General Help

The present version of MoDEL web site allows to browse the stored simulations, download them in a limited way, and examine basic analysis. More specialized analysis are available on demand.

Navigation through MoDEL web site whould be done following the links provided, please, do not use browser's navigation buttons as they may have unexpected behaviour.

Selection of Simulations

Simulations in MoDEL can be selected in several ways.

KEYWORD SEARCH

Keywords provided are used in a fulltext query against Uniprot and PDB headers. A list of hits mapped on simulations available are provided, ordered according to the match with the query. Hit descriptions are provided to allow user to asses the validity of the search performed.

IDs and SEQUENCE SEARCH

PDB id's and UniprotKB Accession and Ids can be searched for. Hits from a precalculated Blast search (standard settings) are produced, so not only the exact hit but also homologous sequences are provided. When the query is an user provided sequence, a Blast search with the same settings is perfomed. Blast hits are limited to E-Values lower than 1.10-5 to assure that a reasonable homology exists. In any case, the hit's EValue is provided together with the alignment€ coverage, to allow the user to assess the validity of the results.

BROWSE BY ID

The section is a direct access to the full list of simulations. Output can be limited by group of simulation, program, PDB Id or length of simulations, and ordered accordingly

BROWSE BY FOLD

The available simulations are grouped according the two top categories of CATH hierarchy (Class, Architecture).

Selection of Analysis

Once structure has been selected, a list of the simulations available for that structure is presented. User should choose the desired simulation and go into the analysis section. Please note that more than one simulation may be available for the same structure and program, as some simulations are duplicated using different conditions.

Analysis section is self explanatory. It provides 4 types of informations. 1) The original strucure is provided as picture or 3D (Jmol visualiser), and a series of links to known structure databases allows to complete the information. 2) Coordinates of the analysis: simulation, trajectory time slice, and structure fragment are provided as selection controls, so the user can switch to different results on the same structure. In the present version of MoDEL, only one analysis can be visualized at a time. 3) A short summary of the simulation details is shown. A link leads to the full details of the simulation. 4) A menu with the available analysis is shown below once the appropriate coordinates are selected.

Visualizing and downloading trajectories

Trajectories in MoDEL database can be visualized in 3D using a JMol applet. Data sent includes a series of snapshots of the dehydrated trajectory as packed PDB files, The visualization servlet allows to visulaize trajectories either as animations or as a superposition of snapshots, but user can modify the view using JMol features. Due to the potentially large size of the data, downloading may take some time depending on the network bandwidth. Jmol applet is very memory demanding in the browser's side. This may result in the fail of loading of large structures. The number of snapshots is balanced according to the size of the system to avoid this, please report to model@mmb.pcb.ub.es any difficulties experienced. Additionally, a video in stanrdard format of the trajectory is available. Video does not allow 3D maniopulation but has a much lower download time, then animations.

PCZ compressed dehydrated trajectories, from CA, heavy or all atoms, packed at 90% of accurancy can be downloaded. For additional information about the PCZ format please consult Meyer, T., et al. (2006) Essential Dynamics: A Tool for Efficient Trajectory Compression and Management. J. Chem.Theor.Comput 2, 251-258.. PCZ compression at 90% of accurancy recovers most of the molecule flexibility losing only higher frequency movements, with a significant reduction of the file size, Trajectories can be transformed to more usual formats using the PCASuite software, To do so:

  1. Download and install PCAsuite, Pre-compiled binaries and source code are available.
  2. To obtain a information about the PCZ file contents use
    pczdump -i input_pcz_file --info
  3. To obtain a PDB file with the average structure use
    pczdump --avg --pdb -i input_pcz_file -o output_pdb_file
  4. To uncompress the trajectory in Amber CRD format
    pczunzip -i input_pcz_file -o output_crd_file
    This command may take a while and generate a large file.
  5. To uncompress the trajectory as a single PDB file
    pczunzip --pdb -i input_pcz_file -o output_pdb_file

For other options, please, consult the PCAsuite guide. Complete trajectories are not available to anonymous users, but can be obtained on demand.