Hi Nigel, It worked! Thanks a lot! Best, Mengbin On Tue, Aug 20, 2013 at 3:03 PM, Nigel Moriarty wrote:

Mengbin

You can use the intra_chain=True option to automatically link the ring. If that fails send me the model and I'll provide the files used in an older method.

Nigel

On Tue, Aug 20, 2013 at 11:32 AM, Mengbin Chen wrote:

...

Dear Phenix Users,

My colleague has got into trouble when he was refining a peptide ligand with a coumarin ring attached via a peptide bond. The peptide part is composed of natural amino acids, which does not require a cif file. On the other hand, a cif file has been created for the coumarin ring. Unfortuantely, after the refinement run, the peptide and the coumarin ring fell apart, and we could not figure out why this is happening. We are using the Phenix-dev-1370 version. Any help would be appreciated!

Thank you in advance, Mengbin

-- Mengbin Chen Department of Chemistry University of Pennsylvania

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-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

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-- Mengbin Chen Department of Chemistry University of Pennsylvania

can you send me the files directly with only the two residues if you desire. Cheers Nigel NB. Any files sent to me will be held in strictest confidence. On Tue, Aug 20, 2013 at 1:40 PM, Mengbin Chen wrote:

Hi

I guess I just rushed to a conclusion. Actually, the peptide bond is not planar after the refinement run...

Mengbin

On Tue, Aug 20, 2013 at 4:36 PM, Mengbin Chen wrote:

...

Hi Nigel,

It worked! Thanks a lot!

Best, Mengbin

On Tue, Aug 20, 2013 at 3:03 PM, Nigel Moriarty wrote:

...

Mengbin

You can use the intra_chain=True option to automatically link the ring. If that fails send me the model and I'll provide the files used in an older method.

Nigel

On Tue, Aug 20, 2013 at 11:32 AM, Mengbin Chen wrote:

...

Dear Phenix Users,

My colleague has got into trouble when he was refining a peptide ligand with a coumarin ring attached via a peptide bond. The peptide part is composed of natural amino acids, which does not require a cif file. On the other hand, a cif file has been created for the coumarin ring. Unfortuantely, after the refinement run, the peptide and the coumarin ring fell apart, and we could not figure out why this is happening. We are using the Phenix-dev-1370 version. Any help would be appreciated!

Thank you in advance, Mengbin

-- Mengbin Chen Department of Chemistry University of Pennsylvania

_______________________________________________ phenixbb mailing list [email protected] http://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 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- Mengbin Chen Department of Chemistry University of Pennsylvania

-- Mengbin Chen Department of Chemistry University of Pennsylvania

_______________________________________________ phenixbb mailing list [email protected] http://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 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov