· 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
occupation column: this is actually what is called the PQR format.
N.B. Learn more about the APBS format here!
- 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. This is the default value as this is the physical one for water. 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 either
First you need to save on your disk and untar the maps.tar file by typing
$ untar xvf maps.tar
For Pymol it is best to rename the .cns files into .xplor files and use load and isomesh commands in pymol to load the maps.
See Pymol wiki here.
For Coot, make sure you load the map as a difference map to contour both positive and negative ions.
In both cases, you need to save the mol_center.pqr file, because the map is contoured around this recentered molecule.