For years I've wondered how useful it would be to visualize pockets, cavities, tunnels, channels etc. in proteins by filling them with pseudoatoms. Eventually I couldn't resist and I have made a program to do this: *Pockets And Cavities Using Pseudoatoms in Proteins (PACUPP)*. Snapshots of results probably won't survive this email list server, so I've put them here: https://urldefense.com/v3/__https://www.dropbox.com/sh/0a6isj97md3km8n/AAC0sS31qCUxGtFgE_bZrhdqa?dl=0__;!!Mih3wA!TDDXQXiWve3q2RCEbpSwpOhxZ1Qwk2y_w8TRS239yGLD2kSKazq33FahQMnGe-0$ One shows the major cavity of a *proteasome* (1pma). The other shows the *nascent peptide exit channel* in a 50S *ribosome* (5np6). There is a YouTube video and a slideshow that show more examples, and demonstrate how to use PACUPP. Download the free, open-source program and all documentation  here: https://urldefense.com/v3/__http://molviz.org/pacupp__;!!Mih3wA!TDDXQXiWve3q2RCEbpSwpOhxZ1Qwk2y_w8TRS239yGLD2kSKazq33FahHf8EZg8$ PACUPP (Jmol) is Java-based, and thus works in Windows, macOS, and linux. Here are some advantages of this method: * Provides easy tools to see what is *inside* a cavity, see the *mouths* of cavities, see and list (spreadsheet ready) atoms *lining* a cavity, and *measure cavity dimensions*. Also, cavity *volumes* are reported. * You see the *actual size and shape* of each pocket, tunnel or cavity -- not an idealized radially-symmetric representation. * Output PDB files include pseudoatoms (holmium, Ho, think "holes") and can be explored in software of the user’s choice, such as*PyMOL* or Chimera. * *Animations*of the types in the slides are *easy to make* using the animation kit <https://urldefense.com/v3/__http://molviz.org/pacupp/animation_kit_instructions.pdf__;!!Mih3wA!TDDXQXiWve3q2RCEbpSwpOhxZ1Qwk2y_w8TRS239yGLD2kSKazq33Fahaow8Qt0$ > that is included. * Provides easy tools to *limit display to one or a few cavities* of interest, and *trim *off fenestrations or “wings” if desired. * *Two thirds*of entries in the Protein Data Bank process in *< 15 sec* each (with cavity detail at the default setting of /fine/). * Very large models (proteasomes, ribosomes, etc.) can be set up as *batch jobs that process unattended*. The output PDB files can be visualized later in Jmol with all PACUPP commands <https://urldefense.com/v3/__http://molviz.org/pacupp/commands-alphabetical.pdf__;!!Mih3wA!TDDXQXiWve3q2RCEbpSwpOhxZ1Qwk2y_w8TRS239yGLD2kSKazq33Fah2onGqls$ > available, or in PyMOL, etc.. * Most small to medium-sized cavities are shown automatically with *no adjustments* to settings. * There are simple adjustments for large cavities or cavity detail. * Handles multiple models and alternate locations by ignoring them automatically. * No knowledge of Jmol command language is needed. ** ** I will be interested in your comparisons with other cavity software, as well as your comments, feedback, and suggestions for improvement. -Eric * * Eric Martz, Professor Emeritus, Dept Microbiology (he/him/his) U Mass, Amherst -- Martz.MolviZ.Org <https://urldefense.com/v3/__http://martz.molviz.org/__;!!Mih3wA!TDDXQXiWve3q2RCEbpSwpOhxZ1Qwk2y_w8TRS239yGLD2kSKazq33FahMhxpjtU$ > Guided Exploration of Macromolecules: FirstGlance.Jmol.Org <https://urldefense.com/v3/__http://firstglance.jmol.org/__;!!Mih3wA!TDDXQXiWve3q2RCEbpSwpOhxZ1Qwk2y_w8TRS239yGLD2kSKazq33FaheLs0JUs$ > Protein 3D Structure Wiki: Proteopedia.Org <https://urldefense.com/v3/__http://proteopedia.org/__;!!Mih3wA!TDDXQXiWve3q2RCEbpSwpOhxZ1Qwk2y_w8TRS239yGLD2kSKazq33FahaJoLsig$ > Top Five 3D MolVis Tools: Top5.MolviZ.Org <https://urldefense.com/v3/__http://top5.molviz.org/__;!!Mih3wA!TDDXQXiWve3q2RCEbpSwpOhxZ1Qwk2y_w8TRS239yGLD2kSKazq33FahK66MBQI$ > Education: Biochem in 3D at MolviZ.Org <https://urldefense.com/v3/__http://molviz.org/__;!!Mih3wA!TDDXQXiWve3q2RCEbpSwpOhxZ1Qwk2y_w8TRS239yGLD2kSKazq33FahSGgRFoM$ > Find Functional Patches in Proteins: ConSurf.tau.ac.il Atlas of Macromolecules: Atlas.MolviZ.Org <https://urldefense.com/v3/__http://atlas.molviz.org/__;!!Mih3wA!TDDXQXiWve3q2RCEbpSwpOhxZ1Qwk2y_w8TRS239yGLD2kSKazq33FahL0axmM0$ > Interactive Molecules in Architectural Spaces: MolecularPlayground.Org <https://urldefense.com/v3/__http://molecularplayground.org/__;!!Mih3wA!TDDXQXiWve3q2RCEbpSwpOhxZ1Qwk2y_w8TRS239yGLD2kSKazq33Fahd-_qb8A$ > Workshops: Workshops.MolviZ.Org <https://urldefense.com/v3/__http://workshops.molviz.org/__;!!Mih3wA!TDDXQXiWve3q2RCEbpSwpOhxZ1Qwk2y_w8TRS239yGLD2kSKazq33Fah6ujiFPE$ >

 included.

 in PyMOL, etc..

For voids (but not pockets), you can do this with AVP ( https://urldefense.com/v3/__http://www.bioinf.org.uk/software/avp/__;!!Mih3wA!WrW4NNDUepbTbCcsryXi9qqXHlz1zBeOevzGarpQq4DOcsHZG4yAWbyL51PaD3g$ ) Programs like surfnet and pocketfinder will do something similar (though not with spheres) for pockets. Best wishes Andrew On Thu, 10 Dec 2020, 23:19 Eric Martz, <emartz@microbio.umass.edu> wrote: > For years I've wondered how useful it would be to visualize pockets, > cavities, tunnels, channels etc. in proteins by filling them with > pseudoatoms. Eventually I couldn't resist and I have made a program to > do this: *Pockets And Cavities Using Pseudoatoms in Proteins (PACUPP)*. > Snapshots of results probably won't survive this email list server, so > I've put them here: > > > https://urldefense.com/v3/__https://www.dropbox.com/sh/0a6isj97md3km8n/AAC0sS31qCUxGtFgE_bZrhdqa?dl=0__;!!Mih3wA!TDDXQXiWve3q2RCEbpSwpOhxZ1Qwk2y_w8TRS239yGLD2kSKazq33FahQMnGe-0$ > > One shows the major cavity of a *proteasome* (1pma). The other shows the > *nascent peptide exit channel* in a 50S *ribosome* (5np6). > > There is a YouTube video and a slideshow that show more examples, and > demonstrate how to use PACUPP. Download the free, open-source program > and all documentation here: > > > https://urldefense.com/v3/__http://molviz.org/pacupp__;!!Mih3wA!TDDXQXiWve3q2RCEbpSwpOhxZ1Qwk2y_w8TRS239yGLD2kSKazq33FahHf8EZg8$ > > PACUPP (Jmol) is Java-based, and thus works in Windows, macOS, and linux. > > Here are some advantages of this method: > > * Provides easy tools to see what is *inside* a cavity, see the > *mouths* of cavities, see and list (spreadsheet ready) atoms > *lining* a cavity, and *measure cavity dimensions*. Also, cavity > *volumes* are reported. > > * You see the *actual size and shape* of each pocket, tunnel or cavity > -- not an idealized radially-symmetric representation. > > * Output PDB files include pseudoatoms (holmium, Ho, think "holes") > and