Updated on March 4, 2026
Release Notes
New features
- #8777 – Change the logic for activation of 'Arrange as a Ring' tool and context menu item
- #8781 – Change the logic for attachment points editing drop-down in the monomer creation wizard
- #8857 – Monomer saving - presets in the monomer creation wizard
- #8856 – Defining other monomer properties - presets in the monomer creation wizard
- #8866 – Defining the preset - presets in the monomer creation wizard
- #8851 – Highlighting presets in the monomer creation wizard
- #8854 – Defining the preset - presets in the monomer creation wizard
- #8849 – Entering the wizard - presets in the monomer creation wizard
- #8852 – Additions to the structure - presets in the monomer creation wizard
- #8850 – Add "Mark as a..." context menu option for Nucleotide (preset) in monomer creation wizard
- #8008 – Implementation of Copolymer S-Group type
Bugfixes and improvements
- #8437 – If no selection made, system doesn't define attachment points for monomer
- #5701 – It is possible to connect all APs to same atom
- #8800 – The hover on a selected atom differs in micro mode and in macro mode
- #7797 – Underline colour for the base counter in the Calculate Properties window doesn't fit the requirement
- #7789 – Fragment selection highlighting inconsistent between Micro and Macro modes
- #7325 – Right-click copy option does not work for microstructures on macro canvas
- #8837 – No bad valence indication on Macromolecules canvas
- #8792 – Rename monomer symbol to monomer code in the monomer creation wizard
- #8898 – Selection ignored in Ketcher API calls
- #7128 – Molecular formula letters are not on the same level
- #8641 – Tooltip in popup Ketcher sequence mode appears beyond view area for sequences at the top
- #4724 – After clicking the "Clear Canvas" button multiple times, a user has to click the "Undo" button multiple times to return the structure
- #6071 – Change event does not trigger after switching to Micro mode
- #6236 – Cycled aromatic bond looks wrong on Macro canvas
- #7123 – Deleting one of multiple monomers does not trigger recalculation in Calculate Properties window
- #5170 – Fixed "Process is not defined" error is displayed in console after Clearing Canvas in Macro Mode with the element with an attachment point and switching to Micro
- #5125 – Fixed after copying and pasting, structure under cursor causes Uncaught TypeErrors in DevTool console when approaching the edges of canvas
- #8205 – System shouldn't allow to upload monomers with no base IDT alias defined
- #5656 – Bond properties are not implemented
- #8954 – Undo/redo operations doesn't work for atoms, arrows and pluses after changing their positions in Macro mode
- #7188, #7190, #7255 – Unknown peptide, sugar, unknown base and unknown phosphate looks like chems (in addition ketcher wrongly considers R3-R1 connection between unknown sugar and/or unknown base as side chain connection)
- #9047 – Leaving group atom position is incorrect for nucleotides created in monomer wizard
- #9032 – Flex mode icon is active after ketcher close and open again
- #8965 – Migrate to Indigo v1.40.0 in-browser module
- #8918 – Update the help document (3.11.)
Github link: https://github.com/epam/ketcher/releases/tag/v3.12.0
Updated on March 4, 2026
Release Notes
New features
- #8248 – Define nucleotide presets using the monomer creation wizard (POC)
- #8254 – Allow for stereo bonds up and down to be a bond between AA and LGA
- #8383 – Introduce library searching using HELM aliases, AxoLabs aliases, and modification types
- #7915 – Enable flipping of all expanded monomers in a structure
- #8363 – Include 'Arrange as a Ring' button for Flex mode
Bugfixes and improvements
- #8386 – Update the help document (3.10.)
