], "v": [1, 3], "valu": [1, 4], "ve": 4, "verbos": [1, 4], "veri": [0, 4, 5], "version": [1, 3], "via": [0, 1, 3, 4, 5], "vicin": 3, "visual": [0, 3, 4], "voxel": [0, 1, 4], "wa": [2, 3], "wai": [0, 3, 5], "walkthrough": 2, "want": [0, 3, 4, 5], "warm": 3, "water": 0, "we": [0, 3, 4, 5], "weight": [0, 1], "weird_solvent_1": 3, "weird_solvent_2": 3, "welcom": [2, 4], "well": [1, 3], "went": 3, "were": 3, "what": [3, 4], "when": [3, 4, 5], "where": [3, 4], "wherein": 0, "wherev": 5, "which": [0, 1, 2, 3, 4, 5], "while": 4, "wise": 0, "wish": 5, "within": [0, 4], "without": 5, "work": [0, 1, 2, 3, 4], "workaround": 5, "would": [0, 3, 4, 5], "write": [3, 4], "written": [1, 3, 4], "wrong": 3, "wt": [1, 3], "x": [0, 2], "yet": 3, "yield": 0, "you": [0, 1, 2, 3, 4, 5], "your": [0, 1, 2, 3, 4, 5], "zero": 0}, "titles": ["About the matchmaps algorithm", "matchmaps command-line interface", "matchmaps Documentation", "Getting started with matchmaps", "Troubleshooting and advanced usage", "Visualizing matchmaps results"], "titleterms": {"A": 3, "The": [0, 2], "about": 0, "abstract": 0, "addit": 3, "advanc": 4, "algorithm": 0, "align": 0, "basic": 3, "boundari": 5, "brief": 2, "bulk": 4, "chain": 4, "command": [1, 5], "compar": 4, "condit": 5, "coot": 5, "cut": 4, "data": 3, "depend": 3, "detail": 0, "document": 2, "each": 4, "error": 4, "exampl": 3, "expans": 5, "file": [3, 5], "fourier": 0, "from": 3, "function": 2, "get": 3, "individu": 4, "input": 3, "instal": 3, "interfac": 1, "line": 1, "map": 5, "mask": [0, 4], "matchmap": [0, 1, 2, 3, 5], "mention": 5, "miscellan": 4, "molecul": 4, "mr": [0, 1], "multipl": 4, "nc": [0, 1], "normal": 5, "note": 3, "off": 3, "option": 4, "other": 4, "output": 3, "overview": 0, "page": 5, "period": 5, "protein": 4, "pymol": 5, "question": 0, "real": 0, "refin": [0, 4], "relat": 4, "resolut": 4, "result": 5, "run": 3, "scale": [0, 4], "script": 3, "solvent": [0, 4], "space": 0, "start": 3, "symmetri": [4, 5], "thought": 0, "transform": 0, "troubleshoot": 4, "us": 4, "usag": [3, 4], "variant": 0, "visual": 5, "weight": 4, "wiki": 5, "work": 5}})
\ No newline at end of file
+Search.setIndex({"alltitles": {"A note on \u201con\u201d and \u201coff\u201d data": [[3, "a-note-on-on-and-off-data"]], "About the matchmaps algorithm": [[0, "about-the-matchmaps-algorithm"]], "Abstract": [[0, "abstract"]], "Additional dependencies": [[3, "additional-dependencies"]], "Algorithm overview": [[0, "algorithm-overview"]], "Algorithmic details": [[0, "algorithmic-details"]], "Basic usage": [[3, "basic-usage"]], "Comparing chains to each other": [[4, "comparing-chains-to-each-other"]], "Examples": [[3, "examples"]], "Getting started with matchmaps": [[3, "getting-started-with-matchmaps"]], "Input files": [[3, "input-files"]], "Installation": [[3, "installation"]], "Miscellaneous useful options": [[4, "miscellaneous-useful-options"]], "Multiple protein chains": [[4, "multiple-protein-chains"]], "Normalization": [[5, "normalization"]], "Output files": [[3, "output-files"]], "Periodic boundary conditions in Coot": [[5, "periodic-boundary-conditions-in-coot"]], "PyMOL Wiki pages for the commands mentioned": [[5, "pymol-wiki-pages-for-the-commands-mentioned"]], "Questions or thoughts?": [[0, "questions-or-thoughts"]], "Real-space alignment": [[0, "real-space-alignment"]], "Refinement": [[0, "refinement"]], "Refining chains individually": [[4, "refining-chains-individually"]], "Resolution cuts and error weighting": [[4, "resolution-cuts-and-error-weighting"]], "Running matchmaps from a script": [[3, "running-matchmaps-from-a-script"]], "Scaling": [[0, "scaling"]], "Solvent masking": [[0, "solvent-masking"]], "Solvent masking and bulk-solvent scaling": [[4, "solvent-masking-and-bulk-solvent-scaling"]], "Symmetry expansion": [[5, "symmetry-expansion"]], "Symmetry-related molecules": [[4, "symmetry-related-molecules"]], "The Fourier transform": [[0, "the-fourier-transform"]], "The matchmaps functions in brief": [[2, "the-matchmaps-functions-in-brief"]], "Troubleshooting and advanced usage": [[4, "troubleshooting-and-advanced-usage"]], "Variants of matchmaps": [[0, "variants-of-matchmaps"]], "Visualizing