Python-based
Hierarchical
ENvironment
for
Integrated
Xtallography
Contents
sculpt_ensemble is a unified model preparation program that internally uses Sculptor and Ensembler. When these two programs are run separately, the result is dependent on what order these programs are run, and no matter what order the programs are run, there are corner cases that it is suboptimal. In the unified program no information loss occurs and there are further benefits as well.
The program sculpt_ensemble is available from the command line and will also be available from the PHENIX GUI.
Structures (compulsory): structures to be superposed and modified. For each structure, specific parts can be selected using PHENIX atom selection syntax, and assembly information can be associated with the using the assembly keyword, or the convenience keyword read_single_assembly_from_file (for more information please see the Ensembler documentation).
Error files associated with the input PDB file can also be input using the errors scope. See the Sculptor documentation for more details (please note that there is no input for superposition errors, since those are calculated within the ensembling step and passed onto Sculptor).
Accepted formats: PDB. Recognized extensions: .pdb, .ent.
Sequence files: target sequences (for each assembly position). This is used to identify the target sequence for each alignment. In case no alignment is available, and the target sequence for the given assembly position is available, sculpt_ensemble prepares an alignment using the sequence of the model chain (if no target sequence available, and no suitable alignment is found, a dummy alignment will be used instead). Accepted extensions are .fasta, .faa or .fa for FASTA format, .pir for PIR-format and .seq or .dat for a relaxed PIR/FASTA-like format.
Alignments: sequence alignment with the target sequence. The alignment contains information that can be exploited in model improvement (this is currently only implemented for protein chains). The chains are automatically associated with the corresponding alignment based on a sequence comparison. The target sequence is also automatically identified if it is provided through the target_sequence keyword (see above), otherwise the first sequence in the alignment is used as target. Alignment input is optional, in case it is not provided, an alignment will be made up using the chain sequence with itself. Accepted extensions (with the corresponding format) are .aln (CLUSTAL format), .pir (PIR-format) and .ali (relaxed PIR-like format).
Homology search files: hits from a homology search. These work very similarly to a set of alignment files. It is assumed that the first sequence in each alignment is the target sequence (the sequence used for searching homologues). Accepted extensions (with the corresponding format) are .xml (BLAST-family XML output) and .hhr (HHPRED output).
The fully processed structure is output. The file is named according to the following convention: root_merged.pdb, where root is a user-defined parameter (accessible from the output scope), and is similar to merged output style from Ensembler.
The program reads in the input files, creates assembly, and runs ensembling first. The assemblies are then transformed, superposition error is associated with respective chains, and processed sequentially according to the corresponding Sculptor protocol (note that although the superposition errors are always present, these are not used unless requested explicitly by enabling a protocol). See the respective documentation for more details.
In case there is only a single assembly present, the superposition step is skipped, and the program works as the standalone Sculptor. It is also possible to disable the processing step (sculpting.disable), in which case the program works as the standalone Ensembler.
sculpt_ensemble also supports chain trimming, but unlike the explicit option in Ensembler, this is available as the superposition option within the mainchain processing section in the sculpting machinery. In addition, this can also be used in combination with polishing options.
phenix.sculpt_ensemble \
[ command-line switches ] \
[ PHIL-format parameter files ] \
[ PHIL command-line assignments ] \
[ PDB-files ] \
[ alignment files ] \
[ sequence files ]
-h, --help show this help message and exit --show-defaults print PHIL and exit -i, --stdin read PHIL from stdin as well -v, --verbosity set verbosity level (info,debug,verbose) --version show program's version number and exit --text-logfile FILE Verbatim copy of log stream --html-logfile FILE Verbatim copy of log stream in HTML
Everything not starting with a dash ('-') is interpreted as a PHIL argument. This can be a PHIL-format file containing parameters, command-line assignment or a file whose type is automatically recognized (based on file extension). Note that sequence files are not accepted on the command line, since associated chains could not easily be guessed and require a fully specified parameter scope.