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CeSymm.md

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CE-Symm

Usage

The easiest way to run CE-Symm is via the included wrapper script.

usage:  runCESymm.sh [OPTIONS] [structures...]

CE-Symm can also run directly through java without using the wrapper script. On many systems, double clicking the JAR file should open the program in interactive mode. From the command line, it can be run as

java -Xmx500M -jar cesymm-*.jar [OPTIONS] [structures...]

Options

Options are specified in gnu style. Boolean options can be negated by prefixing with "no". All common options have short forms.

Short Option Long Option Description
-h --help Print usage information 
| --version         | Print CE-Symm version

-i | --input=file | File listing whitespace-delimited query structures -v | --verbose | Output verbose logging information. -q | --noverbose | Disable verbose logging information, as well as the default (--simple) output. -o | --simple=file | Output result in a simple format (default) | --stats=file | Output a tsv file with detailed symmetry info. | --tsv=file | Output alignment as a tsv-formated list of aligned residues. | --xml=file | Output alignment as XML | --fatcat=file | Output alignment as FATCAT output | --fasta=file | Output alignment as FASTA alignment output -j | --show3d | Force jMol display for each structure [default for <10 structures when specified on command line] -J | --noshow3d | Disable jMol display [default with --input or for >=10 structures] | --ordermethod=Class | Order detection method: SEQUENCE_FUNCTION (default), GRAPH_COMPONENT, ANGLE, or USER_INPUT | --order | Force a particular order. If positive, implies --ordermethod=USER_INPUT. | --refinemethod=Class | Refiner method: SEQUENCE_FUNCTION (default), NOT_REFINED, or GRAPH_COMPONENT | --symmtype=Class | Restrict symmetry to: CLOSED, OPEN, or AUTO (default) | --pdbfilepath=dir | Download directory for new structures [default tmp folder]. Can also be set with the PDB_DIR environmental variable. | --threads=int | Number of threads | --maxgapsize=float| This parameter configures the maximum gap size G, that is applied during the AFP extension. The larger the value, the longer the calculation time can become, Default value is 30. Set to 0 for no limit. | --scoringstrategy=str | Which scoring function to use: CA_SCORING, SIDE_CHAIN_SCORING, SIDE_CHAIN_ANGLE_SCORING, CA_AND_SIDE_CHAIN_ANGLE_SCORING, or SEQUENCE_CONSERVATION | --winsize=int | This configures the fragment size m of Aligned Fragment Pairs (AFPs). | --maxrmsd=float | The maximum RMSD at which to stop alignment optimization. (default: unlimited=99) | --nointernalgaps | Force alignment to include a residue from all repeats. (By default only 50% of repeats must be aligned in each column.) | --gapopen=float | Gap opening penalty during alignment optimization [default: 5.0]. | --gapextension=float | Gap extension penalty during alignment optimization [default: 0.5]. | --symmlevels=int | Run iteratively the algorithm to find multiple symmetry levels. The parameter controls the maximum symmetry levels allowed. 0 means unbounded. [default: 0]. | --noopt | Disable optimization of the resulting symmetry alignment. | --scorethreshold=float | The score threshold. TM-scores above this value will be considered significant results [default: 0.4, interval [0.0,1.0]]. | --ssethrehold=int | The minimum number of secondary structure elements (SSE) for each symmetric subunit, for the result to be singificant [default: 2]. | --maxorder=int | The maximum number of symmetric subunits [default: 8]. | --rndseed=int | The random seed used in optimization, for reproducibility of the results [default: 0]. | --minlen=int | The minimum length, expressed in number of core aligned residues, of a symmetric subunit [default: 15]. | --dcutoff=float | The maximum distance, in A, allowed between any two aligned residue positions [default: 7.0]. | --scopversion=version | Version of SCOP or SCOPe to use when resolving SCOP identifiers [defaults to latest SCOPe]

Interactive mode

By default, running CE-Symm will enter interactive mode. It will prompt you for an input structure and display the result in a jMol window.

runCESymm.sh

You can also pass one or more structures to the program to bypass the input dialog. A number of common ways to specify protein structures are supported, including PDB IDs, SCOP domain identifiers, PDP domains, and filenames. See BioJava's StructureID.getStructure() method for the complete syntax.

runCESymm.sh 1HIV
runCESymm.sh 1GEN.A d1tl2a_ PDP:1RI6Aa

Batch mode

To run CE-Symm on many structures, specify input and output files. The input should contain a list of whitespace separated structure identifiers. Lines beginning with '#' are ignored. Note that using --input disables jMol display by default. Use --jmol to override this behavior.

runCESymm.sh --input=queries.txt --xml=output.xml

An important feature in the batch mode is the multithreading implementation. By default, all the allowed CPUs are used to run the symmetry analyses in parallel. The option -threads N can be used to set the number N of threads to use. Note that the scaling efficiency of the multithreading is not perfect, and the thread overhead becomes significant with more than 8 threads.