matchmaps results": [[5, "visualizing-matchmaps-results"]], "Working with .map files in Coot": [[5, "working-with-map-files-in-coot"]], "Working with .map files in PyMOL": [[5, "working-with-map-files-in-pymol"]], "matchmaps": [[1, "matchmaps"]], "matchmaps Documentation": [[2, "matchmaps-documentation"]], "matchmaps command-line interface": [[1, "matchmaps-command-line-interface"]], "matchmaps.mr": [[0, "matchmaps-mr"], [1, "matchmaps-mr"]], "matchmaps.ncs": [[0, "matchmaps-ncs"], [1, "matchmaps-ncs"]]}, "docnames": ["about", "cli", "index", "quickstart", "troubleshooting", "visualization"], "envversion": {"sphinx": 61, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2}, "filenames": ["about.md", "cli.md", "index.md", "quickstart.md", "troubleshooting.md", "visualization.md"], "indexentries": {"--alpha": [[1, "cmdoption-matchmaps-alpha", false], [1, "cmdoption-matchmaps.mr-alpha", false]], "--dmin": [[1, "cmdoption-matchmaps-dmin", false], [1, "cmdoption-matchmaps.mr-dmin", false], [1, "cmdoption-matchmaps.ncs-dmin", false]], "--eff": [[1, "cmdoption-matchmaps-eff", false], [1, "cmdoption-matchmaps.mr-eff", false], [1, "cmdoption-matchmaps.ncs-eff", false]], "--help": [[1, "cmdoption-matchmaps-h", false], [1, "cmdoption-matchmaps.mr-h", false], [1, "cmdoption-matchmaps.ncs-h", false]], "--input-dir": [[1, "cmdoption-matchmaps-input-dir", false], [1, "cmdoption-matchmaps.mr-input-dir", false], [1, "cmdoption-matchmaps.ncs-input-dir", false]], "--keep-temp-files": [[1, "cmdoption-matchmaps-keep-temp-files", false], [1, "cmdoption-matchmaps.mr-keep-temp-files", false], [1, "cmdoption-matchmaps.ncs-keep-temp-files", false]], "--ligands": [[1, "cmdoption-matchmaps-ligands", false], [1, "cmdoption-matchmaps.mr-ligands", false], [1, "cmdoption-matchmaps.ncs-ligands", false]], "--mapname": [[1, "cmdoption-matchmaps.ncs-mapname", false]], "--mtz": [[1, "cmdoption-matchmaps.ncs-mtz", false]], "--mtzoff": [[1, "cmdoption-matchmaps-mtzoff", false], [1, "cmdoption-matchmaps.mr-mtzoff", false]], "--mtzon": [[1, "cmdoption-matchmaps-mtzon", false], [1, "cmdoption-matchmaps.mr-mtzon", false]], "--ncs-chains": [[1, "cmdoption-matchmaps.ncs-ncs-chains", false]], "--no-bss": [[1, "cmdoption-matchmaps-no-bss", false], [1, "cmdoption-matchmaps.mr-no-bss", false], [1, "cmdoption-matchmaps.ncs-no-bss", false]], "--on-as-stationary": [[1, "cmdoption-matchmaps-on-as-stationary", false], [1, "cmdoption-matchmaps.mr-on-as-stationary", false]], "--output-dir": [[1, "cmdoption-matchmaps-output-dir", false], [1, "cmdoption-matchmaps.mr-output-dir", false], [1, "cmdoption-matchmaps.ncs-output-dir", false]], "--pdb": [[1, "cmdoption-matchmaps.ncs-pdb", false]], "--pdboff": [[1, "cmdoption-matchmaps-pdboff", false], [1, "cmdoption-matchmaps.mr-pdboff", false]], "--phases": [[1, "cmdoption-matchmaps.ncs-phases", false]], "--phenix-version": [[1, "cmdoption-matchmaps-phenix-version", false], [1, "cmdoption-matchmaps.mr-phenix-version", false], [1, "cmdoption-matchmaps.ncs-phenix-version", false]], "--rbr-selections": [[1, "cmdoption-matchmaps-rbr-selections", false], [1, "cmdoption-matchmaps.mr-rbr-selections", false]], "--script": [[1, "cmdoption-matchmaps-script", false], [1, "cmdoption-matchmaps.mr-script", false], [1, "cmdoption-matchmaps.ncs-script", false]], "--spacing": [[1, "cmdoption-matchmaps-spacing", false], [1, "cmdoption-matchmaps.mr-spacing", false], [1, "cmdoption-matchmaps.ncs-spacing", false]], "--unmasked-radius": [[1, "cmdoption-matchmaps-unmasked-radius", false], [1, "cmdoption-matchmaps.mr-unmasked-radius", false]], "--verbose": [[1, "cmdoption-matchmaps-verbose", false], [1, "cmdoption-matchmaps.mr-verbose", false], [1, "cmdoption-matchmaps.ncs-verbose", false]], "-f": [[1, "cmdoption-matchmaps-mtzoff", false], [1, "cmdoption-matchmaps.mr-mtzoff", false]], "-h": [[1, "cmdoption-matchmaps-h", false], [1, "cmdoption-matchmaps.mr-h", false], [1, "cmdoption-matchmaps.ncs-h", false]], "-i": [[1, "cmdoption-matchmaps-input-dir", false], [1, "cmdoption-matchmaps.mr-input-dir", false], [1, "cmdoption-matchmaps.ncs-input-dir", false]], "-k": [[1, "cmdoption-matchmaps-keep-temp-files", false], [1, "cmdoption-matchmaps.mr-keep-temp-files", false], [1, "cmdoption-matchmaps.ncs-keep-temp-files", false]], "-l": [[1, "cmdoption-matchmaps-ligands", false], [1, "cmdoption-matchmaps.mr-ligands", false], [1, "cmdoption-matchmaps.ncs-ligands", false]], "-m": [[1, "cmdoption-matchmaps.ncs-mtz", false]], "-n": [[1, "cmdoption-matchmaps-mtzon", false], [1, "cmdoption-matchmaps.mr-mtzon", false], [1, "cmdoption-matchmaps.ncs-ncs-chains", false]], "-o": [[1, "cmdoption-matchmaps-output-dir", false], [1, "cmdoption-matchmaps.mr-output-dir", false], [1, "cmdoption-matchmaps.ncs-output-dir", false]], "-p": [[1, "cmdoption-matchmaps-pdboff", false], [1, "cmdoption-matchmaps.mr-pdboff", false], [1, "cmdoption-matchmaps.ncs-pdb", false]], "-r": [[1, "cmdoption-matchmaps-rbr-selections", false], [1, "cmdoption-matchmaps.mr-rbr-selections", false]], "-s": [[1, "cmdoption-matchmaps-spacing", false], [1, "cmdoption-matchmaps.mr-spacing", false], [1, "cmdoption-matchmaps.ncs-spacing", false]], "-v": [[1, "cmdoption-matchmaps-verbose", false], [1, "cmdoption-matchmaps.mr-verbose", false], [1, "cmdoption-matchmaps.ncs-verbose", false]], "matchmaps command line option": [[1, "cmdoption-matchmaps-alpha", false], [1, "cmdoption-matchmaps-dmin", false], [1, "cmdoption-matchmaps-eff", false], [1, "cmdoption-matchmaps-h", false], [1, "cmdoption-matchmaps-input-dir", false], [1, "cmdoption-matchmaps-keep-temp-files", false], [1, "cmdoption-matchmaps-ligands", false], [1, "cmdoption-matchmaps-mtzoff", false], [1, "cmdoption-matchmaps-mtzon", false], [1, "cmdoption-matchmaps-no-bss", false], [1, "cmdoption-matchmaps-on-as-stationary", false], [1, "cmdoption-matchmaps-output-dir", false], [1, "cmdoption-matchmaps-pdboff", false], [1, "cmdoption-matchmaps-phenix-version", false], [1, "cmdoption-matchmaps-rbr-selections", false], [1, "cmdoption-matchmaps-script", false], [1, "cmdoption-matchmaps-spacing", false], [1, "cmdoption-matchmaps-unmasked-radius", false], [1, "cmdoption-matchmaps-verbose", false]], "matchmaps.mr command line option": [[1, "cmdoption-matchmaps.mr-alpha", false], [1, "cmdoption-matchmaps.mr-dmin", false], [1, "cmdoption-matchmaps.mr-eff", false], [1, "cmdoption-matchmaps.mr-h", false], [1, "cmdoption-matchmaps.mr-input-dir", false], [1, "cmdoption-matchmaps.mr-keep-temp-files", false], [1, "cmdoption-matchmaps.mr-ligands", false], [1, "cmdoption-matchmaps.mr-mtzoff", false], [1, "cmdoption-matchmaps.mr-mtzon", false], [1, "cmdoption-matchmaps.mr-no-bss", false], [1, "cmdoption-matchmaps.mr-on-as-stationary", false], [1, "cmdoption-matchmaps.mr-output-dir", false], [1, "cmdoption-matchmaps.mr-pdboff", false], [1, "cmdoption-matchmaps.mr-phenix-version", false], [1, "cmdoption-matchmaps.mr-rbr-selections", false], [1, "cmdoption-matchmaps.mr-script", false], [1, "cmdoption-matchmaps.mr-spacing", false], [1, "cmdoption-matchmaps.mr-unmasked-radius", false], [1, "cmdoption-matchmaps.mr-verbose", false]], "matchmaps.ncs command line option": [[1, "cmdoption-matchmaps.ncs-dmin", false], [1, "cmdoption-matchmaps.ncs-eff", false], [1, "cmdoption-matchmaps.ncs-h", false], [1, "cmdoption-matchmaps.ncs-input-dir", false], [1, "cmdoption-matchmaps.ncs-keep-temp-files", false], [1, "cmdoption-matchmaps.ncs-ligands", false], [1, "cmdoption-matchmaps.ncs-mapname", false], [1, "cmdoption-matchmaps.ncs-mtz", false], [1, "cmdoption-matchmaps.ncs-ncs-chains", false], [1, "cmdoption-matchmaps.ncs-no-bss", false], [1, "cmdoption-matchmaps.ncs-output-dir", false], [1, "cmdoption-matchmaps.ncs-pdb", false], [1, "cmdoption-matchmaps.ncs-phases", false], [1, "cmdoption-matchmaps.ncs-phenix-version", false], [1, "cmdoption-matchmaps.ncs-script", false], [1, "cmdoption-matchmaps.ncs-spacing", false], [1, "cmdoption-matchmaps.ncs-verbose", false]]}, "objects": {"matchmaps": [[1, 0, 1, "cmdoption-matchmaps-alpha", "--alpha"], [1, 0, 1, "cmdoption-matchmaps-dmin", "--dmin"], [1, 0, 1, "cmdoption-matchmaps-eff", "--eff"], [1, 0, 1, "cmdoption-matchmaps-h", "--help"], [1, 0, 1, "cmdoption-matchmaps-input-dir", "--input-dir"], [1, 0, 1, "cmdoption-matchmaps-keep-temp-files", "--keep-temp-files"], [1, 