Adding Command-line tools section

sbliven · sbliven · commit 4e40f5e9c912 · 2014-10-16T16:51:23.000+02:00
Also moved up the database search section &amp; fixed some spellings.
diff --git a/structure/alignment.md b/structure/alignment.md
@@ -28,25 +28,30 @@ in 3D. See below for descriptions of the algorithms.
 
 ## Alignment User Interface
 
-Before going the details how to use the algorithms programmatically, let's take a look at the user interface that cames with the *biojava-structure-gui* module.
+Before going the details how to use the algorithms programmatically, let's take
+a look at the user interface that cames with the *biojava-structure-gui* module.
 
-<pre>
-        AlignmentGui.getInstance();
-</pre>
+```java
+AlignmentGui.getInstance();
+```
 
-shows the following user interface.
+This code shows the following user interface:
 
 ![Alignment GUI](img/alignment_gui.png)
 
-You can manually select protein chains, domains, or custom files to be aligned. Try to align 2hyn vs. 1zll. This will show the results in a graphical way, in 3D:
+You can manually select protein chains, domains, or custom files to be aligned.
+Try to align 2hyn vs. 1zll. This will show the results in a graphical way, in
+3D:
 
 ![3D Alignment of PDB IDs 2hyn and 1zll](img/2hyn_1zll.png)
 
 and also a 2D display, that interacts with the 3D display
 
 ![2D Alignment of PDB IDs 2hyn and 1zll](img/alignmentpanel.png)
 
-The functionality to perform and visualize these alignments can of course be used also from your own code. Let's first have a look at the alignment algorithms:
+The functionality to perform and visualize these alignments can of course be
+used also from your own code. Let's first have a look at the alignment
+algorithms.
 
 ## The Alignment Algorithms
 
@@ -60,7 +65,7 @@ structure, and then combining those to try to align the most residues possible
 while keeping the overall RMSD of the superposition low.
 
 CE is a rigid-body alignment algorithm, which means that the structures being
-compared are kept fixed during superpositon. In some cases it may be desirable
+compared are kept fixed during superposition. In some cases it may be desirable
 to break large proteins up into domains prior to aligning them (by manually
 inputing a subrange, using the [SCOP or CATH databases](externaldb.md), or by
 decomposing the protein automatically using the [Protein Domain
@@ -77,7 +82,7 @@ related by a circular permutation, the N-terminal part of one protein is related
 to the C-terminal part of the other, and vice versa. CE-CP allows circularly
 permuted proteins to be compared.  For more information on circular
 permutations, see the
-[wikipedia](http://en.wikipedia.org/wiki/Circular_permutation_in_proteins) or
+[Wikipedia](http://en.wikipedia.org/wiki/Circular_permutation_in_proteins) or
 [Molecule of the
 Month](http://www.pdb.org/pdb/101/motm.do?momID=124&evtc=Suggest&evta=Moleculeof%20the%20Month&evtl=TopBar)
 articles.
@@ -140,7 +145,7 @@ The following methods are not presented in the user interface by default:
 
 * [BioJavaStructureAlignment](http://www.biojava.org/docs/api/org/biojava/bio/structure/align/BioJavaStructureAlignment.html)
   A structure-based alignment method able of returning multiple alternate
-  alignments. It was writen by Andreas Prlic and based on the PSC++ algorithm
+  alignments. It was written by Andreas Prli&#263; and based on the PSC++ algorithm
   provided by Peter Lackner.
 * [CeSideChainMain](http://www.biojava.org/docs/api/org/biojava/bio/structure/align/ce/CeSideChainMain.html)
   A variant of CE using CB-CB distances, which sometimes improves alignments in
@@ -152,6 +157,40 @@ Additional methods can be added by implementing the
 [StructureAlignment](http://www.biojava.org/docs/api/org/biojava/bio/structure/align/StructureAlignment.html)
 interface.
 
