[phenixbb] Adding H atoms onto ligand

Nigel W Moriarty NWMoriarty at lbl.gov
Tue Jun 16 09:18:50 PDT 2009


If you opened the CIF in REEL you can right-click on the P-N bond and 
change the order to single.  You can then use the menu Action -> Build 
-> Add Atom to add a hydrogen to the nitrogen by clicking on the nitrogen.


On 6/16/09 9:03 AM, Young-Jin Cho wrote:
> 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.
> Cheers,
> YoungJin
> ----- 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
> Young-Jin
> 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 
> ligand.
> Nigel
> 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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