0, 1, "cmdoption-matchmaps-ligands", "--ligands"], [1, 0, 1, "cmdoption-matchmaps-mtzoff", "--mtzoff"], [1, 0, 1, "cmdoption-matchmaps-mtzon", "--mtzon"], [1, 0, 1, "cmdoption-matchmaps-no-bss", "--no-bss"], [1, 0, 1, "cmdoption-matchmaps-on-as-stationary", "--on-as-stationary"], [1, 0, 1, "cmdoption-matchmaps-output-dir", "--output-dir"], [1, 0, 1, "cmdoption-matchmaps-pdboff", "--pdboff"], [1, 0, 1, "cmdoption-matchmaps-phenix-version", "--phenix-version"], [1, 0, 1, "cmdoption-matchmaps-rbr-selections", "--rbr-selections"], [1, 0, 1, "cmdoption-matchmaps-script", "--script"], [1, 0, 1, "cmdoption-matchmaps-spacing", "--spacing"], [1, 0, 1, "cmdoption-matchmaps-unmasked-radius", "--unmasked-radius"], [1, 0, 1, "cmdoption-matchmaps-verbose", "--verbose"], [1, 0, 1, "cmdoption-matchmaps-mtzoff", "-f"], [1, 0, 1, "cmdoption-matchmaps-h", "-h"], [1, 0, 1, "cmdoption-matchmaps-input-dir", "-i"], [1, 0, 1, "cmdoption-matchmaps-keep-temp-files", "-k"], [1, 0, 1, "cmdoption-matchmaps-ligands", "-l"], [1, 0, 1, "cmdoption-matchmaps-mtzon", "-n"], [1, 0, 1, "cmdoption-matchmaps-output-dir", "-o"], [1, 0, 1, "cmdoption-matchmaps-pdboff", "-p"], [1, 0, 1, "cmdoption-matchmaps-rbr-selections", "-r"], [1, 0, 1, "cmdoption-matchmaps-spacing", "-s"], [1, 0, 1, "cmdoption-matchmaps-verbose", "-v"]], "matchmaps.mr": [[1, 0, 1, "cmdoption-matchmaps.mr-alpha", "--alpha"], [1, 0, 1, "cmdoption-matchmaps.mr-dmin", "--dmin"], [1, 0, 1, "cmdoption-matchmaps.mr-eff", "--eff"], [1, 0, 1, "cmdoption-matchmaps.mr-h", "--help"], [1, 0, 1, "cmdoption-matchmaps.mr-input-dir", "--input-dir"], [1, 0, 1, "cmdoption-matchmaps.mr-keep-temp-files", "--keep-temp-files"], [1, 0, 1, "cmdoption-matchmaps.mr-ligands", "--ligands"], [1, 0, 1, "cmdoption-matchmaps.mr-mtzoff", "--mtzoff"], [1, 0, 1, "cmdoption-matchmaps.mr-mtzon", "--mtzon"], [1, 0, 1, "cmdoption-matchmaps.mr-no-bss", "--no-bss"], [1, 0, 1, "cmdoption-matchmaps.mr-on-as-stationary", "--on-as-stationary"], [1, 0, 1, "cmdoption-matchmaps.mr-output-dir", "--output-dir"], [1, 0, 1, "cmdoption-matchmaps.mr-pdboff", "--pdboff"], [1, 0, 1, "cmdoption-matchmaps.mr-phenix-version", "--phenix-version"], [1, 0, 1, "cmdoption-matchmaps.mr-rbr-selections", "--rbr-selections"], [1, 0, 1, "cmdoption-matchmaps.mr-script", "--script"], [1, 0, 1, "cmdoption-matchmaps.mr-spacing", "--spacing"], [1, 0, 1, "cmdoption-matchmaps.mr-unmasked-radius", "--unmasked-radius"], [1, 0, 1, "cmdoption-matchmaps.mr-verbose", "--verbose"], [1, 0, 1, "cmdoption-matchmaps.mr-mtzoff", "-f"], [1, 0, 1, "cmdoption-matchmaps.mr-h", "-h"], [1, 0, 1, "cmdoption-matchmaps.mr-input-dir", "-i"], [1, 0, 1, "cmdoption-matchmaps.mr-keep-temp-files", "-k"], [1, 0, 1, "cmdoption-matchmaps.mr-ligands", "-l"], [1, 0, 1, "cmdoption-matchmaps.mr-mtzon", "-n"], [1, 0, 1, "cmdoption-matchmaps.mr-output-dir", "-o"], [1, 0, 1, "cmdoption-matchmaps.mr-pdboff", "-p"], [1, 0, 1, "cmdoption-matchmaps.mr-rbr-selections", "-r"], [1, 0, 1, "cmdoption-matchmaps.mr-spacing", "-s"], [1, 0, 1, "cmdoption-matchmaps.mr-verbose", "-v"]], "matchmaps.ncs": [[1, 0, 1, "cmdoption-matchmaps.ncs-dmin", "--dmin"], [1, 0, 1, "cmdoption-matchmaps.ncs-eff", "--eff"], [1, 0, 1, "cmdoption-matchmaps.ncs-h", "--help"], [1, 0, 1, "cmdoption-matchmaps.ncs-input-dir", "--input-dir"], [1, 0, 1, "cmdoption-matchmaps.ncs-keep-temp-files", "--keep-temp-files"], [1, 0, 1, "cmdoption-matchmaps.ncs-ligands", "--ligands"], [1, 0, 1, "cmdoption-matchmaps.ncs-mapname", "--mapname"], [1, 0, 1, "cmdoption-matchmaps.ncs-mtz", "--mtz"], [1, 0, 1, "cmdoption-matchmaps.ncs-ncs-chains", "--ncs-chains"], [1, 0, 1, "cmdoption-matchmaps.ncs-no-bss", "--no-bss"], [1, 0, 1, "cmdoption-matchmaps.ncs-output-dir", "--output-dir"], [1, 0, 1, "cmdoption-matchmaps.ncs-pdb", "--pdb"], [1, 0, 1, "cmdoption-matchmaps.ncs-phases", "--phases"], [1, 0, 1, "cmdoption-matchmaps.ncs-phenix-version", "--phenix-version"], [1, 0, 1, "cmdoption-matchmaps.ncs-script", "--script"], [1, 0, 1, "cmdoption-matchmaps.ncs-spacing", "--spacing"], [1, 0, 1, "cmdoption-matchmaps.ncs-verbose", "--verbose"], [1, 0, 1, "cmdoption-matchmaps.ncs-h", "-h"], [1, 0, 1, "cmdoption-matchmaps.ncs-input-dir", "-i"], [1, 