[ccp4bb] Generating Restraints for a Synthetic Peptide
Dear CCP4 Users, I have a structure containing a synthetic alpha helical peptide (similar to the one found in PDB: 2YJD) for which I need to generate the restraints (.cif). I have the PDB coordinates for the peptide but need the .cif for refinement/fitting. Does anyone have any suggestions on how I could generate this file? Thank you very much, Sean Fanning
Re: [ccp4bb] Generating Restraints for a Synthetic Peptide
Dear Sean Fanning, you could try the grade server (grade.globalphasing.org). I don't know its size limit. It recognizes the ligand YJD from 2YJD and produces restraints for it. In your case you may need to generate the mol2 file or SMILES string. I think openbabel could generate the mol2 file from the PDB file, I haven't tried. Best, Tim On 06/23/2015 05:17 PM, Sean Fanning wrote: Dear CCP4 Users, I have a structure containing a synthetic alpha helical peptide (similar to the one found in PDB: 2YJD) for which I need to generate the restraints (.cif). I have the PDB coordinates for the peptide but need the .cif for refinement/fitting. Does anyone have any suggestions on how I could generate this file? Thank you very much, Sean Fanning -- -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A signature.asc Description: OpenPGP digital signature
Re: [ccp4bb] Generating Restraints for a Synthetic Peptide
Phenix should also work nicely: phenix.elbow inputfile.smi --opt Inputfile can be one of many different file formats (ie: smiles, sdf, pdb, etc.) The --opt flag runs an AM1 geometry optimization that usually produces superior restraints as compared to running without it. Cheers, Jim On Tue, Jun 23, 2015, 10:27 AM Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear Sean Fanning, you could try the grade server (grade.globalphasing.org). I don't know its size limit. It recognizes the ligand YJD from 2YJD and produces restraints for it. In your case you may need to generate the mol2 file or SMILES string. I think openbabel could generate the mol2 file from the PDB file, I haven't tried. Best, Tim On 06/23/2015 05:17 PM, Sean Fanning wrote: Dear CCP4 Users, I have a structure containing a synthetic alpha helical peptide (similar to the one found in PDB: 2YJD) for which I need to generate the restraints (.cif). I have the PDB coordinates for the peptide but need the .cif for refinement/fitting. Does anyone have any suggestions on how I could generate this file? Thank you very much, Sean Fanning -- -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A
Re: [ccp4bb] Generating Restraints for a Synthetic Peptide
Dear Sean, For a synthetic peptide, you should only make restraints for the non-standard amino acids that are not already in the dictionary. You can do this graphically in jLigand which is part of CCP4. If you give the atoms names consistent with regular amino acids and define the compounds as ‘peptide’ you don’t even have to create LINK records to make things run in Refmac/COOT. Note that the PDB will break up a synthetic peptide into residues and rename things if you do treat the peptide a one compound. This may cause conflicts between the final structure model and the figures in the paper describing it. It’s better to avoid the issue by doing things properly in the first place. Cheers, Robbie From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jim Fairman Sent: Tuesday, June 23, 2015 20:14 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Generating Restraints for a Synthetic Peptide Phenix should also work nicely: phenix.elbow inputfile.smi --opt Inputfile can be one of many different file formats (ie: smiles, sdf, pdb, etc.) The --opt flag runs an AM1 geometry optimization that usually produces superior restraints as compared to running without it. Cheers, Jim On Tue, Jun 23, 2015, 10:27 AM Tim Gruene t...@shelx.uni-ac.gwdg.de mailto:t...@shelx.uni-ac.gwdg.de wrote: Dear Sean Fanning, you could try the grade server (grade.globalphasing.org http://grade.globalphasing.org ). I don't know its size limit. It recognizes the ligand YJD from 2YJD and produces restraints for it. In your case you may need to generate the mol2 file or SMILES string. I think openbabel could generate the mol2 file from the PDB file, I haven't tried. Best, Tim On 06/23/2015 05:17 PM, Sean Fanning wrote: Dear CCP4 Users, I have a structure containing a synthetic alpha helical peptide (similar to the one found in PDB: 2YJD) for which I need to generate the restraints (.cif). I have the PDB coordinates for the peptide but need the .cif for refinement/fitting. Does anyone have any suggestions on how I could generate this file? Thank you very much, Sean Fanning -- -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A
Re: [ccp4bb] Generating Restraints for a Synthetic Peptide
You can also do it using ReadySet! which makes all the calls to eLBOW. phenix.ready_set 2yjd.pdb phenix.geometry_minimization 2yjd.updated.pdb 2yjd.link.edits 2yjd.ligands.cif Cheers Nigel --- 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 On Tue, Jun 23, 2015 at 11:13 AM, Jim Fairman fairman@gmail.com wrote: Phenix should also work nicely: phenix.elbow inputfile.smi --opt Inputfile can be one of many different file formats (ie: smiles, sdf, pdb, etc.) The --opt flag runs an AM1 geometry optimization that usually produces superior restraints as compared to running without it. Cheers, Jim On Tue, Jun 23, 2015, 10:27 AM Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear Sean Fanning, you could try the grade server (grade.globalphasing.org). I don't know its size limit. It recognizes the ligand YJD from 2YJD and produces restraints for it. In your case you may need to generate the mol2 file or SMILES string. I think openbabel could generate the mol2 file from the PDB file, I haven't tried. Best, Tim On 06/23/2015 05:17 PM, Sean Fanning wrote: Dear CCP4 Users, I have a structure containing a synthetic alpha helical peptide (similar to the one found in PDB: 2YJD) for which I need to generate the restraints (.cif). I have the PDB coordinates for the peptide but need the .cif for refinement/fitting. Does anyone have any suggestions on how I could generate this file? Thank you very much, Sean Fanning -- -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A
