Re: [ccp4bb] Issue about cif file of ligand
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/-0001-8857-9464 On Mon, Apr 3, 2023 at 9:38 AM Robbie Joosten 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 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=1 > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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=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/
Re: [ccp4bb] Issue about cif file of ligand
Wonderful! Grade solves my problem, thank you Pietro and Robbie! Cheers On Mon, Apr 3, 2023 at 12:38 PM Robbie Joosten 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 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=1 > > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] Issue about cif file of ligand
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 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=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
[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 [image: image.png] To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
