Usage

PDB-IHM Validation System

The easiest way to run PBD-IHM Validation pipeline it to use standalone validation server https://validate.pdb-ihm.org. Register an account using Globus, upload your IHMCIF file, and in 5-115 minutes you will get both full and summary validation reports in the PDF format.

Local deployment

Building runtime image

IHMValidation pipeline is designed to work inside the Apptainer (previously Singularity) container with all 3rd-party dependencies.

To build the image:

  1. Navigate to the directory holding Singularity.def file: cd IHMValidation/singularity

  2. Download Chimera and place in the same directory. The current pipeline was tested with Chimera-1.19 for headless servers.

  3. Download ChimeraX .deb package for Ubuntu 22.04 and place in the same directory. The current pipeline was tested with ChimeraX-1.9.

  4. Select an appropriate timezone. For example America/Los_Angeles

  5. Build the image: apptainer build --build-arg TZ=America/Los_Angeles --build-arg CHIMERA=./chimera-1.19-linux_x86_64_osmesa.bin --build-arg CHIMERAX=./ucsf-chimerax_1.11.1ubuntu22.04_amd64.deb ihmv.sif Singularity.def

which will generate ihmv.cif image file.

NB 1: To get a date-tagged name, use ihmv_$(date +%Y%m%d).sif as an image name.

NB 2: It takes about ~25 minutes on a modern workstation to build the image from scratch.

Running the pipeline

A typical IHMValidation run looks like this:

singularity run --pid ihmv.sif --cache-root cache --output-root . -f input/8ZZU.cif

where

  • --pid ensures that in case of error or termination all subprocesses will be killed;

  • ihmv.sif name of the apptainer image with the IHMValidation pipeline;

  • --cache-root cache path to a cache directory. Some validation steps, like MolProbity assesment or assessment of model fit to 3DEM density can be resource and time consuming, thus we recommend preserving these intermidiate results in a dedicated directory. Otherwise you can point to /tmp or current directory .;

  • --output-root . path to the directory where output will be created. . means the current directory. The actual output directory will have the same stem as the input file;

  • -f 8ZZU.cif path to the input file in the IHMCIF format. Entry 8ZZU is provided only as an example.

The output will have a following structure:

  • 8ZZU - directory with the results;

  • 8ZZU/8ZZU_full_validation.pdf - full validation report in the PDF format;

  • 8ZZU/8ZZU_summary_validation.pdf - summary table in the PDF format;

  • 8ZZU/8ZZU_html.tar.gz - compressed archive with the full validation report in HTML format. NB: If you’re planning to review HTML version of the report, you should add --html-mode local flag to the pipeline call, this will replace links to PDB-IHM resources with local copies.

To get a full list of available options you can call the pipeline with a -h flag:

singularity run --pid ihmv.sif -h

Interpreting the reports

If you’re not an expert in structral biology or integrative modeling, we recommend checking a detailed user guide with descriptions of all metrics and plots presented in the report.