Dear reader,

Hope you are doing well. Here I outline the files contained in this dossier and provide some pointers to where things may be found and how to display certain files.

The project is organized accoriding to the experiment performed.
Namely:
1. highres_core
2. lowres_a
3. lowres_b
4. lowres_c
5. lowres_d
6. xls_alone

Each of these folders contains three subfolders.
These subfolders are as follows:
1. data
2. modeling
3. analysis
4. analysis_G (Analysis focused on a specific NTD, available for lowres_b and lowres_d experiments)
In the data folder, you will find all resources used for modeling, such as:

- topology.txt (Topology files)
- PaFS_NTD.pdb (PDB files containing initial positions for each domain)
- PaFS.fasta.txt (FASTA File containing sequence info)
- faylo_xlms.csv (CSV file containing XL-MS information)
- PaFS.map.LR_a.resampled.mrc (map used to create GMM)
- calculate_gmm.com (A file containing the command used to generate the GMM)
- PaFS.map.LR_a.resampled.mrc.gmm.200.txt (Gaussian Mixture Model (GMM) text file)
- PaFS.map.LR_a.resampled.mrc.gmm.200.gmm (GMM file for displaying)
- PaFS.map.mrc (High-res core map)

In the modeling folder, you will find modeling scripts, and information used for downstream analyses. These files are contained in the following folders:
- run1 or run2 (contains all modeling information, scripts and raw outputs)
- filter (intermediate files used to find good scoring models during analyses)
- good_scoring_models (folder containing the top scoring models from modeling for analysis)

In the analysis folder, you will find statistical and modeling results including the following:
- PaFS.Cluster_Population.pdf (and similar pdf files summarizing the findings as well as the .txt files from where this data is obtained)
- cluster.0 (multiple folders output during analysis containing the localization probability density envelopes and integrative models that best describe each domain's position)
- top_cluster_assessment.cxc (a Chimera X script to display the results from the analysis)

Hope this helps and if any questions remain, feel free to email me, Jose Gorbea, at the following address:

gorbea@pennmedicine.upenn.edu

Best regards,

Jose Gorbea