Ning Can you send the SMILES and the output directly to me?
Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : nwmoria...@lbl.gov Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464 On Mon, Apr 3, 2023 at 9:38 AM Robbie Joosten <robbie_joos...@hotmail.com> wrote: > 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/ > ######################################################################## 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/
