My software notes

February 24, 2012

add protons (hydrogens) to structure

Filed under: pymol/ molmol,servers,softwares and scripts — kpwu @ 6:08 pm
Tags: , ,

A list of online servers or programs as I know which can add hydrogens on the structures (most likely determined by X-ray crystallography).

  1. WHATIF server (
    –> check “Hydrogen (bonds)” in the left frame
  2. Molprobity server (
    –> after uploading a PDB file, you will see “add hydrogen” in the online interface.
  3. HAAD: (a computer algorithm for constructing hydrogen atoms from protein heavy-atom structures)
  4. PyMOL (Win/Linux/Mac)
  5. SPDB (Swiss PDB Viewer)

In my own test, WHATIF is more friendly for other CNS/Xplor-NIH/Haddock-related works because WHATIF generates CNS/Xplor compatible PDB format.

Molprobity generates PDB with added hydrogens but the added hydrogens are ALL numbered as “0”. Thus I have to use other program to reset all atom numbers.

PyMOL adds hydrogens,too (object -> A -> hydrogens -> add) but the nomenclature of hydrogens in proteins seems weird (see below). The hydrogens are named as H01, H02, H03.. etc. I don’t think CNS/Xplor-NIH can take it for further calculation purposes.



  1. Thanks for the info. A couple of days back i was looking for options other than PYMOL for the same reason you mentioned. Also, there is suite of programs at Mayachemtools ( Esp. for changing the sequence number of the protein. I was trying to use TENSOR2 to calculate diffusion tensor, it came always with error, no matching residue found in the PDB file. The crystal structure started from Residue 1, where as the NMR data started as the original protein sequence 300+. Mayachemtools worked fine for changing numbers of the residue uniformly from whatever starting number provided.

    Comment by Siva — February 24, 2012 @ 6:56 pm | Reply

  2. My earlier post “” about a JAVA program called PDB editor can help you do similar task using friendly graphic interface. I use this PDBeditor very often.

    Comment by kpwu — February 25, 2012 @ 11:33 pm | Reply

  3. Actually, CNS will add protons that do not match the forcefield naming, or just are just missing. So it doesn’t really matter if you keep them or not. For example in HADDOCK, this is the case.

    Comment by João — March 4, 2012 @ 4:58 am | Reply

  4. Thank you, João. Good to know CNS/HADDOCK can handle this issue.

    Comment by kpwu — March 10, 2012 @ 4:21 pm | Reply

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