Re: [ccp4bb] restraints for cis-bonds, ACD cif file
Nathaniel The atom names in the file I sent have the correct atom names as defined by the PDB for ACD. Naturally, the atom names in your PDB file and the restraints CIF file should match and given that you need the correct names to deposit your structure into the PDB, then I would recommend doing it sooner later than later. PHENIX has a number of tools to do this for you and we can talk off-line about them. Nigel On Tue, Nov 30, 2010 at 8:16 AM, Nathaniel C. Gilbert wrote: > I appreciate the input Paul and Nigel. The cif dictionary file you sent me > doesn't have matching restraint definitions for 53 atoms in the ACD file. I > opened the cif file you sent and extracted the SMILES code for ACD. Then I > ran it in phenix.elbow to have it generate a pdb of the ACD. Then i would use > the cif file you sent and import it into coot or phenix.refine, but it would > not match the cif and pdb. I can wait for the new nightly build to come out, > but I was wondering why this process wouldn't work. > > Paul, I'm not as familiar with the CCP4 suite. Refmac5 doesn't give me as > many new Fo-Fc peaks to build more model into as does phenix.refine even > though Rfree numbers are comparable. > -- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : nwmoria...@lbl.gov Fax : 510-486-5909 Web : CCI.LBL.gov
Re: [ccp4bb] restraints for cis-bonds, ACD cif file
I appreciate the input Paul and Nigel. The cif dictionary file you sent me doesn't have matching restraint definitions for 53 atoms in the ACD file. I opened the cif file you sent and extracted the SMILES code for ACD. Then I ran it in phenix.elbow to have it generate a pdb of the ACD. Then i would use the cif file you sent and import it into coot or phenix.refine, but it would not match the cif and pdb. I can wait for the new nightly build to come out, but I was wondering why this process wouldn't work. Paul, I'm not as familiar with the CCP4 suite. Refmac5 doesn't give me as many new Fo-Fc peaks to build more model into as does phenix.refine even though Rfree numbers are comparable.
Re: [ccp4bb] restraints for cis-bonds, ACD cif file
Nathaniel I made a small mod to eLBOW (which will be available in the next nightly build) that allows you to get an all cis ACD from a SMILES string. I have attached the result. Note that the name of the file has for the four cis (zusammen) configurations. As Paul suggested, the torsion value is 0. and the period is 1. Nigel On Mon, Nov 29, 2010 at 9:29 AM, Paul Emsley wrote: > On 29/11/10 16:17, Nathaniel C. Gilbert wrote: >> >> I have arachidonic acid soaked into my crystal structure and want to model >> it. The phenix.refine is allowing my cis double bonds to distort to a gauche >> or trans form. Is it the cif file or the refinement restraints in the >> program that I need to correct. >> > > It is not entirely clear to me what you are asking - I'd say that "the cif > file" and "the refinement restraints" are pretty much synonymous. > > I suggest that you clear up (by using idealization and checking the starting > conformer) whether the "bad" resulting conformation is due the the > restraints or the density. > > Incidentally arachidonic acid is in the PDB (and CCP4's copy of SBase). I > took that idealized structure and fed it into Prodrg, the resulting torsion > restraints look good to me. > > If you want to brute-force/hand-edit the restraints, make sure that the > torsions across the double bonds (C5-C6, C8-C9, C11-C12 and C14-C15) have a > value_angle of 0 and a period of 1. > > (The torsions from the (rather old) version of libcheck I have here > (generated from a SMILES string) were not great and seem to be consistent > with your question.) > > Paul. > -- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : nwmoria...@lbl.gov Fax : 510-486-5909 Web : CCI.LBL.gov acd_.cif Description: Binary data
Re: [ccp4bb] restraints for cis-bonds, ACD cif file
On 29/11/10 16:17, Nathaniel C. Gilbert wrote: I have arachidonic acid soaked into my crystal structure and want to model it. The phenix.refine is allowing my cis double bonds to distort to a gauche or trans form. Is it the cif file or the refinement restraints in the program that I need to correct. It is not entirely clear to me what you are asking - I'd say that "the cif file" and "the refinement restraints" are pretty much synonymous. I suggest that you clear up (by using idealization and checking the starting conformer) whether the "bad" resulting conformation is due the the restraints or the density. Incidentally arachidonic acid is in the PDB (and CCP4's copy of SBase). I took that idealized structure and fed it into Prodrg, the resulting torsion restraints look good to me. If you want to brute-force/hand-edit the restraints, make sure that the torsions across the double bonds (C5-C6, C8-C9, C11-C12 and C14-C15) have a value_angle of 0 and a period of 1. (The torsions from the (rather old) version of libcheck I have here (generated from a SMILES string) were not great and seem to be consistent with your question.) Paul.
