Re: [ccp4bb] keep ligand conformation
Garib kindly sorted out this problem and external harmonic works well for ligands now. He said that the next ccp4 update will include this version of refmac (5.8.0070 or later). Thanks again for your help. Best, Koji Dear all, I tried to keep a conformation of a ligand during refinement with Refmac5 (Ver. 5.7.0032), and I put a harmonic restraint as, external harmonic residues from 600 A to 600 A 600 is the residue number of the ligand. I checked structures with and without the harmonic restraint, but no change was found between the two structures at all. I also tried with and without sigma weight, but nothing changed again. external harmonic restraints worked for protein parts. I would appreciate any suggestions and comments. Thank you so much in advance, Koji
Re: [ccp4bb] keep ligand conformation
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Koji, some ligands tend to be where the users wishes them to be. If your ligands moves away, maybe it is not really there? Maybe there is a stereochemical clash which acts more strongly than the restraints you are applying? And maybe harmonic restraints only make sense when applied to a large number of atoms, not only a few - this would depend on the implementation, though. Best, Tim On 02/20/2014 08:42 AM, Koji Yonekura wrote: Dear all, I tried to keep a conformation of a ligand during refinement with Refmac5 (Ver. 5.7.0032), and I put a harmonic restraint as, external harmonic residues from 600 A to 600 A 600 is the residue number of the ligand. I checked structures with and without the harmonic restraint, but no change was found between the two structures at all. I also tried with and without sigma weight, but nothing changed again. external harmonic restraints worked for protein parts. I would appreciate any suggestions and comments. Thank you so much in advance, Koji - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTBdAOUxlJ7aRr7hoRAtNeAKDITbOxnPeTcTcoLjhOx4PLAXSmwQCfSuE1 ydSoXKpSmeFjh+WLbs32r+g= =aZu9 -END PGP SIGNATURE-
Re: [ccp4bb] keep ligand conformation
Dear Koji, In addition to all the things Tim said, you may also have a conflict between the ligand conformation you modelled and the conformation described in your restraint file. The Refmac logfile will mark any really severe outliers, but smaller problems can still exist. Try regularising your ligand in Coot to check whether your restraints are what you want. Cheers, Robbie Sent from my Windows Phone Van: Tim Gruene Verzonden: 20-2-2014 10:51 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: Re: [ccp4bb] keep ligand conformation -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Koji, some ligands tend to be where the users wishes them to be. If your ligands moves away, maybe it is not really there? Maybe there is a stereochemical clash which acts more strongly than the restraints you are applying? And maybe harmonic restraints only make sense when applied to a large number of atoms, not only a few - this would depend on the implementation, though. Best, Tim On 02/20/2014 08:42 AM, Koji Yonekura wrote: Dear all, I tried to keep a conformation of a ligand during refinement with Refmac5 (Ver. 5.7.0032), and I put a harmonic restraint as, external harmonic residues from 600 A to 600 A 600 is the residue number of the ligand. I checked structures with and without the harmonic restraint, but no change was found between the two structures at all. I also tried with and without sigma weight, but nothing changed again. external harmonic restraints worked for protein parts. I would appreciate any suggestions and comments. Thank you so much in advance, Koji - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTBdAOUxlJ7aRr7hoRAtNeAKDITbOxnPeTcTcoLjhOx4PLAXSmwQCfSuE1 ydSoXKpSmeFjh+WLbs32r+g= =aZu9 -END PGP SIGNATURE-
[ccp4bb] keep ligand conformation
Dear all, I tried to keep a conformation of a ligand during refinement with Refmac5 (Ver. 5.7.0032), and I put a harmonic restraint as, external harmonic residues from 600 A to 600 A 600 is the residue number of the ligand. I checked structures with and without the harmonic restraint, but no change was found between the two structures at all. I also tried with and without sigma weight, but nothing changed again. external harmonic restraints worked for protein parts. I would appreciate any suggestions and comments. Thank you so much in advance, Koji
