[phenixbb] Adding H atoms onto ligand

Young-Jin Cho yjcho at brandeis.edu
Tue Jun 16 09:03:11 PDT 2009

Thanks Nigel,
I opened ANP and truncated the terminal PO3 and ran phenix.ready_set.  When I opened through phenix.reel, N atom has double bond to PB, thus has only one H atom, which I thought it should be single bond thus has two H atoms like any N6 of adenine.

So if you can tell me how I can handle to put correct geometry, it will be great.


----- Original Message -----
From: "Nigel W Moriarty" <NWMoriarty at lbl.gov>
To: "PHENIX user mailing list" <phenixbb at phenix-online.org>
Sent: Tuesday, June 16, 2009 11:21:18 AM GMT -05:00 US/Canada Eastern
Subject: Re: [phenixbb] Adding H atoms onto ligand


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

phenix.reel --chemical-components=ANP

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:
>   refinement.refine.occupancies.remove_selection
>   refinement.geometry_restraints.remove.angles
>   refinement.geometry_restraints.remove.dihedrals
>   refinement.geometry_restraints.remove.chiralities
>   refinement.geometry_restraints.remove.planarities
> Thanks in advance,
> YoungJin
> ps. Tanks Nat!
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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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Postdoctoral Fellow, Kern Lab
Biochemistry Department/HHMI
Brandeis University

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