+## PDB-wide database searches
+
+The Alignment GUI also provides functionality for PDB-wide structural searches.
+This systematically compares a structure against a non-redundant set of all
+other structures in the PDB at either a chain or a domain level. Representatives
+are selected using the RCSB's clustering of proteins with 40% sequence identity,
+as described
+[here](http://www.rcsb.org/pdb/static.do?p=general_information/cluster/structureAll.jsp).
+Domains are selected using either SCOP (when available) or the
+ProteinDomainParser algorithm.
+
+![Database Search GUI](img/database_search.png)
+
+To perform a database search, select the 'Database Search' tab, then choose a
+query structure based on PDB ID, SCOP domain id, or from a custom file. The
+output directory will be used to store results. These consist of individual
+alignments in compressed XML format, as well as a tab-delimited file of
+similarity scores and statistics. The statistics are displayed in an interactive
+results table, which allows the alignments to be sorted. The 'Align' column
+allows individual alignments to be visualized with the alignment GUI.
+
+![Database Search Results](img/database_search_results.png)
+
+Be aware that this process can be very time consuming. Before
+starting a manual search, it is worth considering whether a pre-computed result
+may be available online, for instance for
+[FATCAT-rigid](http://www.rcsb.org/pdb/static.do?p=general_information/cluster/structureAll.jsp)
+or [DALI](http://ekhidna.biocenter.helsinki.fi/dali/start). For custom files or
+specific domains, a few optimizations can reduce the time for a database search.
+Downloading PDB files is a considerable bottleneck. This can be solved by
+downloading all PDB files from the [FTP
+server](ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/) and setting
+the `PDB_DIR` environmental variable. This operation sped up the search from
+about 30 hours to less than 4 hours.
 
 
 ## Creating alignments programmatically
@@ -186,45 +225,25 @@ GuiWrapper.display(afpChain, ca1, ca2);
 // Or StructureAlignmentDisplay.display(afpChain, ca1, ca2);
 ```
 
-Note that these require that you include the structure-gui package and the jmol
+Note that these require that you include the structure-gui package and the jMol
 binary in the classpath at runtime.
 
 ## Command-line tools
 
-## PDB-wide database searches
-
-The Alignment GUI also provides functionality for PDB-wide structural searches.
-This systematically compares a structure against a non-redundant set of all
-other structures in the PDB at either a chain or a domain level. Representatives
-are selected using the RCSB's clustering of proteins with 40% sequence identity,
-as described
-[here](http://www.rcsb.org/pdb/static.do?p=general_information/cluster/structureAll.jsp).
-Domains are selected using either SCOP (when available) or the
-ProteinDomainParser algorithm.
-
-![Database Search GUI](img/database_search.png)
-
-To perform a database search, select the 'Database Search' tab, then choose a
-query structure based on PDB ID, SCOP domain id, or from a custom file. The
-output directory will be used to store results. These consist of individual
-alignments in compressed XML format, as well as a tab-delimited file of
-similarity scores and statistics. The statistics are displayed in an interactive
-results table, which allows the alignments to be sorted. The 'Align' column
-allows individual alignments to be visualized with the alignment GUI.
+Many of the alignment algorithms are available in the form of command line
+tools. These can be accessed through the main methods of the StructureAlignment
+classes. Tar bundles are also available with scripts for running
+[CE and FATCAT](http://source.rcsb.org/jfatcatserver/download.jsp).
 
-![Database Search Results](img/database_search_results.png)
+Example:
+```bash
+runCE.sh -pdb1 4hhb.A -pdb2 4hhb.B -show3d
+```
 
-Be aware that this process can be very time consuming. Before
-starting a manual search, it is worth considering whether a pre-computed result
-may be available online, for instance for
-[FATCAT-rigid](http://www.rcsb.org/pdb/static.do?p=general_information/cluster/structureAll.jsp)
-or [DALI](http://ekhidna.biocenter.helsinki.fi/dali/start). For custom files or
-specific domains, a few optimizations can reduce the time for a database search.
-Downloading PDB files is a considerable bottleneck. This can be solved by
-downloading all PDB files from the [FTP
-server](ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/) and setting
-the `PDB_DIR` environmental variable. This operation sped up the search from
-about 30 hours to less than 4 hours.
+Using the command line tool it is possible to run pairwise alignments, several
+alignments in batch mode, or full database searches. Some additional parameters
+are available which are not exposed in the GUI, such as outputting results to a
+file in various formats.
 
 
 ## Acknowledgements