0, 1, "cmdoption-matchmaps.ncs-keep-temp-files", "-k"], [1, 0, 1, "cmdoption-matchmaps.ncs-ligands", "-l"], [1, 0, 1, "cmdoption-matchmaps.ncs-mtz", "-m"], [1, 0, 1, "cmdoption-matchmaps.ncs-ncs-chains", "-n"], [1, 0, 1, "cmdoption-matchmaps.ncs-output-dir", "-o"], [1, 0, 1, "cmdoption-matchmaps.ncs-pdb", "-p"], [1, 0, 1, "cmdoption-matchmaps.ncs-spacing", "-s"], [1, 0, 1, "cmdoption-matchmaps.ncs-verbose", "-v"]]}, "objnames": {"0": ["std", "cmdoption", "program option"]}, "objtypes": {"0": "std:cmdoption"}, "terms": {"": [0, 1, 2, 3, 4, 5], "0": [0, 1, 3, 4], "006": 5, "1": [0, 1, 3, 4], "15": 3, "2": [0, 1, 3, 4, 5], "20": [1, 3, 5], "21": 3, "25": [0, 4], "3": 3, "4": 0, "5": [0, 1, 3, 4], "6": 3, "7": 0, "9": 3, "90": 5, "A": [0, 1, 2, 4], "As": [3, 5], "At": 3, "But": [0, 5], "By": [0, 1, 3, 4], "For": [0, 2, 3, 4], "If": [0, 1, 2, 3, 4, 5], "In": [0, 3, 4, 5], "It": 3, "NOT": 1, "No": 3, "ON": [0, 4], "Of": 5, "On": 3, "One": [0, 4], "Such": 0, "The": [1, 3, 4], "Then": [0, 5], "There": [3, 4, 5], "These": [0, 3], "To": [0, 3, 4], "_unmask": [0, 4], "about": [2, 4, 5], "abov": [0, 3, 5], "abruptli": 5, "absolut": 3, "accordingli": 0, "account": 0, "across": [0, 2, 4], "action": 2, "activ": [1, 3], "actual": 3, "ad": [0, 3], "add": 3, "addit": 0, "addition": 3, "address": 4, "admittedli": 4, "affect": 1, "after": [0, 3, 4], "afterward": 0, "again": 3, "against": 4, "aim": 4, "algorithm": [3, 4], "align": [1, 2, 3, 4], "all": [0, 2, 3, 4, 5], "allow": 0, "along": [0, 1, 2, 3, 5], "alpha": [0, 1, 4, 5], "alreadi": 5, "also": [0, 1, 3, 4], "alter": 4, "altern": [3, 4], "altogeth": 0, "alwai": [3, 4, 5], "ambigu": 4, "amplitud": [0, 1, 3], "an": [0, 1, 2, 3, 4, 5], "analysi": [0, 3], "analyz": [1, 4], "angstrom": [0, 1, 3], "ani": [0, 1, 3, 4, 5], "anisotrop": 0, "annoi": [1, 4], "anoth": [4, 5], "anstrom": 1, "anyth": 4, "apo": [1, 3, 4], "apo_data": 3, "appar": 3, "appli": [0, 1, 3, 4, 5], "approach": [0, 4, 5], "appropri": 0, "approxim": [0, 1, 4], "ar": [0, 1, 2, 3, 4, 5], "argument": 3, "aris": 5, "around": [4, 5], "artif": 5, "artifact": 0, "artifactu": 4, "assist": 0, "assum": [1, 3, 4, 5], "asymmetr": 0, "atom": 0, "attempt": [1, 5], "automat": 1, "avail": 0, "averag": 4, "avoid": 0, "awai": [0, 1, 3, 4], "b": [0, 1, 3, 4], "bad": 4, "balanc": 0, "base": 1, "basic": [1, 2], "becaus": [0, 1, 4, 5], "becom": [3, 4], "been": 3, "befor": 3, "behavior": 5, "behind": 0, "being": [3, 4], "believ": 0, "belong": 0, "below": [0, 1, 3, 4, 5], "best": [0, 5], "better": 4, "between": [0, 1, 2], "bia": [0, 3], "big": 4, "biolog": 0, "black": 0, "bodi": [0, 1, 4], "booster": 0, "both": [0, 1, 3], "bottom": 5, "bound": [0, 1, 3, 4], "bound_data": 3, "box": 0, "brief": 5, "briefli": [2, 5], "bright": 1, "brookner": 2, "bss": [1, 4], "bug": [4, 5], "built": 1, "bulk": [0, 1], "c": [0, 1], "calcul": 0, "call": [1, 3], "can": [0, 1, 2, 3, 4, 5], "carri": 0, "case": [0, 4, 5], "catch": 5, "ccp4": [0, 1, 3, 4, 5], "cell": [0, 1, 2, 5], "chain": [0, 1], "chang": [0, 2, 3, 4], "check": [0, 2, 5], "chosen": 0, "cif": [1, 3], "clariti": 3, "close": 5, "code": [0, 4], "coerc": 5, "cold": [1, 3], "column": [0, 1, 3], "com": 3, "combin": 0, "come": 4, "command": [0, 2, 3], "common": 0, "compat": 3, "complet": 3, "complex": 0, "complic": 3, "comput": [0, 1, 2, 3, 4, 5], "conceiv": 2, "conda": 3, "conform": 0, "consid": 4, "consist": 2, "contain": [0, 1, 2, 3, 4], "content": 3, "contour": 5, "conveni": 0, "convers": 0, "convinc": 5, "coordin": 3, "coot": [0, 4], "copi": [0, 5], "core": [0, 2], "corner": 5, "correct": 0, "correspond": [1, 3], "cost": 4, "could": [0, 1, 3, 4], "counterintuit": 5, "cours": [4, 5], "creat": [0, 1, 3], "creation": 1, "critic": 0, "cryo": 5, "crystal": [0, 1, 2], "crystallograph": [0, 2, 4, 5], "crystallographi": [0, 2], "cube": 0, "curiou": 3, "current": [1, 3], "custom": [0, 1, 4], "cut": 0, "cutoff": 1, "d": [2, 3], "dark": [1, 3], "data": [0, 1, 2, 4], "dataset": [0, 2, 3, 4], "deactiv": 0, "deal": 5, "debug": 4, "decid": 4, "default": [0, 1, 3, 4, 5], "defin": [0, 2, 4], "defint": 4, "delet": [1, 3], "denni": 2, "densiti": [0, 4, 5], "depend": [0, 