Chat

Code and materials to create sources for Phenix user Chat, CCTBX developer chat. For CCTBX developer chat, see cctbx_dev_docs subdirectory.

phenix_docs include current Phenix user documentation, reference material (pdf of papers), Phenix newsletters, selected documentation for atom selection and Phil

cctbx_dev_docs include CCTBX developer documentation and cctbx code

MATERIALS

phenix_docs: documentation: directory containing Phenix documentation as of 2025-06-11

papers: PDF versions of many papers describing Phenix

newsletters: PDF versions of all Phenix newsletters

phil_etc: documentation on Phil and atom selections

info.txt: source describing priming the chatbot

info_for_audio.txt: Text to paste in to control the generation of default-length audio summary

videos.list: list of youtube videos to include in documentation

HOW TO CREATE PHENIX DOCUMENTATION CHAT WITH NOTEBOOKLM AND THESE MATERIALS

1. Start a new NotebookLM project. You may need to have a paid account to be allowed to use the number of sources present here (over 100).

2. Select "Add source" in the notebook and select and drag all the PDF files in phenix_doc/( documentation, papers, newsletters, phil_etc), as well as info.txt on to the "+" screen that appears.

3. Individually select "Add source" and then "Add youtube video" and paste in the url for each video in phenix_doc/videos.list, one at a time.

4. To generate an audio transcript, go to the Studio tab, hit Configure, and paste the contents of info_for_audio.txt (or equivalent) into the suggestion box that guides the AI. Then generate the audio. If you are not pleased with it, delete it and add text to the suggestions box to discourage the AI from focusing on things you do not want and to encourage it to discuss things you are interested in seeing.

HOW TO UPDATE THE DOCUMENTATION MATERIALS FOR PHENIX DOCUMENTATION CHAT

The documentation PDF files were created from a nightly build Phenix documentation web site with the following protocol:

Work in a directory that contains crawler.py, sort_urls.py, combine.py, run_combine.csh (from code/), combine_a.html, and combine_c.html (from helper_files)

Run a web crawler to look up all the pages in this version:

python crawler.py https://phenix-online.org/version_docs/2.0-5725 urls.list >& crawler.log

Result is the file urls.list

Sort the urls by category and create separate lists for each

python sort_urls.py urls.list

Result are files with lists of urls: phenix_faqs.list phenix_overviews.list phenix_top_level.list

phenix_misc.list phenix_reference.list phenix_tutorials.list

Create dummy html files that contain all the web pages from each list

Header is the file a.html, body is created from one of the files with list of urls, footer is c.html

./run_combine.csh > run_combine.log

Result are html files that display all of the material from all the pages from one of the files

with list of urls: combine_phenix_faqs.html combine_phenix_reference.html combine_phenix_misc.html

combine_phenix_top_level.html combine_phenix_overviews.html combine_phenix_tutorials.html

Now load each combine_phenix_xxx.html into Orion or Safari and save as PDF

Put these files in documentation/