[phenixbb] Adding H atoms onto ligand

Pavel Afonine PAfonine at lbl.gov
Mon Jun 15 20:45:29 PDT 2009

Hi YoungJin,

> I was now modifying AMPPNP ('ANP' in its library name). Although it came from coot/ccp4 library, phenix does not recognize so I had to generate .cif file from the pdb.
>  As it turned out AMPPNP is hydrolyzed in the crystal having AMPPN (terminal Phosphate group needs to be removed), I made from coot (simply deleted  atoms) and made another .cif file. One question what I have now is while I am adding H atoms into a whole molecule, how I can add H atoms onto terminal AMPPN (N atom). Unlike ATP case, it is very certain that terminal N atom should have 2 H's.  I did Molprobity as in the general case to add H atoms, but it didn't make it.

I hope Nigel will comment on this (he is the author of phenix.ready_set 
- a program that is designed to be smart about adding H atoms to 
everything and creating corresponding CIF files).

> Another questions is how I can remove H atoms from the pdb file. 

I'm wondering about why you need to do this? Anyway, here is how:

phenix.reduce -trim model.pdb > model_no_h.pdb


phenix.pdbtools model.pdb xxx.cif remove="element H"

or equivalently:

phenix.pdbtools model.pdb xxx.cif keep="not element H"

More about phenix.pdbtools:



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