4], "describ": [0, 3], "descript": 5, "design": 5, "desir": [4, 5], "detail": 3, "detect": [0, 1], "determin": 1, "dialog": 5, "differ": [0, 1, 2, 3, 4, 5], "difference_map": 5, "differencemesh_posit": 5, "different_dir_with_input_fil": 3, "dimens": [1, 2], "dir": [1, 3], "direct": 3, "directli": [3, 4, 5], "directori": [1, 3], "disabl": 4, "discard": 0, "discuss": 0, "disregard": 4, "distanc": 1, "dmin": [1, 4], "do": [0, 1, 2, 3, 4, 5], "doc": 2, "docum": 3, "document": [3, 4], "doe": [4, 5], "doek": 2, "doesn": [2, 4], "domin": 4, "don": [0, 3, 4, 5], "downgrad": 3, "downstream": 5, "due": 2, "e": [0, 1, 3, 4], "each": [0, 1, 3], "earlier": 3, "easi": [0, 4, 5], "easiest": 0, "edg": 5, "editor": 5, "eff": [0, 1, 4], "effect": 4, "either": 3, "electron": 0, "elegantli": 4, "em": 5, "encount": 5, "end": [0, 4, 5], "enough": 5, "ensur": 3, "env": 3, "environ": [0, 1, 3], "equal": [3, 4], "equat": 0, "error": [0, 1, 3], "essenti": [0, 4, 5], "estim": 4, "etc": [1, 3], "even": [0, 2, 4, 5], "ever": 5, "everyth": [1, 3, 4], "exactli": [0, 3, 4], "examin": 3, "exampl": 0, "excit": 1, "excitedli": 3, "exclus": 3, "exit": 1, "expand": 5, "expect": [0, 3, 4], "experi": 5, "explicit": 0, "explor": [2, 3], "extend": 0, "extern": 3, "extraordinari": 0, "f": [0, 1, 4], "factor": [0, 1, 3], "fals": 1, "famili": 2, "familiar": 5, "far": [0, 3, 4], "farther": 4, "featur": [0, 3, 4], "figur": [3, 4, 5], "file": [0, 1, 4], "filenam": [1, 3], "filter": 0, "final": [0, 3, 4], "find": [0, 2, 4, 5], "fine": [3, 4, 5], "finer": 4, "finish": 3, "finnicki": 4, "first": 3, "fit": 0, "fixed_chain": 1, "flag": [1, 3, 4], "flatten": 4, "flexibl": 0, "floatgrid": 1, "fly": 5, "fob": 3, "foff": 1, "follow": [1, 3, 4], "fon": 1, "form": 0, "format": 1, "formula": [0, 4], "found": [0, 1, 2, 3], "fourier": [1, 4, 5], "fp": 3, "frac": 4, "free": 3, "fresh": 3, "from": [0, 1, 4, 5], "full": [0, 3, 4], "fulli": 0, "function": [0, 1, 4], "further": 4, "futur": 3, "g": [0, 1, 3, 4], "gemmi": 0, "gener": [0, 1, 3, 4], "get": 0, "git": 3, "github": [0, 1, 3, 4, 5], "given": 5, "global": 4, "go": 3, "goal": 4, "good": [3, 4, 5], "grid": 0, "ground": 1, "group": 1, "guid": [0, 2, 4], "h": 1, "ha": [0, 4], "hand": 3, "handl": 0, "happi": 5, "hard": [4, 5], "harvard": 2, "hasn": 3, "have": [0, 2, 3, 4, 5], "headach": 4, "hear": 0, "hekstra": 2, "help": [0, 1, 3, 4, 5], "here": [0, 2, 3, 4, 5], "hesit": [0, 4], "high": 0, "highest": [1, 4], "homo": 4, "hope": 3, "hopefulli": 5, "hot": 1, "how": [0, 3, 4, 5], "howev": [0, 1, 4, 5], "html": 1, "http": [1, 3], "i": [0, 1, 2, 3, 4, 5], "idea": [0, 3, 4], "ident": 0, "identifi": 4, "ignor": 3, "immedi": 4, "impercept": 5, "implement": [0, 4], "import": [0, 4], "importantli": 3, "includ": [0, 1, 4], "increas": 4, "index": 1, "indic": 4, "inform": [1, 2, 3, 4], "input": [0, 1, 4, 5], "input_dir": 1, "input_fil": 3, "insid": [3, 5], "inspect": 3, "instal": [1, 2], "instead": 4, "instruct": [0, 2], "instuct": 0, "integ": 1, "interest": [0, 3, 4], "intermedi": 1, "intern": [0, 1, 2], "interpolate_grid_of_aligned_model2": 0, "introduct": 0, "involv": 4, "io": 1, "isn": 4, "isomesh": 5, "isomorph": [0, 2], "issu": [0, 3, 4, 5], "its": [0, 3], "journal": 0, "just": [4, 5], "k": 1, "keep": [0, 1, 3, 5], "keep_temp_fil": 1, "kei": 5, "kept": 3, "know": [0, 3], "l": 1, "lab": 2, "larg": 4, "larger": 4, "later": 5, "latest": 3, "laxli": 4, "learn": [0, 2], "left": 5, "let": [0, 3], "level": 5, "librari": 0, "lie": 5, "ligand": [0, 1, 3, 4], "light": [1, 3], "like": [0, 2, 3, 4, 5], "likelihood": 5, "limit": 1, "line": [0, 2, 3, 4], "lit": 3, "littl": 4, "live": 3, "ll": [3, 5], "load": 5, "log": 4, "long": [3, 4], "look": [0, 3, 4, 5], "lot": 4, "love": 0, "lower": 1, "luck": 5, "m": 1, "macromolecul": 0, "made": 3, "mai": [0, 1, 3, 4], "main": [0, 4], "maintain": 1, "make": [0, 3, 4, 5], "manag": 3, "mani": 5, "manner": 3, "map": [0, 1, 2, 3, 4], "map_auto_expand_sym": 5, "map_from_matchmap": 5, "mapnam": 1, "mask": [1, 3], "match": 0, "matchmap": 4, "mate": 4, "maximum": [0, 1], "me": [0, 4], "mean": [4, 5], "meantim": 3, "measur": 0, "mediat": 0, "medium": 4, "messag": 1, "method": 