Data specification


The data to render must be in the Protein Data Bank format (PDB).
It can be specified either on the form or a PDB Id , or by uploading the data. PDB Ids must be on the form: 1tim for the whole 1tim PDB entry, or 1timA for the chain A of the 1 tim entry. PDB identifier (the first 4 characters) are not case sensitive, hence 1Tim, 1TIM or 1tim are equivalent.
Uploading data or specifying a PDBId, you can also specify a list of chain Ids in the "Chains to visualize" field (e.g. AB, or A,B to select chains A and B of the PDB entry). Specifying "All" or nothing  will result in keeping all chains.Chain identifier are case sensitive. 1timA and 1tima are NOT equivalent.

Pay attention with the Blank character as a chain identifier. For a multi-chains protein wihch have one of them identify with the blank character, PMG will not recognize it because of the Dino3D language scripting. Also, try to rename it.
To make an image including several PDB entries, you can however concatenate them into one file, labeling each file using separate chain Ids.

The PDB NMR format file is well recognize by PMG. So any PDB which contains MODEL fields can be used for NMR scenarii animation (slideshow of models). As a result you could use the result file generated by :
  - morph and normal mode analysis software (see links)
  - pdb snapshot of macromolecular movement from the Database of Macromolecular Movements.
  - pdb snapshot of molecular dynamic simulation from the Molecular Dynamics Extended Library.
  - models generated by docking sofwares (like Cluspro).
  - oligomer generated by the PQS - Protein Quaternary Structure server in the mmol format file (like PDB format) or by the Pita- Protein InTerfaces and Assemblies server/program.

Optionally, you can upload a trajectory generated by a molecular dynamic simulation in the .xtc, .dcd and .crd format (gromacs, charmm and cns). Thus, by choosing the DM scenario, you will be able to produce an animation displaying the choosen number of frame by choosen step (see the animation parameters).
Note : There is a length limitation for upload. You could be redirect to an error page, if the size of your file is greater than this max length.