- #8739 – Migrate to Indigo v1.39.0-rc.1 in-browser module
- #4188 – Choosing wedged/hashed bond direction doesn't work from right-clicking context menu
- #7148 – Number of selected elements in context menu is wrong for sense/antisense chain
- #7735 – System shows inner circles of aromatized benzene rings from collapsed monomers on Molecules canvas
- #6855 – Labels for empty ambiguous monomer categories are present in the library
- #7244 – File format name for Sequence is cut off in Save Structure modal dropdown
- #5578 – Peptide section for ambiguous monomers should have "Ambiguous Amino Acids" name
- #5580 – Order of sections for ambiguous bases is wrong - Ambiguous Bases should come first
- #5927 – Font size and label position should be corrected at "Open structure" dialog
- #7995 – Unable to create more than one attachment point per atom
- #8395 – "Attachment points are set
- #5481 – Ambiguous CHEM shown wrong at Sequence mode
- #5799 – S-Group properties window should be disabled for monomers
- #7385 – Cannot delete and copy microstructures via right-click context menu in macromolecule canvas
- #4772 – Fix Platinum valence
- #8403 – There is no way to remove HELM alias
- #7506 – Tooltip is shown in wrong place for ambigous monomers in popup mode
- #8461 – Function calls should not pass extra arguments
- #6737 – 5NitInd unsplit nucleotide should be shown as X symbol instead of @ one
- #8459 – Getters and setters should access the expected fields
- #5361 – getInChIKey returns just the InChI string as JSON
- #5751 – Establishing connection between ambiguous CHEMs works wrong
- #5214 – The tooltip does not appear below the cursor when hovering over the “plus” button and stripe
- #6725 – Ambiguous sugars (alternatives and mixed) in sequence shown as % symbol instead of @ symbol
- #4891 – When using the “ketcher.setMode(mode)” method, the icon of the "Type mode" drop-down does not change
- #8554 – System losts AxoLabs alias while save it KET
- #8556 – System losts Modification types values while save it KET
- #7372 – "Ghost image" doesn't satisfy the UX design
- #6731 – Ambiguous phosphates (alternatives and mixed) in sequence shown as % symbol instead of @ symbol
- #8584 – Tooltip for attachment points appears too far from attachment point
- #8397 – Context menu remains visible after creating cyclic structure via right-click menu
- #7776 – In Macro mode clicking on Selection tool icon does not open dropdown menu as in Micro mode
- #4645 – In the “Modify RNA Builder” mode, when hovering over the buttons “Yes” and “Cancel” in the “Update Sequence” window, tooltips are displayed
- #7610 – R-groups are not shown if to Open from file as New project
- #7559 – Charge tools doesn't work for "star" atoms
- #7022 – Dropdown for units (Da/kDa/MDa) is not aligned in width with the selector button
- #5677 – Preview for chain of CHEMs works wrong in sequence mode
- #5664 – Selection circle is different on micro and macro mode
- #5469 – Preview tooltips for monomers loaded from HELM with inline smiles are wrong
- #7956 – Presence of R32 group in molecule makes impossible to create monomer from it
- #5534 – Ambiguous monomer tooltip content doesn't sorted properly in case of equal quantities
- #5382 – System shouln't allow user to load empty mol file - Add to Canvas should be disabled
- #7689 – No tooltip shown and invalid attachments allowed when adding monomers consecutively without moving mouse from arrow button
- #5567 – System losts height data during copy/paste operation
- #7191 – Change 3SS6 monomer type to Phosphate
- #8726 – Name should not be mandatory any more, Symbol value should be used instead if user left it empty
- #8723 – User should be able to type ambiguous monomers symbols in edit sequence mode (current sequence type should be taken in to account)
- #6730 – System doesn't unite ambiguous bases (alternatives and mixed) into one @ symbol
- #8721 – Create a monomer button remain selected (colored) after user done with monomer creation (creation wizard got closed)
- #8720 – Library update event is triggered after API usage
- #7578 – Undo/Redo restores partial selection after cancelling monomer creation
- #8752 – All types of ambiguous monomers alone represented on sequence canvas as @ symbol should be represented
- #7519 – In case of multiple R1 or R2 groups second R1/R2 groups should be assigned to the smallest available Rn (n>2) if available
- #5922 – Non-polar amino acid (with W as natural analog) should have shade of green but currently it is violet
- #5445 – Labels for ambiguous monomers at Bond Preview tooltip are wrong
- #7189 – Unknown unsplit nucleotide looks like chem
- #8846 – Unable to create more than one nucleotide monomer - system throws exception
- #8845 – Creation nucleortide preset causes som bonds to disappear
- #8847 – Former molecule selection causes invalid attachment point creation in Monomer creation wizard
Github link: https://github.com/epam/ketcher/releases/tag/v3.11.0
Updated on February 27, 2026
Release Notes
New features
- #7500 – Update the monomer preview
- #7633 – Allow for setting of modification type in the monomer creation wizard
- #7932 – Add warning messages to the monomer creation wizard in case of unusual leaving group atoms
- #7928 – Allow for setting of HELM alias in the monomer creation wizard
- #8200 – Add parameter to Editor to disable saving new monomers to local storage
- #8281 – Adjust subscription to library update event of Ketcher API
- #7905 – Selection logic change and toolbar icons enabling for the monomer creation wizard
- #7970 – Include 'Create cyclic structure' option in the context menu for Flex mode
Bugfixes and improvements
- #8602 – Migrate to Indigo v1.38.0 in-browser module
- #7971 – Update the help document (3.9.)
