Cavity programs: Difference between revisions

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Limited to channels with two entrances. Can display only one channel at a time. Channels are represented as overlapping spheres, thus radially symmetric. Offers a channel profile graph showing channel diameter that can be colored by many different properties. A list of channel-lining atoms is provided (not spreadsheet-ready), and these can be displayed as yellow atoms on the blue channel.

Personal experience: For SARS-CoV-2 spike protein [[6zgi]], I specified a ''User Defined Site'' as 3 residues that encircle the deepest part of the membrane-proximal cavity (Asn 907 in all 3 chains of the homotrimer). The result was 45 channels that passed through this site. Visualization is in JSmol but the macromolecule rendering options are limited as all obscure the channel. It would be useful to have a thin backbone trace that would less obscure the channel, or to provide translucency e.g. for cartoon. Also, translucency for the channel, which would enable seeing any ligands within, is not offered.

Personal experience: For SARS-CoV-2 spike protein [[6zgi]], I specified a ''User Defined Site'' as 3 residues that encircle the deepest part of the membrane-proximal cavity (Asn 907 in all 3 chains of the homotrimer). The result was 45 channels that passed through this site. Visualization is in JSmol but the macromolecule rendering options are limited as all obscure the channel. It would be useful to have a thin backbone trace that would less obscure the channel, or to provide translucency e.g. for cartoon. Also, translucency for the channel, which would enable seeing any ligands within, is not offered. [[User:Eric Martz|Eric Martz]] 21:33, 18 December 2020 (UTC)

==Jmol==

Cavity programs: Difference between revisions

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 Limited to channels with two entrances. Can display only one channel at a time. Channels are represented as overlapping spheres, thus radially symmetric. Offers a channel profile graph showing channel diameter that can be colored by many different properties. A list of channel-lining atoms is provided (not spreadsheet-ready), and these can be displayed as yellow atoms on the blue channel.
-Personal experience: For SARS-CoV-2 spike protein [[6zgi]], I specified a ''User Defined Site'' as 3 residues that encircle the deepest part of the membrane-proximal cavity (Asn 907 in all 3 chains of the homotrimer). The result was 45 channels that passed through this site. Visualization is in JSmol but the macromolecule rendering options are limited as all obscure the channel. It would be useful to have a thin backbone trace that would less obscure the channel, or to provide translucency e.g. for cartoon. Also, translucency for the channel, which would enable seeing any ligands within, is not offered.
+Personal experience: For SARS-CoV-2 spike protein [[6zgi]], I specified a ''User Defined Site'' as 3 residues that encircle the deepest part of the membrane-proximal cavity (Asn 907 in all 3 chains of the homotrimer). The result was 45 channels that passed through this site. Visualization is in JSmol but the macromolecule rendering options are limited as all obscure the channel. It would be useful to have a thin backbone trace that would less obscure the channel, or to provide translucency e.g. for cartoon. Also, translucency for the channel, which would enable seeing any ligands within, is not offered. [[User:Eric Martz|Eric Martz]] 21:33, 18 December 2020 (UTC)
 ==Jmol==