· Delarue web servers|
· PDB_Hydro Flow chart
· Modify PDB structures
· Fix missing side chains
· Flip HNQ side chains
· Refine sidechain torsions
· Single point mutations
· Change sequence (decorate)
· Generate missing loops
· Solvate PDB structures
· Assign charges (PQR)
· Solvate using GPBL
· Place Waters
· All in one
· NEW ! AQUASOL
· Run AquaSol
· Job queue status
Input data formats
- The e-mail address is used to send an e-mail containing the address
of the directory where the results will be stored for 15 days. You can do without it
and reply 'nothanks' if you want.
- The job title is just for your own identification, but note that
it will show up in the public job queue (but your results will not be public).
- The coordinate file should be in PDB format, with only a single
structure (no multiple models). Atoms marked with alternate residue
flags will be removed. Charges should be in the B-factors column and atomic radius in the
N.B. This is the APBS format!
- The choice of the surface type: The solvent accessible surface (SAS) corresponds to the Lee and Richards definition (Lee B. and Richards F. M., 1971, J. Mol. Biol., 55: 379). The molecular surface (MS) corresponds to the calculation described by Jiang and Brunger (J. Mol. Biol., 1994, 243: 100).
- The dipole moment of 2.35 Debye corresponds to epsilon=19.5 for the solvent. The scale law is such that epsilon is proportional to the square of p_0.
Output data formats
- To visualize the CNS/Xplor maps (ion densities, electrostatic potential) you can use PyMol:
untar the map.tar file, rename the .cns files into .xplor files and use load and isomesh commands in pymol to load the maps.
See Pymol wiki here.