- #7887 – Molecule rotation causes error in console: Uncaught TypeError: Cannot read properties of undefined (reading 'pp')
- #4467 – Ket label should be renamed to Ket Format
- #7746 – System replace few spaces in monomer name to one space on monomer preview
- #7421 – "Ghost image" of CHEM is white (different from "ghost image" of other monomer types)
- #7740 – System should not allow to fill Symbol and Name fields if Type is not selected on Monomer creation wizard
- #3742 – Wrong tooltip for "minimize window" button (shows "expand window")
- #7373 – "Grabbing hand" mouse cursor is absent on grabbing monomers from the library
- #5570 – PNG and SVG exported images should be identical to how the canvas looks like in case of Chiral label
- #8294 – Do allow to collapse s-groups (superatom type) without name
- #7936 – Add tooltips to some attachment points in the monomer creation wizard
- #7997 – For non-potential-AAs the related context menu option (Mark as connection point,) should be disabled
- #8328 – Modification drop-down list is not ordered as required (Natural Amino Acid first, others alphabetically)
- #8377 – Add data-topology and data-reacting-center attributes for bonds
- #7553 – Dropdown for switching between Macro and Micro modes does not appear in fullscreen mode
- #5520 – Percentages for mixed bases ain't sorted from biggest to smallest in tooltip
- #8414 – System should throw The following string cannot be interpreted as an AxoLabs string. error if symbols without brackets cannot be interpreted
- #8039 – Ketcher doesn't send input_format parameter to Indigo in case of AxoLab load request
- #8418 – All monomers from SDF loaded via updateMonomersLibrary appear in Base group instead of their correct classes
- #8404 – No documentation for libraryUpdate event subscription
- #8463 – Batch monomer import aborts on a single invalid entry and does not indicate which record failed Standalone mode
- #8599 – Correct the stereo-bonds of sugars
Github link: https://github.com/epam/ketcher/releases/tag/v3.10.0
Updated on February 27, 2026
Release Notes
New features
- #7690 – Allow for modification of the structure in the monomer creation wizard
- #7730 – Continuation of attachment points editing in the monomer creation wizard
- #7748 – AxoLabs format support
- #7674 – Add ability to update monomers library API in SDF format
- #7560 – Improving snake layout logic to include small molecules
- #7709 – Update the help document (3.8.)
- #8270 – Migrate to Indigo v1.37.0 in-browser module
Bugfixes and improvements
- #7572 – "Create a monomer" option is missing in right-click menu when selection meets conditions
- #7443 – Save to SDF button is missed on Salts and Solvents tab in Structure Library dialog
- #7359 – Stereochemistry dialog crashes Ketcher if only one stereo bond on the canvas
- #7697 – IDT alias of CHEM 5TAMRA is displayed wrong
- #7919 – Change the symbol of CHEM Cy5.5 dye
- #5417 – IDT aliases not shown at preview tooltip at Monomer Library
- #5202 – Update visuals in Right-click context menu
- #7395 – Line between Paste option and Create RNA antisense strand option is missing in the context menu
- #7364 – Gap between icon and Delete label is twice bigger than it should be in Molecules mode
- #7327 – Missing separator line above "Delete" in context menu
- #7256 – Ketcher losts aliasHELM property for unknown monomers that makes export to HELM incorrect
- #7912 – Errors in console in dev mode "Cannot update a component"
- #7770 – Pressing Right Scroll Arrow button of top menu cause exception to console
- #7700 – System allow to delete monomers leaving connected bonds on the canvas
- #7934 – Export to SVG Documents works wrong for unsplite nucleotides with dash symbole (-) in alias
- #7649 – Undo/redo works wrong for monomer reposition corrected by snapping
- #7783 – Microstructure disappears from canvas in Sequence mode when adding new sequence row
- #7918 – Change the IDT alias format in the library file and adjust the logic for IDT aliases on preview
- #7581 – Undo/Redo buttons become inactive and canvas Up, Bottom, Left and Right toolbars remain active inside Monomer Wizard
- #7893 – System shouldn't allow to create monomers for selection with aromatic bonds to non-selected part
- #7923 – Undo after deleting RNA preset connected to benzene ring leaves undeletable artifacts in Flex, Snake, and Sequence modes
- #7914 – Microstructure not removed properly with Redo, duplicates on repeated Undo/Redo in Sequence mode
- #7978 – Create monomer process changes atom of not related part of the molecule
- #7979 – Pressing right Command key on Mac causes errors in DevTool Console (left Command works fine)
- #8000 – Monomer Wizard allows creation of monomer with Functional Group
- #8002 – No validation message shown for minimal monomer structure in Monomer Wizard
- #8005 – Changing name for attachment points works wrong
- #8040 – R2 attachment point is missing for vinU monomer
- #8041 – System loads invdC monomer as unresolved monomer from AxoLabs
- #8067 – Do not save added or updated monomer in local storage
- #8068 – Unable to update monomer library via API on Remote Ketcher – input format error
- #8070 – Existing Presets in the library disappear after adding new preset via API
- #8123 – HELM (and IDT) alias collision is possible after library update
- #8296 – Create Monomer tool can not be hidden by toolbar buttons config
GitHub release: https://github.com/epam/ketcher/releases/tag/v3.9.0
Updated on October 17, 2025
Release Notes
New features
- #6287 – Expanding the snap functionality to monomer groups inside of a structure
- #7441 – Allow for modification of the attachment points in the monomer creation wizard
- #6657 – Bump react to ^19.0.0 in ketcher-react package
- #6358 – Add lasso selection/fragment selection tool in macromolecules mode
- #7554 – Correct existing and add new structures to the library with appropriate IDT codes
- #7221 – Change the colour of nucleobases
- #7384 – Create documentation for hiding toolbar buttons
- #7505 – Update the help document (3.7.)
