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Last Update: 2006.05.16 | ||||||||||
Introduction | Manual | Examples | Download | ||||||||||
Examples I. Convert [*.pdb] tnto [*.env] format: %./lsheba -e [*.pdb] | ||||||||||
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The [*.env] file is created in the same directory and the content is like this: | ||||||||||
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If the PDB file is from NMR experiment, there might be more than one model of the structure in that pdb file. LSHEBA only takes the first model and converts it into [*.env] format.
It shows the number of residues in each protein, in each domain and those with C-alpha distance less than 35 Angstron. The output is on the screen. %./lsheba [query.env/.pdb] [subject.env/.pdb] | ||||||||||
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[back to Manual] To parse the result to a file, use -p option. Default output will be displayed on the screen and the result in a easy parsing format will be stored in the file. %./lsheba -p [query.env/.pdb] [subject.env/.pdb] | ||||||||||
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[back to Manual]
LSHEBA has several different alignment output options which users can view it on the screen or save it in a file with or without secondary structure information. In brief, LSHEBA groups local alignments into a domain and if one domain contains more than one chain, the alignments are displayed seperately. In each domain, if there are more than 20 residues in a continuous sequence that are not matched with subject sequence, those un-matched ones are not considered to be in that domain and are represented in <<n>> , where n is the number of unmatched residues. LSHEBA can take either [*.pdb] file or [*.env] file and the output are either stdout or in a file. The naming convention of the output file is [query structure file name]-[subject structure file name]-[option].out. 1. Alignment output with color on the screen to indicate different kinds of secondary structures: % ./lsheba -a [query.env/.pdb] [subject.env/.pdb] | ||||||||||
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[back to Manual] 2. Alignments saved in the file without secondary structure code: Default output will be displayed on the screen and the alignments will be saved in the file. %./lsheba -n [query.env/.pdb] [subject.env/.pdb] | ||||||||||
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[back to Manual] 3. Alignments with secondary structure information saved in the file: Default output will be displayed on the screen and the alignments with secondary structure code: C for Coil, H for Helix, S for Sheet and T for turns, will be saved in the file. [back to Manual] % ./lsheba -s [query.env/.pdb] [subject.env/.pdb] | ||||||||||
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