[{"data":1,"prerenderedAt":531},["ShallowReactive",2],{"blog-post-nanome-v2.7:-comments-pocket-minimization-ligand-builder-upgrades-and-more":3,"blog-posts-nav":22},{"data":4,"meta":18},[5],{"id":6,"attributes":7},158,{"title":8,"content":9,"createdAt":10,"updatedAt":11,"publishedAt":12,"date":13,"description":14,"keywords":15,"slug":16,"category":17},"Nanome v2.7: Comments, Pocket Minimization, Ligand Builder Upgrades, and More","v2.7 puts the conversation next to the atoms. Comments now live inside the workspace, threaded and tied to the exact atoms they're about.\n\nThe Ligand Builder also gets its largest update since it shipped in v2.3: attachment points that follow valence, torsion snapping, ring fusion, and pocket minimization against a receptor. Atoms and bonds are drawn with a new renderer that holds up at any zoom. Desktop and web gained hover, selection, and measurement. And the fixes list runs to 36 entries.\n\nHere's the tour.\n\n## Comments, attached to the atoms they're about\n\n\u003C!-- IMAGE_NEEDED: Screen recording of a threaded comment in a workspace: a reply with an @mention and an emoji reaction, then clicking the atom chip so the view highlights and zooms to those atoms -->\n\nComments in v2.7 can hang off an annotation, a scene, or the whole workspace. Threads take replies, @mentions, and emoji reactions, and they update live for everyone in the session.\n\nA comment can carry an **atom chip**. Clicking the chip highlights the atoms it refers to and zooms to them, so \"this carbonyl\" always means one specific carbonyl.\n\nWatched threads and unread indicators keep track of what changed since the last visit. Annotations and comments now share one menu.\n\nThe reasoning behind a design decision now stays in the same place as the structure it's about.\n\n## A Ligand Builder that follows the chemistry\n\n\u003C!-- IMAGE_NEEDED: Screen recording of the Ligand Builder in XR: bringing a fragment to an attachment point, the preview, twisting around the bond with torsion snapping, release to attach, and a ring closing automatically -->\n\nAttachment points now follow each atom's valence and geometry. Bringing a fragment to an attachment point previews it. Twisting it around the new bond snaps to favorable torsions, and releasing attaches it. Rings close automatically.\n\nReplace mode can fuse a fragment onto a ring, merging every overlapping atom, with an aromatic preview before anything is committed.\n\nA new Auto Relax button cleans up nearby geometry after each edit, and aromaticity is recalculated every time.\n\n### Pocket minimization\n\n\u003C!-- IMAGE_NEEDED: Screen recording of pocket minimization in the Ligand Builder: choosing a receptor and a mode, setting the pocket radius, and the result panel with energy, ligand RMSD, and pocket RMSD -->\n\nWhen ligand minimization shipped in v2.4, we noted that minimizing inside a binding site would come later. It's here.\n\nPocket minimization takes a receptor, one of 3 modes (rigid receptor, flexible pocket, or flexible side chains), and a pocket radius, then minimizes the ligand in place. The result reports energy along with ligand RMSD and pocket RMSD. A run can be cancelled or undone.\n\nOne limit: ligands that contain metal atoms can't be minimized.\n\n## Atoms and bonds, redrawn\n\n\u003C!-- IMAGE_NEEDED: Close-up comparison of atom and bond rendering on a large structure, zoomed far in, showing smooth antialiased spheres and cylinders -->\n\nSpheres and cylinders are now drawn as GPU impostors. They stay smooth and antialiased at any zoom, with much higher frame rates on large structures. The same renderer covers structures being edited, selection highlights, and the web viewer.\n\nMolecular surfaces are generated at higher resolution too, so they come out smoother and more detailed.\n\nThe backdrop changed as well. Skyboxes are now procedurally generated mountains in each theme's colors, which trims about 30 MB off the Quest download. Skybox themes and night mode also arrive in the web viewer.\n\n## Hover, select, and measure on desktop and web\n\n\u003C!-- IMAGE_NEEDED: Screen recording of the web viewer: hovering residues, clicking atoms to measure a distance and an angle, and double-clicking to zoom to a residue -->\n\nOn desktop and in the web viewer, atoms, bonds, and residues highlight on hover and select on click. Clicking atoms measures distances and angles. Double-clicking zooms to a residue or an entry.\n\nRotation and zoom pivot on the selection, or on the highlighted residue under the cursor, so the thing being inspected stays in the middle of the screen.\n\nThe web viewer can also create and remove interaction components: polymer-ligand, polymer-polymer, and chain-chain. On desktop, Escape shows or hides the main menu.\n\n## Pointing in XR\n\nThe default pointer now highlights whole residues. A trigger pull adds the hovered residue to the selection, or removes it.\n\nThe off-hand always works as a pointer for hovering and selecting atoms, whatever tool the other hand is holding.\n\nPointing at an interaction, a measurement, or a text annotation shows a tooltip with its details: interaction type, distance, and the groups involved.\n\nX on the off-hand controller (left by default) mutes and unmutes the microphone.\n\n## Following shows the work in progress\n\n\u003C!-- IMAGE_NEEDED: Screen recording from a follower's point of view while another user builds a ligand or adjusts a torsion, showing their tool, hover highlights, and the in-progress edit before it is committed -->\n\nFollowing someone used to show where they were looking. In v2.7 it also shows their current tool and mode, the atoms they hover and select, and their edits as they happen. Ligand building, torsions, and rotamers appear live, before they're committed.\n\nChains resolve too. Following someone who is following another person leads to the person at the end of the chain, and the view smoothly re-aligns to what the leader is looking at.