[phenixbb] Adding H atoms onto ligand
Nigel W Moriarty
NWMoriarty at lbl.gov
Tue Jun 16 08:21:18 PDT 2009
You need to check that you and the PDB ligand database are talking about
the same thing. You can see what the ligand ANP is by
If you have the non-hydrogen atoms of your truncated ligand,
phenix.ready_set will add the hydrogens and may even add the correct
number of hydrogens to the terminal nitrogen. But what about its name?
I would recommend find the three-letter code that corresponds to your
On 6/15/09 7:01 PM, Young-Jin Cho wrote:
> Let me excuse to post another similar issue.
> 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.
> Another questions is how I can remove H atoms from the pdb file. I did "phenix.refine model.pdb remove="element H" but got a message as below:
> Processing inputs. This may take a minute or two.
> Sorry: Ambiguous parameter definition: remove = element H
> Best matches:
> Thanks in advance,
> ps. Tanks Nat!
> phenixbb mailing list
> phenixbb at phenix-online.org
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709
Fax : 510-486-5909
Email : NWMoriarty at LBL.gov
Web : CCI.LBL.gov
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