- #7760 – Migrate to Indigo v1.36.0 in-browser module
Bugfixes and improvements
- #7222 – Incorrect leaving group atoms for expanded monomers
- #6993 – Atoms and "monomer to atom bonds" are not removed when all other bonds are removed from atom
- #7619 – Pressing ? key at Text Editor form while creation text label opens Macromolecules help link
- #7525 – Specify a target origin for this message. vulnerability
- #6747 – Unnecessary leaving groups (R-groups) appear upon "Removing Abbreviation" of expanded monomer when an attachment point is occupied
- #7571 – Ctrl+M does not open monomer creation wizard when selection meets conditions
- #7683 – Remove Add attachment point functionality
- #7578 – Undo/Redo restores partial selection after cancelling monomer creation
- #7509 – Export to SVG doesn't work in Ketcher mode
- #7788 – Tooltip and restriction not triggered when selecting monomer without R2 in Macro mode
- #7794 – Selection remains on original structure after creating Antisense RNA/DNA and cannot be cleared by canvas click
- #7782 – In Macro mode selection tool resets to Rectangle when switching between Flex, Snake, and Sequence modes
- #7791 – Highlight is not secured for clicked r label in monomer creation wizard
- #7152 – Copy keyboard shortcut works wrong for text content
- #7837 – Unable to create monomer if molecule loaded from KET
- #7846 – Connection between created monomer and the rest of molecule got lost after monomer creation
- #7814 – Connection point enumeration is wrong if they are already enumerated form range [3-8]
- #7688 – Attached groups are lost when saving and reopening monomer created via Monomer Wizard in KET format
- #7828 – Unable to assign atom as a leaving group event if it is eligable
- #7806 – Problematic points are not highlighted in red when validation is failed
- #7877 – Ketcher losts attachment point name on loading s-group from mol v3000
- #7786 – In Snake mode after Undo bonds remain on canvas and cause console errors
- #7777 – Incorrect shortcut displayed for selection tools in Macro mode
- #7854 – Ketcher api doesn't work in proper order
- #7785 – Clicking toolbar buttons resets selection tool from Lasso/Fragment to Rectangle
- #7784 – In Sequence mode selection tool resets to Rectangle when entering or exiting sequence edit mode
- #7850 – System doesn't add the leaving group atom (a hydrogen) by default at the end of the bond connecting the attachment atom and the non-selected part of the structure
- #7807 – Selection of cyclic molecule causes application crash: Uncaught ReferenceError: process is not defined
- #7817 – Connection point enumeration is wrong R-groups outside [1-8] range
- #7838 – The leaving group atom (a hydrogen) is not added by default at the end of the bond
- #7821 – Connection point enumeration is wrong R-groups outside [3-8] range
- #7813 – System should not allow to create monomer if atom with many R-groups in the selection
- #7815 – System changes right connection point (R2) to left one (R1) if no R1 group defined
- #7816 – System swaps left connection point (R2) and right connection point (R1) if R2 group was created early that R1
- #7606 – Pasting text into Symbol or Name fields in Monomer Wizard triggers unrelated "Convert error"
- #7801 – Incorrect edit dialog behaviour when right-clicking on attachment atom
- #7798 – Atom label is not correct in attributes panel for leaving atoms different from hydrogen
- #7804 – Incorrect atom label upon monomer saving when removing automatically assigned attachment point via R-group
Github link: https://github.com/epam/ketcher/releases/tag/v3.8.0
Updated on September 19, 2025
Release Notes
New features
Here’s the converted list with links added for each item:
- #6552 – Create a monomer from a selected part of the structure
- #6785 – Support aliases from HELM
- #3253 – Introduce the arrow button on library cards for easy monomer/preset addition to canvas
- #7430 – Adjust sgroup hover rendering to remove overlapping parts
- #6150 – Add the star atom to the special nodes section of the extended table
- #7535 – Add API for switching between macromolecules and molecules modes
- #7660 – Migrate to Indigo v1.35.0 in-browser module
Bugfixes and improvements
Here’s the updated list with links added for each item:
- #7377 – Update the help document (3.6.)
