Dear Ning, There is a separate bulletin board for anything Phenix. You can try the CCP4 program AceDRG to generate restraint from a SMILES string.
Cheers, Robbie > -----Original Message----- > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Ning Li > Sent: Monday, April 3, 2023 18:17 > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Issue about cif file of ligand > > Hi everyone, > > My crystal structure contains a ligand and I generated the cif file of the > ligand > using phenix.elbow from the smiles file of the ligand. The ligand was drawn > and > the smiles file was generated from > https://pubchem.ncbi.nlm.nih.gov//edit3/index.html. My problem is that the > double bond (shown in the picture) is longer than the single bond in the > generated elbow pdb file. Although the bond can be recognized correctly in the > Coot (display the correct double bond), the simulation software doesn't > recognize them correctly because of the bond length. In my theory, the double > bond of the ring should be shorter than the single bond, is there any reason > why phenix elbow generate this or any parameters I can set to overcome this? > Thank you for your suggestions. > > Ning > > > > > ________________________________ > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
