Cavity programs: Difference between revisions
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[http://molviz.org/pacupp PACUPP]], '''P'''ockets '''A'''nd '''C'''avities '''U'''sing '''P'''seudoatoms in '''P'''roteins, identifies cavities by filling them with pseudoatoms (holmium, Ho, think "holes"; see comparison note<ref name="hitormiss" />). Cavities are identified as spaces between macromolecule atoms large enough to accomodate a ''cavity probe'' (default cavity probe radius 1.5 Å, configurable), or pockets between a smoothed macromolecular surface (default surface probe radius 10 Å, configurable) and atoms of the macromolecule. Starting point(s) are not relevant. An example is presented in some detail at [[PACUPP: Pockets And Cavities Using Pseudoatoms in Proteins]]. Further examples with demonstrations of how to use PACUPP are in a YouTube video and a slideshow, available from [http://molviz.org/pacupp molviz.org/pacupp], where you can also download the program. | [http://molviz.org/pacupp PACUPP]], '''P'''ockets '''A'''nd '''C'''avities '''U'''sing '''P'''seudoatoms in '''P'''roteins, identifies cavities by filling them with pseudoatoms (holmium, Ho, think "holes"; see comparison note<ref name="hitormiss" />). Cavities are identified as spaces between macromolecule atoms large enough to accomodate a ''cavity probe'' (default cavity probe radius 1.5 Å, configurable), or pockets between a smoothed macromolecular surface (default surface probe radius 10 Å, configurable) and atoms of the macromolecule. Starting point(s) are not relevant. An example is presented in some detail at [[PACUPP: Pockets And Cavities Using Pseudoatoms in Proteins]]. Further examples with demonstrations of how to use PACUPP are in a YouTube video and a slideshow, available from [http://molviz.org/pacupp molviz.org/pacupp], where you can also download the program. | ||
PACUPP offers a number of [http://molviz.org/pacupp/commands-alphabetical.pdf simple commands specialized for visualizing cavities], mostly single letter commands. Some call up a dialog where the use enters information. Lists cavity-lining atoms in a spreadsheet-ready text file. Learning the PACUPP commands is much easier than learning Jmol commands. | PACUPP offers a number of [http://molviz.org/pacupp/commands-alphabetical.pdf simple commands specialized for visualizing cavities], mostly single letter commands. Some call up a dialog where the use enters information. Lists cavity-lining atoms in a '''spreadsheet-ready''' text file. Learning the PACUPP commands is much easier than learning Jmol commands. | ||
PACUPP is a Jmol script. It processes 2/3 of the entries in the [[Protein Data Bank]] in ≤15 sec each. For large models such as ribosomes or proteasomes that may take many minutes, PACUPP offers an unattended batch mode. | PACUPP is a Jmol script. It processes 2/3 of the entries in the [[Protein Data Bank]] in ≤15 sec each. For large models such as ribosomes or proteasomes that may take many minutes, PACUPP offers an unattended batch mode. | ||