- #7351 – Profiling and optimization for many monomers on molecules canvas
- #6270 – Add "About" (i) and "Help" (?) buttons to the main toolbar in macromolecules mode
- #7222 – Incorrect leaving group atoms for expanded monomers
- #7168 – Opening the 3D Templates section in Structure Library causes multiple errors in the DevTools console
- #7252 – Integrate with SonarQube
- #7273 – System loads micro-macro connected structure on snake canvas and created understandable bond
- #7283 – Context menu is wrong if clicked on top of sequence
- #7205 – Layout shift when changing mode from sequence to flex and back upon first macromolecules mode initialization
- #7245 – Missing tooltip for standalone input field in ruler control
- #7440 – Area selection doesn't work till bond/atom reposition
- #7381 – Create documentation for 'change' event subscription
- #7152 – Copy keyboard shortcut works wrong for text content
- #7423 – It is possible to drag monomer from library and drop it to sequence canvas
- #7512 – Library doesn't fit view port in Sequence mode in Popup mode
- #7513 – "Ghost image" doesn't position below mouse cursor if dragged from Library to canvas in popup mode
- #7531 – Arrow icon appears in Sequence mode, violating requirement for Snake and Flex modes only
- #7538 – Unable to add ambiguous monomers via arrow button - no preview and errors in console
- #7539 – No tooltip shown and invalid attachment allowed when adding a monomer without R1 to selected monomer with free R2
- #7548 – Tooltip not shown and addition allowed when multiple monomers with free R2 are selected
- #7551 – Monomer drag-n-drop from Library to the canvas doesn't work for peptides if they were clicked on Sequence canvas
- #7562 – Tooltip overlaps monomers when hovering over arrow button on monomer card
- #7575 – Monomer creation wizard opens despite selection being connected via non-simple bond
- #7576 – Create monomer wizard is available for structures containing S-groups, R-groups, or extended table atoms
- #7577 – "Create a monomer" button becomes active for disconnected structures
- #7563 – Selection after chain/monomer addition (autochain improvement)
- #7580 – Zoom actions in Monomer Wizard throw errors in the console
- #7601 – Wizard allows editing atoms and bonds via right-click menu without showing an error
- #7604 – Name, Symbol, Natural analogue input fields are not highlighted when left empty and Submit is clicked in Monomer Wizard
- #7606 – Pasting text into Symbol or Name fields in Monomer Wizard triggers unrelated "Convert error"
- #7607 – Missing S-group name in KET after saving a monomer via the wizard
- #7609 – Symbol uniqueness validation is missing in Monomer Wizard (no error, no highlight)
- #7612 – Natural analogue is not cleared when monomer type changes
- #7614 – After creating a monomer via wizard, switching to macro mode shows two separate entities instead of one
- #7615 – Phantom structure remains on canvas after closing wizard and is visible in exported files
- #7620 – Creating a monomer from a partial benzene selection causes console errors and no hover highlight on created region
- #7624 – Created Sugars and Phosphates via wizard are not added to Macro library
- #7625 – No validation against existing monomers - newly created monomer with duplicate name overwrites the existing one in the library
- #7627 – Selection tools stop working after creating first monomer via wizard when many structures are on canvas
- #7629 – API does not implement library change subscription
- #7684 – Only selected atoms connected with bonds should be taken into account on monomer creation
- #7714 – System shouldn't allow to create monomer for selected structure that have any non-simple single bonds to non-selected parts of the structure
- #7692 – System shouldn't allow to create monomer for molecules with R-Groups attachment points
- #7691 – System shouldn't allow to create monomer for molecules with R-Groups
- #7725 – Hand tool and Area Selection Tool buttons close Monomer creation wizard if pressed
- #7722 – Connection preview does not follow cursor and AP to AP connection is not possible
- #6581 – Monomer placement offset from cursor when Ketcher runs in a popup with increased browser zoom
Github link: https://github.com/epam/ketcher/releases/tag/v3.7.0
Updated on September 17, 2025
Release Notes
New features
- #6404 – Drag and drop for the library elements in macromolecules mode
- #7164 – Introduce marking of nucleotide components
- #7125 – Support for reaction arrows and reaction pluses in macromolecules mode
- #7132 – Update and add icons to right-click drop-down menus in all modes
- #7347 – Migrate to Indigo v1.34.0 in-browser module
Bugfixes and improvements
Here is the list converted into the desired Markdown format with links:
- #7231 – Update the help document (3.5)
- #7073 – Unable to create hydrogen bond: Uncaught RangeError: Maximum call stack size exceeded
- #7178 – The tooltip appears behind the context menu options
- #7187 – IDT code shown wrong for SS3 chem
- #6410 – Incorrect bond attachment to micro molecules in Macro Mode
- #7277 – Cannot open multiple instances of Ketcher in one window
- #6986 – Context menu appears on both canvases in molecules mode for several Ketcher instances on the same page
- #7207 – Rectangular input field should be wide enough to fit any (at least 4) digit number
- #7117 – Chemical elements disappear when attempting to Expand the Structure in Micro mode after selecting one in Macro mode
- #7170 – Monomer tooltip appears and remains in place even if the mouse cursor moves away
- #7209 – The ruler is limited to 190 divisions
- #7365 – Console errors appear when using actions on structures with nucleotide component marking
- #7386 – Delete operation causes exception: Uncaught (in promise) Error: Minified Redux error
- #7432 – Security: form-data uses unsafe random function in form-data for choosing boundary
- #7371 – Mouse cursor doesn't position at the top left corner of the preset
Github link: https://github.com/epam/ketcher/releases/tag/v3.6.0
Updated on August 26, 2025
Release Notes
New features
- #6738 – Ability to change the number of monomers in a line
- #5208 – Allow modifying amino acids on canvas
- #6995 – Smart positioning of CIP stereo labels for atoms
- #6852 – Improve the hydrophobicity graph in the "Calculate Properties" window
- #6589 – API lacks support for 3 letter code sequence export in macro mode
- #7070 – Include the removed versions of some 3D templates in the templates library in addition to the corrected ones
- #7224 – Migrate to Indigo v1.33.0 in-browser module
Bugfixes and improvements
Here is the list converted to the desired Markdown format with links:
- #7094 – Update the help document (3.4.)