\n\nSpotlight is steadier. People who join or reconnect mid-session follow the presenter automatically, a briefly disconnected presenter returns as the same participant, and web viewers start following without the old 6-second delay.\n\n## Trajectories and file loading\n\nPlayback is smoother. Upcoming frames are precomputed in the background, and interactions, annotations, and residue labels stay visible and update as frames advance.\n\nMD trajectories load faster and take much less storage and server memory. Large GROMACS (.gro) systems load far faster, GRO files split into chains where residue numbering restarts, and terminal caps (ACE, NME, NH2) stay part of the protein.\n\nBonding is more accurate. Ligand bonds for PDB and mmCIF files now come from the RCSB Chemical Component Dictionary, and metal coordination is no longer drawn as covalent bonds. Structures containing DNA or RNA load faster, with more accurate bonds and formal charges.\n\nCovalently bound ligands keep their bond to the protein. A modified residue with an attached group is split: the standard amino acid stays in the protein, and the attached group is treated as a ligand.\n\n## The rest of the list\n\n- **Structure alignment** runs on the server, with a choice of CE-Align or TM-Align. Aligning trajectory entries keeps their current frame.\n- **Residue editing** can score rotamer clashes and hydrogen bonds against visible atoms only, or against all atoms. Rotamer suggestions calculate much faster in large workspaces.\n- **Components** have a Delete Atoms action (with a confirmation), show their atom count on hover, and gray out when empty. Distance components can include atoms from every entry in the workspace.\n- **Clash markers** scale in size and brightness with how much the atoms overlap.\n- **Metal coordination** detection now includes methionine sulfur, iron-sulfur cluster sulfides, and aromatic nitrogen donors such as porphyrin and imidazole rings.\n- **Annotations** can be hidden and shown with an eye toggle on each row, or all at once with Hide All and Show All, so nothing has to be deleted to clear the view.\n- **Scene analysis export.** Chemical interactions, measurements, and minimization history download as a ZIP of CSV files.\n- **MCP.** AI assistant tools can read a summary of each workspace's contents: chains, residue ranges, ligands, and ions.\n- **Tables.** The Projects, Workspaces, Ligands, and rotamer lists share a new table with column sorting, a loading indicator, and an empty-state message.\n- **Presence.** Teammates' online status, workspace invites, and join requests update instantly, including for colleagues in the web viewer.\n\n## Licenses and sign-in\n\n3 account changes ship with v2.7.\n\nFree licenses now have limits: 1 owned project, 3 owned workspaces, 5 structures per workspace, and view-only access to shared workspaces and projects. The app shows a clear message when a limit is reached.\n\nNanome warns when a license expires within 30 days, and signs out with a clear notice when it does.\n\nSign-in errors explain what went wrong: wrong credentials, an account that has to use Google, Microsoft, Apple, or SSO sign-in, an organization IP restriction, or a network problem.\n\n## Fixes\n\nThe fixes list has 36 entries. A few of them:\n\n- Cancelling a load, or leaving a workspace while a large structure is rendering, no longer freezes the app.\n- The Components menu stays responsive in large workspaces, and opening the Sequence menu no longer stalls.\n- Sound annotations that reach the 5-minute limit are no longer lost, and the recorder shows elapsed and maximum time.\n- Following resumes after a headset wakes from sleep.\n- File loading errors show a short readable message in place of a stack trace.\n- Wrist menu buttons no longer intermittently stop responding.\n\nThe full changelog is on the [setup page](https:\u002F\u002Fnanome.ai\u002Fsetup\u002F).\n\n## How to get it\n\nHeadset builds of v2.7 are on the [setup page](https:\u002F\u002Fnanome.ai\u002Fsetup\u002F). Nanome Web runs in a browser at [app.nanome.ai](https:\u002F\u002Fapp.nanome.ai), with nothing to install.\n\nSee you in the workspace.\n","2026-10-13T18:33:09.922Z","2026-10-13T18:38:01.313Z","2026-10-13T18:38:01.307Z","2026-10-13","Nanome v2.7 adds threaded comments, pocket minimization, a valence-aware Ligand Builder, a new atom renderer, desktop selection, and 36 fixes.","Nanome v2.7, molecular visualization, pocket minimization, ligand builder, threaded comments, XR collaboration, structure-based drug design, molecular dynamics trajectories, structure alignment, TM-align, web molecular viewer, drug discovery software","nanome-v2.7:-comments-pocket-minimization-ligand-builder-upgrades-and-more","releases",{"pagination":19},{"page":20,"pageSize":21,"pageCount":20,"total":20},1,100,{"data":23,"meta":528},[24,29,34,39,44,49,54,59,64,69,74,80,85,90,96,101,106,111,116,121,126,131,136,141,146,152,157,162,167,172,177,182,187,192,197,202,207,212,217,222,227,232,237,242,247,252,257,262,267,272,277,282,287,292,297,302,308,313,318,323,328,333,338,343,349,354,359,364,369,374,379,384,389,394,399,404,409,414,419,424,429,434,439,444,449,454,459,464,469,474,479,484,489,493,498,503,508,513,518,523],{"id":20,"attributes":25},{"slug":26,"title":27,"category":28},"spy-stories-and-rational-drug-design","Spy stories & rational drug design","case-studies",{"id":30,"attributes":31},2,{"slug":32,"title":33,"category":17},"meta-quest-pro-and-a-new-version-of-nanome-(v1.24)","Meta Quest Pro & a new version of Nanome (v1.24)",{"id":35,"attributes":36},3,{"slug":37,"title":38,"category":28},"beating-the-pandemic-in-virtual-reality","Beating the Pandemic in Virtual Reality",{"id":40,"attributes":41},4,{"slug":42,"title":43,"category":28},"a-new-era-in-drug-discovery-the-first-ai-generated-drug-is-going-to-clinical-trial","A new era in drug discovery? 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