Start a new simulation

This tutorial can be downloaded as a pdf-file.

Required input

A new eBDIMS simulation is initiated here. The minimal set of input data comprises:

  • a job name (< 150 alphanumeric characters). The job name can be used to identify the submitted job in the public server queue.
  • two distinct configurations of the same atomic protein strucutre (referred to as start and target end-states, respectively).

End-state structures

Start and target end-state structures can be either

  • retrieved automatically from by providing structure PDB IDs, or
  • manually uploaded as coordinate files in strict PDB format.
In both cases, end-state structures should not have any missing residues, and both sequence and residue numbering should match perfectly between them.

If start and target structures present different number of chains, only the number of chains in the shorter pdb structure will be accounted for
Curated and correctly formatted input files are available for each resolved example and can be used as template when preparing new end-state strucutres.
PDB code examples:

Type 1NQL or 1nql to fetch the entire PDB structure 1NQL.

One can specify chains of interest by indicating them immediately after the strucutre ID (separated by a colon). PDB IDs are case insensitive. Valid chain identifiers are A-Z (i.e. single characters). See examples below:

Example Interpretation
3NJP All chains of PDB structure 3NJP (i.e. A,B,C,D)
3NJP:B Chain B of PDB structure 3NJP
3NJP:A,B,C Chains A,B,C of PDB structure 3NJP
3NJP:A-C Chains A,B,C of PDB structure 3NJP
PDB file examples:

Uploaded PDB files should have file extension .pdb. The PDB header is optional.

Please double check for missing atoms, alternative conformations, etc that could potentially result in format errors. Use specialized software to check the integrity of the PDB files (Molprobity, Procheck, What if).

We recommend reconstructing small residue gaps (<5 residues) with specialized software such as Modeller.

Optional input

Job description

Each job can contain an elaborated description (< 500 characters).

Email address

It is possible to associate the job with an email address. When a new email address is entered into the system, a temporary password is sent to the email address which allows the user to log in to the dashboard page.

The dashboard lists all jobs generated by the user. A user account also allows for notifications on job termination.

Ensemble structures

A key feature of the eBDIMS web application is to facilitate classification of protein structures by their projection onto the intrinsic normal mode (NM) and principal component (PC) motion-spaces. For that purpose, input end-state files can be accompanied by a third input file, the ensemble.

A detailed tutorial on how to prepare an ensemble file is available here.

Briefly, the ensemble file should contain at least three structures of the same protein in different conformations in a multi-pdb format with coordinate sets delimited by MODEL and ENDMDL labels (as in NMR pdb-entries. See example below).

      ( coordinate set 1 )
      ( ... )
      ( coordinate set n )
Note that:
  • the ensemble should include both the start and target end-state structures,
  • each coordinate set should be complete (i.e. no missing residues),
  • all coordinate sets must have the same number of residues,
  • 1000 models are considered at most,
  • total file size is limited to 16 Mb.
For help with ensemble preparation, check the Bio3D tool or ProDy packages.

Submitted jobs

When a job is submitted to the eBDIMS server, the input structures are validated server-side against the criteria described above. Carbon-alpha residues are selected and any duplicates removed. The pdbParser script is used to select the common regions of end-state structures. Similarly, individual ensemble structures are checked for integrity and that all models have the same number of residues. Each model is assigned a model index (1–1000).

An error message will be thrown if any anomaly is detected (e.g. missing residues or inconsistent labelling), otherwise the new job will enter the server queue and the user will be automatically redirected to the associated and unique result page.

It is recommended to bookmark the result page if the job was submitted without an email address

Job status

A submitted job acquires a status:

  • pending: the job has been placed in the server queue. When a free job slot is avaialbe, the status will automatically change to "active".
  • active: the job is currently running. When the simulation finishes, the status changes to "finished".
  • finished: the job has finished and results are visualized and available for download.
  • error: the eBDIMS algorithm failed to compute the tranistion.

The job status can be monitored from the job-specific result page, the user dashboard, or the server queue.

Server queue

Submitted jobs enter the server queue. It displays server usage and current status of recent submitted jobs.

A normal-sized transition usually takes a few minutes to complete. Big systems, and especially if they display large-scale transitions, can take several hours to complete. The running time for any eBDIMS simulation is however limited to 4 hours (per direction, and excluding any pre- and postprocessing).


The job-specific result page can be accessed as soon as the job has been successfully submitted. Depending on the job status, it shows the full results or how the job is progressing.


Results are accessed through the unique access key assigned to each job upon submission: eBDIMS/jobs/results/UNIQIUE_KEY
Submitted data and results are not viewable by anyone without the access key.

It is recommended that anonymous users bookmark the result page

Input data files

Input data is analyzed and validated server-side as described above. The definite structures that are used for running the eBDIMS algorithm are listed in the ‘Files’ section on the results page: eBDIMS/jobs/results/UNIQUE_KEY#files

The input data files include the end-state structures start.pdb and target.pdb, and ensemble.pdb if applicable. In addition, a log file that describes the input file validation is available for download.

Active jobs (real-time progress monitoring)

Active jobs can be monitored in real-time as the eBDIMS workflow automatically emits updates to the unique job-result page. Updates are published at the top of the page. Also, the transition progress (%) as well as RMSD distance (Å) between the most current frame and the target end-state structure are continuously updated in the respective charts.
The real-time charts show the progress for both forward and reverse eBDIMS transitions.

  • Plot legend:
  • forward
  • reverse

Finished jobs

When the eBDIMS transitions have approached the corresponding target structure to 99.9% of the initial RMSD they are post-processed for data visualization and the job status changes from “active” to “finished”. The result page automatically updates to show the output of the calculations and associated output data files.

eBDIMS trajectories are visualized as:

  • 3D molecular representations that can be reproduced with the eBDIMS trajectory viewer
  • projections onto the intrinsic 2D motion-space. The computed motion-axes provide automatic reaction coordinates to easily understand how a given transition proceeds in terms of molecular movements.
The motion-space is defined by the first pair of normal modes (NM) of the start structure, or principal components (PC) calculated from the ensemble structures. Both NM and PC motions can be explored in 3D with the eBDIMS trajectory viewer.

eBDIMS trajectory viewer

The eBDIMS trajectory viewer is used to show the eBDIMS trajectories as well as the major intrinsic protein motions (referred to as eBDIMS, NM, or PC modes) as 3D molecular representations. In eBDIMS mode, the viewer is coupled to the motion-space projection chart, so that every frame is also highlighted in the motion-space.

The eBDIMS 3D trajectory viewer loads the forward and reverse transitions in sequence.
The eBDIMS trajectory viewer is built on the NGL Viewer library.
  • AS Rose, AR Bradley, Y Valasatava, JM Duarte, A Prlić and PW Rose. Web-based molecular graphics for large complexes. ACM Proceedings of the 21st International Conference on Web3D Technology (Web3D '16): 185-186, 2016. doi:10.1145/2945292.2945324
  • AS Rose and PW Hildebrand. NGL Viewer: a web application for molecular visualization. Nucl Acids Res (1 July 2015) 43 (W1): W576-W579 first published online April 29, 2015. doi:10.1093/nar/gkv402


The major steps in the eBDIMS workflow can be reproduced locally by downloading and running the corresponding scripts from the eBDIMS stand-alone package. The stand-alone packages allows for fine-tuning algorithm parameters, and to run larger or incomplete structures.

Data storage

  • Finished jobs are stored on the server for a minimum time period of 7 days.
  • Jobs submitted with an email addressed are stored for at least 30 days.