Re: [phenixbb] Adding H atoms onto ligand

YoungJin You can (you may need a newer version of ReadySet!) phenix.ready_set model.pdb cif_file_name=ligand.cif To put hydrogens on the model and use the CIF file for the ligand. Nigel On 6/16/09 10:29 AM, Young-Jin Cho wrote:

Thanks a lot Nigel, I could generate new .cif file. Then I need to combine this ligand information while I am adding H atoms to model.pdb (protein+ligand). when I simply type "phenix.ready_set model.pdb" it will wrongly generate strange.pdb file. My question is how I can add this new geometry information (.cif file) while adding H atoms into modle.pdb file to make protein and ligand has H atoms in correct way.

Thanks again in advace.

YoungJin

----- Original Message ----- From: "Nigel W Moriarty" To: "PHENIX user mailing list" Sent: Tuesday, June 16, 2009 12:18:50 PM GMT -05:00 US/Canada Eastern Subject: Re: [phenixbb] Adding H atoms onto ligand

YoungJin

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.

Nigel

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" To: "PHENIX user mailing list" 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! _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

-- 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 : [email protected] Web : CCI.LBL.gov