Output

CE-Symm can output results in a number of formats. Format options may be followed by a filename (--stats=out.txt). If the filename is empty or '-', output will be sent to the terminal. To prevent structure names from being interpreted as filenames, it is recommended to use the hyphen explicitly (e.g. --stats=-, although --stats may work alone in some contexts).

If no format is specified, CE-Symm will default to printing the simple format to standard out, although this can be surpressed with the -q option.

The following formats are supported. Most formats represent the symmetry as an alignment from the structure to itself.

  • Simple: Intended to be a simple human-readable summary of results. Lists one line per query, giving the symmetry determination and information about how that conclusion was reached.
  • Stats: Provides more detailed statistics about each result. See below for a description of the fields.
  • TSV: A list of aligned residues for each structure, with a line containing only '//' to separate records.
  • FATCAT: A single file containing all alignments in FATCAT's traditional output format, with a line containing only '//' to separate records.
  • XML: All the alignments in a custom XML format suitable for machine parsing.

Statistics Output

The --stats option outputs a tab-delimited file with the following columns:

  • Name Name of the structure
  • NumRepeats Total number of repeats detected by CE-Symm, including multiple levels of symmetry if detected.
  • SymmGroup Symmetry Group of the top level of symmetry. This includes point group symmetry (Cn or Dn), helical symmetry (H), and translational repeats (R).
  • Refined 'true' or 'false', indicating whether refinement was successful
  • SymmLevels Number of symmetry levels detected
  • SymmType OPEN or CLOSED symmetry
  • RotationAngle Angle of rotation at the principal axis (degrees). Closed symmetry may deviate from ideal values due to the superposition procedure.
  • ScrewTranslation Translation parallel the principal axis (Å)
  • UnrefinedTMscore TM-Score of the self-alignment prior to refinement
  • UnrefinedRMSD RMSD of the self-alignment prior to refinement
  • SymmTMscore Average pairwise TM-Score of all repeats in the alignment after refinement
  • SymmRMSD Average RMSD of all repeats in the alignment after refinement
  • RepeatLength Number of aligned residues in each repeat
  • CoreLength Number of ungapped columns in the alignment
  • Length Total length of the protein
  • Coverage Fraction of the protein aligned

License & Availability

CE-Symm is licensed under LGPL 2.1 (see LICENSE, which should have come bundled with the executable).

The source code is available at https://github.com/rcsb/symmetry and as part of the BioJava library. A webserver is also provided at http://source.rcsb.org/jfatcatserver/symmetry.jsp

If you use CE-Symm in your research, please cite:

Douglas Myers-Turnbull, Spencer E Bliven, Peter W Rose, Zaid K Aziz, Philippe Youkharibache, Philip E Bourne, and Andreas Prlic. Systematic detection of internal symmetry in proteins using CE-Symm. 2014. Awaiting publication.

Examples

# Get help
runCESymm.sh -h

# Full interactive mode. Prompts for an input structure & runs CE-Symm,
# displaying the result using jMol
runCESymm.sh

# Run CE-Symm on a single structure or a short list of structures
# and display the results using jMol
runCESymm.sh 1HIV
runCESymm.sh 1GEN.A d1tl2a_ PDP:1RI6Aa
runCESymm.sh ./myprotein.pdb

# Print result summary to standard out, repressing jMol display
runCESymm.sh --noshow3d 1GEN.A 1TL2.A 1RI6.A

# Print detailed alignment information
runCESymm.sh --stats=- 1GEN.A

# Output XML file with full alignments and detailed results
runCESymm.sh --xml=output.xml -J 1GEN.A 1TL2.A 1RI6.A

# Run in batch mode.
# The input file should list one structure per line.
# Accepts PDB IDs ("4hhb"), SCOP identifiers ("d4hhba_"), or ranges ("4hhb.A","4hhb.A_1-141")
# Lines beginning with '#' are ignored.
runCESymm.sh --input=queries.txt --xml=output.xml

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