can be explored in software of the user’s choice, such as*PyMOL* > or Chimera. > > * *Animations*of the types in the slides are *easy to make* using the > animation kit > < > https://urldefense.com/v3/__http://molviz.org/pacupp/animation_kit_instructions.pdf__;!!Mih3wA!TDDXQXiWve3q2RCEbpSwpOhxZ1Qwk2y_w8TRS239yGLD2kSKazq33Fahaow8Qt0$ > > that is > included. > > * Provides easy tools to *limit display to one or a few cavities* of > interest, and *trim *off fenestrations or “wings” if desired. > > * *Two thirds*of entries in the Protein Data Bank process in *< 15 > sec* each (with cavity detail at the default setting of /fine/). > > * Very large models (proteasomes, ribosomes, etc.) can be set up as > *batch jobs that process unattended*. The output PDB files can be > visualized later in Jmol with all PACUPP commands > < > https://urldefense.com/v3/__http://molviz.org/pacupp/commands-alphabetical.pdf__;!!Mih3wA!TDDXQXiWve3q2RCEbpSwpOhxZ1Qwk2y_w8TRS239yGLD2kSKazq33Fah2onGqls$ > > available, or > in PyMOL, etc.. > > * Most small to medium-sized cavities are shown automatically with *no > adjustments* to settings. > > * There are simple adjustments for large cavities or cavity detail. > > * Handles multiple models and alternate locations by ignoring them > automatically. > * No knowledge of Jmol command language is needed. > > ** > > ** > > I will be interested in your comparisons with other cavity software, as > well as your comments, feedback, and suggestions for improvement. > > -Eric > > * * > Eric Martz, Professor Emeritus, Dept Microbiology (he/him/his) > U Mass, Amherst -- Martz.MolviZ.Org < > https://urldefense.com/v3/__http://martz.molviz.org/__;!!Mih3wA!TDDXQXiWve3q2RCEbpSwpOhxZ1Qwk2y_w8TRS239yGLD2kSKazq33FahMhxpjtU$ > > > Guided Exploration of Macromolecules: FirstGlance.Jmol.Org > < > https://urldefense.com/v3/__http://firstglance.jmol.org/__;!!Mih3wA!TDDXQXiWve3q2RCEbpSwpOhxZ1Qwk2y_w8TRS239yGLD2kSKazq33FaheLs0JUs$ > > > Protein 3D Structure Wiki: Proteopedia.Org < > https://urldefense.com/v3/__http://proteopedia.org/__;!!Mih3wA!TDDXQXiWve3q2RCEbpSwpOhxZ1Qwk2y_w8TRS239yGLD2kSKazq33FahaJoLsig$ > > > Top Five 3D MolVis Tools: Top5.MolviZ.Org < > https://urldefense.com/v3/__http://top5.molviz.org/__;!!Mih3wA!TDDXQXiWve3q2RCEbpSwpOhxZ1Qwk2y_w8TRS239yGLD2kSKazq33FahK66MBQI$ > > > Education: Biochem in 3D at MolviZ.Org < > https://urldefense.com/v3/__http://molviz.org/__;!!Mih3wA!TDDXQXiWve3q2RCEbpSwpOhxZ1Qwk2y_w8TRS239yGLD2kSKazq33FahSGgRFoM$ > > > Find Functional Patches in Proteins: ConSurf.tau.ac.il > Atlas of Macromolecules: Atlas.MolviZ.Org < > https://urldefense.com/v3/__http://atlas.molviz.org/__;!!Mih3wA!TDDXQXiWve3q2RCEbpSwpOhxZ1Qwk2y_w8TRS239yGLD2kSKazq33FahL0axmM0$ > > > Interactive Molecules in Architectural Spaces: MolecularPlayground.Org > < > https://urldefense.com/v3/__http://molecularplayground.org/__;!!Mih3wA!TDDXQXiWve3q2RCEbpSwpOhxZ1Qwk2y_w8TRS239yGLD2kSKazq33Fahd-_qb8A$ > > > Workshops: Workshops.MolviZ.Org < > https://urldefense.com/v3/__http://workshops.molviz.org/__;!!Mih3wA!TDDXQXiWve3q2RCEbpSwpOhxZ1Qwk2y_w8TRS239yGLD2kSKazq33Fah6ujiFPE$ > > > TO UNSUBSCRIBE OR CHANGE YOUR SUBSCRIPTION OPTIONS, please see > https://lists.sdsc.edu/mailman/listinfo/pdb-l .