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The Phenix AI analysis tool is designed to help you interpret your output files from a run in the Phenix GUI. It analyzes your log file and any output written to the GUI and the names of any output files that are supplied to the GUI and creates a summary of the run. Then it analyzes this summary in the context of the Phenix documentation to describe how this run fits into the framework of structure determination and suggests next steps. The AI analysis tool can be accessed in the Phenix GUI in the Results section of most Phenix GUI runs, next to the Log file button. You can also access it under the Tools menu.
To run the AI analysis, you will need Google and Cohere API keys. The Google key will let you run Gemini from the Phenix server, and the Cohere key will let you run Cohere Langchain tools. Both are free. You can get the keys from the AI section of the Preferences menu in the Phenix GUI. You can run a few AI analyses without getting your own key (a shared set of keys is supplied), but you should get your own set once you get going so that others can use the shared keys.
The AI analysis is carried out in two steps. In the first step, the log file, along with text written to the GUI and names of output files supplied to the GUI are summarized using a Cohere Langchain analysis. In the second step, the summary from the first step is analyzed in the context of all the Phenix documentation, transcripts of Phenix tutorial videos, and Phenix publications to provide background and to suggest next steps to take.
This type of AI does not save or learn from your questions. However the information in your log file is sent to the Phenix server, and from there, on to Cohere and Google gemini.
The purpose of the AI analysis is to help you interpret your output and to suggest ideas for next steps. You should keep in mind that this tools can make mistakes and give you incorrect interpretations and poor suggestions at times, so you want to just take the information as suggestions to think about.
You can combine this AI analysis with the Phenix chatbot . The chatbot can give you interactive answers to your questions using the same database of information as the AI analysis. This allows you to follow up on the AI analysis with questions to the chatbot. You can also paste part of the output from the AI analysis into the chatbot along with a question to get more context.
The AI analysis is limited to the sources that is supplied with, so it only knows about Phenix, and it only knows what is in the documentation, the videos and newsletters, and the papers we have supplied.
AI tools like this one can also just make mistakes and give incorrect answers. This does not seem to happen too often with this tool, but you need to always be on alert when using it. Use the tool as a helper, don't expect it to always be right.
If a detail is missing in the documentation, the AI analysis will not know it.
If you use the AI analysis tool, your log files are sent to the Phenix server, and from there on to Cohere and Gemini. That means the data could potentially be used by Cohere and Google in any way that they use other AI data that is sent to them.
Note that access to Cohere and Gemini is non-commerical only.