- #6294 – Hiding toolbar buttons doesn't also hide/disable the corresponding keyboard shortcut
- #6930 – Replace File comparison (for MOL files ONLY!) operations with valid helper function - verifyFileExport
- #7032 – Ketcher allows to make changes in sequence while being in nucleotide modification mode
- #5971 – Inconsistent selection sensitivity when highlighting sequences
- #7023 – Hydrophobicity section is missing tooltip icon and description
- #6834 – Clicking on base card in RNA Builder does not scroll to selected base if multiple bases from the same section are selected
- #7031 – Layout shift when entering symbol in sequence mode upon first macromolecules mode initialization
- #6958 – Monomers positions are not preserved when pasting macromolecule in MOL format
- #7200 – App crashes after modifying amino acids and switching to Micro mode
- #7203 – N-methylation is shown as available for Hyp even though it shouldn't be
- #7142 – Monomer selection without bonds should work the same as with bonds
- #7251 – Incorrect tooltips for properties and logic for the hydrophobicity graph in the "Calculate properties" window
- #7130 – Incorrect calculation when part of a microstructure is selected - full structure is sent to Indigo
- #7150 – Molecule mass should be calculated for partial selected micromolecule (ketcher part)
- #7202 – Incorrect order of amino acid modification options in context menu
- #7281 – App crashes when closing Ketcher
- #6985 – Structure appears on incorrect canvas in molecules mode for several ketcher instances on the same page
- #7288 – Monomers shift out of visible area when adjusting layout with ruler in sequence edit mode
- #7318 – Bonds are overlapped by CIP labels when moving the structure or when the structure has small bond angles
Github link: https://github.com/epam/ketcher/releases/tag/v3.5.0
Updated on June 20, 2025
Release Notes
New features
- #6832 – Update the help document 3.3
- #6625 – Support of expanded monomer option
- #6271 – Support for CIP stereo labels in macromolecules mode
- #5727 – Add "Calculate Properties" for macromolecules
- #5797 – Highlighting attachment point of expanded monomers on hover in micromolecules mode
- #7237 – Migrate to Indigo v1.32.0 in-browser module
Bugfixes and improvements
- #4838 – Incorrect structure for Phe-L-Phenylalanine in template library
- #5497 – Refactor (SnakeModePolymerBondRenderer): Create and use SVGPathDAttributeUtil
- #6288 – Incorrect numbering in sequence
- #6871 – Connection points become visible and broken if user switches window focus from one app to another and back
- #6870 – Enter key adds undeletable preset to preset section
- #4476 – Tooltips in sequence mode not disappear after right-click on letters
- #6762 – System shows natural analog monomer as modified if source MOL file contains only 3-letters natural analog name
- #6791 – Change activation area of the New sequence button
- #6788 – Reduce "Add new sequence" control width
- #7008 – Support of expanded monomer options doesn't work if monomer loaded from file/clipboard
- #7007 – Rotation doesn't work for expanded monomers on Molecules mode
- #5791 – It is possible to expand unknown nucleotide on micromolecules canvas
- #5789 – It is possible to expand ambiguous monomers on micromolecules canvas
- #7014 – No tooltip displayed for the “Calculate Properties” button in main toolbar
- #7019 – Data in “Calculate Properties” window disappears after switching browser tabs, selection remains
- #7030 – Missing Celsius symbol (°C) in “Melting temperature” label
- #7039 – App crashes when adding Ambiguous Amino Acids to peptide sequence with open Calculate Properties window
- #7015 – Alt+C / Option+C hotkey does not open the “Calculate Properties” window
- #7033 – calculateMacroProperties API is called immediately on sequence selection, even when Calculate Properties window is closed
- #7018 – Unable to clear monomer selection after switching browser tabs
- #7026 – Calculate properties for peptides are missing in case of mixed peptide and RNA/DNA chain
- #7017 – “Calculate Properties” shows wrong behavior when sequence is connected to microstructure
- #7062 – Rotation is incorrect upon exporting transformed monomer to SVG or PNG
- #7074 – Formula in "Calculate Properties" window is not updated when selecting monomers with connected microstructure
- #7034 – Unipositive ions default value is shown in nM instead of mM for double-stranded sequence selection
- #7085 – Ketcher does not send bond type to Indigo if connection is different from R2–R1, causing missing data in "Calculate Properties"
- #7027 – Incorrect highlight (missing fill) for leaving-group atoms
- #7028 – Turquoise monomer outline has incorrect gap for attachment points and blue outline too thin
- #7096 – Clearing canvas while "Calculate Properties" window is open causes console errors
- #6974 – System removes monomers from Molecules mode canvas is switched from Macro mode (bonds remain!) if Ketcher is in embedded mode (custom style iframe)
- #7118 – Cannot edit concentration values of unipositive ions and oligonucleotides in "Calculate Properties"
- #7249 – Input fields for ion concentration and oligonucleotides become inactive after clearing or entering zero