0, "mi": 0, "might": [3, 4, 5], "mind": 5, "minim": 0, "misalign": 4, "mix": 3, "mmcif": 1, "mmfile": 3, "model": [0, 1, 2, 3, 4, 5], "modest": 0, "modif": 0, "modifi": [0, 4], "molecul": [0, 1], "molecular": 0, "more": [0, 1, 2, 3, 4], "most": [3, 4], "motion": 4, "move": [0, 1, 4], "moving_chain": 1, "mr": [2, 3], "mrc": 5, "mtz": [0, 1, 2, 3, 5], "mtzdump": 3, "mtzfileoff": 1, "mtzfileon": 1, "mtzoff": [1, 3], "mtzon": [1, 3], "much": [0, 3, 4], "multim": 4, "multipl": [0, 1], "must": 1, "mutant": [1, 3], "mutat": 0, "my": 3, "my_new_mesh": 5, "mymtz": 3, "myproject": 3, "n": [1, 3], "name": [0, 1, 3], "nc": [2, 4], "nearest": 0, "nearli": 2, "necessari": [0, 1, 3], "necessarili": 4, "need": [1, 3, 4, 5], "neg": 3, "never": 4, "new": 4, "next": 4, "nicer": 4, "noisi": [0, 4], "nomin": 0, "non": [0, 2, 4], "nonsens": 5, "normal": 0, "normalize_ccp4_map": 5, "note": [0, 1], "number": [0, 1], "o": 1, "ob": [0, 1], "observ": [0, 3], "off": [0, 1, 4, 5], "off_befor": 3, "often": [0, 5], "omit": [0, 1], "on_befor": 3, "on_minus_off": [3, 5], "on_minus_off_unmask": 3, "onc": 5, "one": [0, 1, 3, 4], "onli": [0, 1, 3, 4, 5], "onlin": 1, "onto": 1, "open": [0, 2, 3, 5], "oper": [0, 5], "opportun": 4, "option": [0, 1, 2, 3, 5], "order": 0, "origin": 5, "orthorhomb": 5, "other": [0, 2, 3], "otherwis": 4, "our": 2, "out": [0, 1, 2, 3, 4, 5], "outlin": 5, "output": [0, 1, 4, 5], "output_dir": 1, "outsid": [0, 5], "overal": 0, "overlai": [0, 1], "overwritten": 3, "own": 4, "p": 1, "p1": 5, "pack": [0, 1, 2, 4], "packag": [0, 2, 3], "page": 3, "pair": [2, 3, 4], "paper": 0, "paramet": [0, 1, 3, 4], "part": [2, 5], "particular": 4, "pass": 4, "path": [1, 3], "pdb": [1, 3, 5], "pdb_in_high_symmetry_spacegroup": 5, "pdboff": [1, 3], "peak": 4, "perform": [0, 1, 4], "perhap": 3, "permit": 0, "perturb": [0, 3], "ph2fofcwt": 0, "phase": [0, 1, 2], "phaser": 0, "phenix": [0, 1, 3, 4], "phenix_env": 3, "phenix_vers": 1, "piec": 3, "pip": 3, "pipelin": 3, "place": [0, 1, 3], "plan": 0, "pleas": [0, 1, 2, 3, 4, 5], "plu": 3, "point": [0, 3, 4], "poorli": 0, "popular": 0, "posit": 3, "possibl": [0, 4, 5], "potenti": [4, 5], "pre": 2, "prefer": 5, "preprend": 3, "present": [2, 4], "pretti": [0, 4], "prevent": 0, "previou": 3, "print": [1, 2, 3, 4], "prior": [1, 3, 4], "probabl": [4, 5], "proce": 0, "procedur": 0, "produc": [0, 2, 3, 4, 5], "program": [0, 3], "promin": 3, "properti": 0, "protein": [0, 1, 3, 5], "provid": [0, 1, 3, 4], "pull": 4, "purpos": [4, 5], "pymol": [0, 4], "pypi": 3, "python": [0, 2, 3], "question": [4, 5], "quick": 3, "quickstart": [2, 4], "quirk": 5, "quit": 2, "r": [0, 1, 3], "radiu": [0, 1, 3, 4], "rai": [0, 2], "rang": 0, "rather": [0, 1, 4], "rbr": [1, 4], "rbr_select": 1, "re": [0, 3, 4, 5], "reach": 5, "read": [0, 3, 4], "real": [1, 2, 3, 4, 5], "realli": 4, "reason": [0, 4], "reciproc": 2, "reciprocalspaceship": [0, 3], "recommend": [0, 3, 4], "refer": [0, 1], "refin": [1, 3], "reflect": [0, 1, 2, 4], "regard": 0, "region": [0, 5], "regular": 1, "rel": [0, 3, 4], "relat": [0, 1, 5], "relev": 5, "reli": 3, "remain": [0, 4], "rememb": 3, "remind": 3, "render": [0, 5], "renumb": 0, "reopen": 5, "repeat": 1, "replac": 0, "repres": 3, "reproduc": 3, "request": 4, "requir": [0, 2], "rescu": 0, "resi": 5, "resolut": [0, 1], "resolv": 4, "respect": 3, "restraint": [1, 3], "result": [0, 4], "retain": 0, "revers": 0, "right": 3, "rigid": [0, 1, 4], "rotat": 0, "round": 0, "run": [0, 1, 4, 5], "run_matchmap": [1, 3], "sai": [4, 5], "same": [0, 1, 2, 3], "sampl": 2, "save": 3, "scale": 1, "scaleit": [0, 1], "script": 1, "second": [0, 4], "see": [0, 1, 2, 3, 4], "select": [0, 1, 4, 5], "sens": 0, "sensit": 0, "separ": [0, 4], "seri": 5, "set": [0, 5], "sfcif": 1, "sh": [1, 3], "shift": 0, "short": 3, "shorter": 4, "should": [0, 1, 3, 4, 5], "show": [0, 1], "side": 4, "sigf": [0, 1], "sigfob": 3, "sigfoff": 1, "sigfon": 1, "sigfp": 3, "sigma": 4, "signal": [0, 3, 4], "similar": [2, 3], "simpli": 4, "singl": 2, "situat": 0, "size": [1, 4], "skip": [0, 1], "slightli": [0, 3], "slow": 4, "small": 0, "so": [0, 2, 3, 4], "softwar": [0, 2, 3, 5], "solut": 0, "solvent": [1, 3], "some": [0, 3, 