Chat

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Sending Messages

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Basic Message Types

What is the role of p53 in cancer development?
How does CRISPR-Cas9 target specific DNA sequences?
What are the latest FDA-approved kinase inhibitors?

Search UniProt for human membrane proteins
Find PDB structures of HIV protease
Query ChEMBL for EGFR inhibitors with good bioavailability

Predict the structure of this protein sequence: MKTAYIAK...
Analyze the binding affinity of this ligand to the target protein

Analyze the sequences in @protein_data.fasta
Show me the structures of @model1.pdb and @model2.pdb
Summarize the findings in @research_paper.pdf

Run /protein-analysis on this sequence
Execute the /literature review workflow for "CRISPR gene editing"

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Message Controls

• Type your message in the input box at the bottom
• Press Enter to send (single line)
• Press Shift + Enter for new lines without sending
• Click the arrow button to send

• Stop generation: Click the red stop button
• Scroll up: Read previous messages without interrupting

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Tool Calls and Visualizations

• Tool name: Which service was used (e.g., “PDB Search”, “UniProt Query”)
• Parameters: What was searched for or analyzed
• Status: Running, completed, or failed
• Actions: Options to view details or save results, and view the visualization

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Managing Conversations

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Chat History

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Search and Organization

• Click the search box at the top of the chat history list
• Search across chat with keywords

• Hover over any chat and click the pin icon
• Pinned chats stay at the top regardless of activity
• Perfect for ongoing research projects

• Click the chat title in the header to edit
• Or right-click chat in chat history and select “Rename”
• Use descriptive names for easy identification

• Hover over any chat and click the delete icon
• Deleted chats cannot be recovered

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Advanced Features

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File References

1. Type @ in your message
2. Select from autocomplete suggestions
3. File appears as a blue chip in your message

1. Click the attach button in the chat input
2. Select from autocomplete suggestions
3. File appears as a blue chip in your message

1. Right-click any file in the files panel
2. Select “Add to Chat”
3. File reference inserted

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Workflow Integration

1. Type / in the chat input
2. Select from autocomplete suggestions
3. Workflow appears as a purple chip in your message

1. Click the workflow button (/) in the chat input
2. Select from autocomplete suggestions
3. Workflow appears as a purple chip in your message

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Tool Suggestions

1. Type ! in your message
2. A dropdown appears with available tools
3. Type to search by tool name, display name, or description
4. Select a tool from the suggestions
5. Tool appears as a chip in your message

1. Click the tool button (!) in the chat input toolbar
2. A dropdown appears with all available tools
3. Search or browse tools by category
4. Select a tool from the list
5. Tool appears as a chip in your message

!search_uniprot_tool Find human insulin sequences

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Model Selection

• Claude Sonnet 4: Best overall performance, complex reasoning (use for predictions and complex reasoning tasks)
• Gemini Flash 2.5: Fast responses, general research tasks
• Other models: Additional options for specific needs

1. Click current model name
2. Select from dropdown menu
3. Next message uses the new model
4. Selected model will be used for all future messages

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Code Mode (Data Analysis)

1. Click the code icon (</>) in the chat input area
2. Icon and the chat input area highlights in purple when active
3. Your preference is saved automatically

• Data analysis and visualization
• Statistical calculations
• Scientific computing tasks
• Bioinformatics sequence analysis
• Creating plots and charts

• Stateful Python environment (variables persist across executions)
• Pre-installed data science libraries (pandas, numpy, matplotlib, etc.)
• File upload/download integration with your project
• Rich output support (plots, DataFrames, images)

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Best Practices for Chat

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Troubleshooting

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Next Steps