- #7266 – Oligonucleotides input field becomes unresponsive after entering zero
Github link: https://github.com/epam/ketcher/releases/tag/v3.4.0
Updated on June 20, 2025
Release Notes
New features
- #6508 – Update the logic for recognizing sense and antisense chains
- #6435 – Do not retain snake mode layout when passing through snake mode
- #6519 – Implement the library redesign and modify the RNA builder behavior
- #6620 – Add salts to the "Salts and Solvents" tab in the monomer library
- #6472 – Add "Copy", "Paste", and "Delete" to the right-click drop-down menu in sequence mode
- #5999 – Added "Create Antisense Strand" icon on the toolbar
- #6317 – Introducing the snap to distance functionality for monomers connected via bonds
- #6612 – Update the help documentation (3.2)
- #6987 – Migrate to Indigo v1.31.0 in-browser module
Bugfixes and improvements
Here is the list you provided converted into the desired Markdown format with links:
- #6293 – Remove base monomer border after selection
- #6573 – Incorrect bond length and angle for non-natural monomers in the library
- #6695 – Unable to create antisense RNA/DNA chain in case of multiple chain selection (if not eligible for antisense chain selected)
- #6842 – Single click on already selected monomer causes monomer to stick to mouse cursor and snapping elements to appear on the canvas forever
- #6813 – Click on monomer selection area causes an exception: Uncaught TypeError: Cannot read properties of undefined (reading 'drawingEntity')
- #6774 – Modified bases selected via RNA Builder revert to natural analogs in all modes
- #6495 – System replaces A base with always RNA N base (alternatives of A, C, G, U) even if user selected DNA N base (alternatives of A, C, G, T)
- #6716 – Cursor can escape to the void after certain actions and break the canvas
- #6671 – Removing dash should turn aligned nucleotide to nucleoside
- #6541 – Undo of clear canvas operation causes molecules bonds to overlap atom labels
- #6712 – Adding RNA/DNA before empty space in sense sequence causes an exception and breaks the canvas
- #6776 – Phosphate does not appear immediately when added via keyboard in SYNC mode
- #6780 – Phosphate always added to sense strand in non-SYNC mode when targeting antisense strand
- #6781 – Phosphates added via keyboard in SYNC mode are not reverted by Undo and cause console errors on hover
- #6779 – Unable to add phosphate to antisense strand in SYNC mode via keyboard
- #6775 – Adding monomer to the first position from the left of antisense chain works wrong and causes exception: Uncaught TypeError: Cannot read properties of undefined (reading 'chain')
- #6863 – Horizontal/Vertical snap to distance doesn't work for hydrogen bonds
- #6814 – System should turn nucleotide to nucleoside on sequence break by Enter
- #6783 – Incorrect cursor jumps after phosphate insertion in the middle or at the end of the sequence
- #6824 – Unable to delete multiple sequences at once via right-click menu in Sequence mode
- #6705 – Antisense complement is not skipped when terminal monomer lacks an attachment point (R1/R2), causing incorrect structure on canvas
- #6833 – Tooltips on monomer cards in all sections instantly disappear on hover in popup Ketcher
- #6830 – RNA Builder section does not highlight the corresponding monomer in library on the first click
- #6828 – Star icon for Favorites tab in monomer library is too small compared to design specification
- #6831 – Last row of monomers in Sugars, Bases, and Phosphates sections is not visible in popup Ketcher
- #6834 – Clicking on base card in RNA Builder does not scroll to the selected base if multiple bases from the same section are selected
- #6816 – Incorrect hotkeys are displayed and triggered for RNA and DNA Antisense strand creation
Github link: https://github.com/epam/ketcher/releases/tag/v3.3.0
Updated on April 17, 2025
Release Notes
New features
- #6215 – Introducing the snap to angle and standard bond length for monomers connected via bonds
- #6252 – Allow creation of antisense chains in sequence mode
- #6383 – Introduce the creation of DNA antisense chains
- #6355 – Change attachment points of backbone monomers in automatically created antisense chains
- #6254 – Update the representation of sense and antisense chains in sequence mode (2/2)
- #6284 – Long bonds for uneven double stranded sequences in snake and flex modes
- #6527 – Add ability to pass coordinates to Ketcher addFragment and setMolecule API to position provided structure
- #6357 – Allow insertion of phosphates (p) from the keyboard in sequence mode
- #6596 – Update Indigo to 1.30.0 in browser module
Bugfixes and improvements
- #6219 – Unable to save to HELM hydrogen connection between micromolecule (with AP) and monomer
- #6005 – Move the dot indicating a modified phosphate in sequence mode
- #4145 – Implement popup versions of Ketcher (and routing)
- #5700 – System allows to establish infinite number of bonds from monomer to microstructure
- #6534 – Adding nucleotide to the last position having phosphate in antisense causes exception: ReferenceError: process is not defined
- #6402 – Hydrogen bonds misaligned due to antisense strand direction change when opening or pasting a structure in Macro Mode