4, 5], "someth": [3, 4], "sometim": 5, "somewher": 3, "sort": 4, "sort_hetatm": 0, "sourc": [0, 2, 3, 4], "space": [1, 2, 3, 4, 5], "spacegroup": [0, 1, 2, 5], "specif": [1, 3, 4, 5], "specifi": [0, 1, 3], "spuriou": 5, "start": [0, 2, 4], "state": [0, 1], "station": [1, 2, 3], "stationari": [1, 4], "statist": 4, "step": 0, "still": 4, "strict": 4, "stricter": 4, "strictli": 4, "string": 1, "strong": 4, "strongli": 4, "structur": [0, 1, 3, 4, 5], "subdirectori": 1, "subtract": [0, 1, 2, 3], "success": 5, "successfulli": 3, "suffix": 4, "suggest": 0, "summari": 3, "suppli": [1, 3, 4], "support": [0, 3], "sure": 3, "symmetri": [0, 2], "t": [0, 2, 3, 4, 5], "take": 2, "tell": 4, "temp": [1, 3], "templat": [0, 1, 4], "temporari": 3, "term": 4, "termin": [1, 4], "text": 5, "than": [0, 3, 4, 5], "thei": [0, 1, 2, 3, 5], "them": [1, 2, 3, 5], "thi": [0, 1, 2, 3, 4, 5], "those": [0, 3], "though": [1, 3, 5], "three": [2, 3], "through": [0, 4], "throughout": [1, 3, 4], "thrown": 3, "thu": [4, 5], "tight": 0, "time": [0, 3], "tip": 2, "togeth": 4, "touch": 0, "tour": 3, "transform": [1, 4, 5], "translat": 0, "trick": 4, "troubl": [3, 4], "troubleshoot": [1, 3], "truncat": [0, 4], "try": [4, 5], "turn": [0, 5], "two": [0, 1, 2, 3, 4, 5], "type": [2, 3], "typic": [4, 5], "unbias": [0, 2], "uncertainti": [0, 1, 3], "unfortun": [4, 5], "uniqu": 3, "unit": [0, 1, 2, 5], "unless": 3, "unlik": 5, "unmask": [1, 3, 4], "unmasked_radiu": 1, "unnecessari": 0, "up": [3, 4], "updat": 3, "us": [0, 1, 2, 3, 5], "usag": [1, 2], "useless": 0, "user": [0, 5], "usual": 5, "util": [0, 1, 2, 3], "utilit": [2, 3], "v": [1, 3], "valu": [1, 4], "ve": 4, "verbos": [1, 4], "veri": [0, 4, 5], "version": [1, 3], "via": [0, 1, 3, 4, 5], "vicin": 3, "visual": [0, 3, 4], "voxel": [0, 1, 4], "wa": [2, 3], "wai": [0, 3, 5], "walkthrough": 2, "want": [0, 3, 4, 5], "warm": 3, "water": 0, "we": [0, 3, 4, 5], "weight": [0, 1], "weird_solvent_1": 3, "weird_solvent_2": 3, "welcom": [2, 4], "well": 3, "went": 3, "were": 3, "what": [3, 4], "when": [3, 4, 5], "where": [3, 4], "wherein": 0, "wherev": 5, "which": [0, 1, 2, 3, 4, 5], "while": 4, "wise": 0, "wish": 5, "within": [0, 4], "without": 5, "work": [0, 1, 2, 3, 4], "workaround": 5, "would": [0, 3, 4, 5], "write": [3, 4], "written": [1, 3, 4], "wrong": 3, "wt": [1, 3], "x": [0, 2], "yet": 3, "yield": 0, "you": [0, 1, 2, 3, 4, 5], "your": [0, 1, 2, 3, 4, 5], "zero": 0}, "titles": ["About the matchmaps algorithm", "matchmaps command-line interface", "matchmaps Documentation", "Getting started with matchmaps", "Troubleshooting and advanced usage", "Visualizing matchmaps results"], "titleterms": {"A": 3, "The": [0, 2], "about": 0, "abstract": 0, "addit": 3, "advanc": 4, "algorithm": 0, "align": 0, "basic": 3, "boundari": 5, "brief": 2, "bulk": 4, "chain": 4, "command": [1, 5], "compar": 4, "condit": 5, "coot": 5, "cut": 4, "data": 3, "depend": 3, "detail": 0, "document": 2, "each": 4, "error": 4, "exampl": 3, "expans": 5, "file": [3, 5], "fourier": 0, "from": 3, "function": 2, "get": 3, "individu": 4, "input": 3, "instal": 3, "interfac": 1, "line": 1, "map": 5, "mask": [0, 4], "matchmap": [0, 1, 2, 3, 5], "mention": 5, "miscellan": 4, "molecul": 4, "mr": [0, 1], "multipl": 4, "nc": [0, 1], "normal": 5, "note": 3, "off": 3, "option": 4, "other": 4, "output": 3, "overview": 0, "page": 5, "period": 5, "protein": 4, "pymol": 5, "question": 0, "real": 0, "refin": [0, 4], "relat": 4, "resolut": 4, "result": 5, "run": 3, "scale": [0, 4], "script": 3, "solvent": [0, 4], "space": 0, "start": 3, "symmetri": [4, 5], "thought": 0, "transform": 0, "troubleshoot": 4, "us": 4, "usag": [3, 4], "variant": 0, "visual": 5, "weight": 4, "wiki": 5, "work": 5}})
\ No newline at end of file
diff --git a/troubleshooting.html b/troubleshooting.html
index a70abbb..d5c8234 100644
--- a/troubleshooting.html
+++ b/troubleshooting.html
@@ -17,7 +17,7 @@
   
         
         
-        
+        
         
         
         
diff --git a/visualization.html b/visualization.html
index cc18fdb..d331c77 100644
--- a/visualization.html
+++ b/visualization.html
@@ -17,7 +17,7 @@
   
         
         
-        
+