USE
The installation of the software is left with the care of the user.
To illustrate the use of my plugin, I chose to take as example two pdb files which are 1EVH (Evh1 Domain From Murine Enabled In Complex With Acta Peptide) and 1DDW (Homer Evh1 Domain Unliganded). The superposition of these two files will be good.
In YASARA, the way to lauch my plugin is Analyze and Structural Alignement.
And then, we have to choose the pdb to analyze, and the software(s) to select.
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selected pdb to superpose
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choise of software(s) to launch
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Another interest of the plugin, is the possibility to select one or more softwares.
The results are posted in YASARA; and as it is indicated in the plugin, the meaning of ????_pdb is the result for SSM and SHEBA, joinFull.pdb for MULTIPROT, and transSecond for FLEXPROT.
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superposition with biginning files
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superposition without the beginning files
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Several PDB: MULTIPROT
The superposition of several pdb can only be done with MULTIPROT. I tried with four pdb: 1DDW, 1EVH, 1CBKA (string A from 1CBK) and 1HKA. (but it works with more than 4 pdb too.)
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exemple with 4 pdb
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pdb choise
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The superposition is the same one than if we have two pdb. So the result is:
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choise of MULTIPROT
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result with 4 pdb
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NB: However, it is possible to change the results files. For FLEXPROT and MULTIPROT, other final files are created. There are the files joinPart.pdb, join.pdb for MULTIPROT, and join.pdb for FLEXPROT. To change the file loaded in YASARA, lines 187-189 and 238 should be modified. These modification are carried out if the files loaded, are not those necessary. This program erases the intermediate files created by the software of superpositions, and also the pdb files in the temporary repertories.