- #6464 – Splitting chain with Enter key doesn't work
- #6425 – Hiding of number indicators while in sync editing mode when the triangle overlaps with the number
- #6535 – Unable to add nucleoside to the end of sequence if hanging antisense monomer present
- #6561 – Switching to macromolecules changes CSS in the page
- #6369 – System doesn't switch Library tab to proper one if user changes typing type using keyboard shortcuts
- #6627 – Fix invisible snapping drawings after switching to micro mode
- #6621 – Fix monomer snapping wiping monomer labels
- #6608 – API setMolecule moves molecule off-canvas on second call
- #6607 – README missing coordinate units for setMolecule and addFragment API methods
- #6539 – System should add same thing in antisense chain but not connect it with H-bond if it is not nucleotide/nucleoside
- #6624 – Enter key in single-strand edit mode incorrectly breaks both chains instead of only one
- #6632 – New sequence appears gray after clearing the canvas in non-sync mode
- #6631 – Sync mode causes incorrect letter input after adding a monomer in non-sync mode
- #6606 – Adding nucleotide to the last position having phosphate in antisense works wrong
- #6531 – System can't add nucleotide between phosphate and nucleotide in antisense chain
- #6617 – Empty element appears after undoing line deletion in Sequence mode and switching to Flex/Snake mode
- #6609 – System creates ambiguous RNA nucleotides instead of DNA ones in case of DNA antisense stand creation
- #6615 – Missing warning message when deleting all hydrogen bonds between two chains
- #6619 – System doesn't create antisense phosphate if it situated to the left from nucleotide
- #6623 – Sense and antisense chains switch places during editing based on monomer count
- #6443 – System allows to select single antisense symbol that causes an error if it got deleted
- #4002 – getSmiles and getSmarts on query feature containing aromatic ring raises an error
- #6709 – Unable to paste HELM from clipboard to the canvas. System throws an error: Convert error! option manager: Property "sequence-type" not defined
- #6723 – Forbid moving sequence nodes and snapping by select rectangle tool
- #6729 – Create RNA/DNA Strand doesn't work for B, K, Y and S ambiguous bases
- #6750 – Incorrect R1 attachment atom for natural Ribose (R) in the library
- #6759 – Add pruning of the remaining transient views on clear canvas button click
- #6795 – Incorrect properties of some monomers in the library
- #6829 – Add monomers to the library
- #6786 – Add monomers from HELM Core Library to Ketcher Library
Updated on March 27, 2025
Release Notes
New features
- #6167 – Long bonds for linearly displayed circular structures
- #5942 – Update the representation of sense and antisense chains in sequence mode (1/2)
- #5995 – Synchronize the library tab with typing type switcher in sequence mode
- #6222 – New chain tool behavior
- #6246 – Import indigo with EXPORT_ES6 & USE_ES6_IMPORT_META options
- #6417 – Update Indigo to 1.29.0 in browser module
Bugfixes and improvements
- #6164 – Changing any parameter at Settings cause Undo/Redo work wrong (or delete undo history)
- #6166 – Color schema for Favorites tab at RNA Library is wrong for Peptides
- #6088 – Disable create antisense strand option if antisense-less base present in chain selection
- #5696 – Adding Attachment point to microstructure already connected to monomer - causes problems
- #6201 – Circular hydrogen bond connection between three (or more) chains, those hydrogen bonds isn't considered as side chain connection for layout purposes
- #6195 – Nucleotide wrongly become antisense oriented if have hydrogen connection to sugar
- #6194 – Unknown monomer and CHEM overlap to each other if both are the side chain for same chain
- #6422 – Long bond appears behind monomers when using attachment points
- #6084 – System doesn't allow select ambiguous monomers from the library
- #6085 – Changing of ambiguous base via RNA Builder on Sequence mode causes sequence corruption
- #6098 – Adding second chain with antisense chain to the canvas cause layout problem
- #6446 – System shouldn't merge two antisense chains if separator monomer got deleted
- #6447 – System doesn't split chain pair on two if - symbol deleted
- #6460 – Troubles with switching to Edit mode if - symbol present in sequence
- #5780 – Connection points appear visually disconnected when moving monomers in Flex and Snake mode
- #6462 – Adding peptide between RNA and - symbol breaks sense/antisense chain
- #6456 – Long bond appears behind the structure after Copy-Paste in Flex Mode
- #6471 – Removing peptide from sense/antisense chain cause unnecessary phosphate removal
- #5780 – Connection points appear visually disconnected when moving monomers in Flex and Snake mode
- #6493 – Undo of deleted bond on sequence mode causes "ghost" monomer appearance on the canvas
- #6505 – Hotkey CTRL+ALT+P does not switch library to Peptides
- #6628 – Add export of ketcher-standalone esm module as cjs
- #6159 – Aromatizing doesn't work for Pyridone and Pyrone (molecules from Template library)
- #6588 – Peptide sequence not pasting directly on canvas
- #6661 – Adjust ketcher-standalone entrypoints to work for all builders
