[ccp4bb] ANN: CCP4 6.5 for 32-bit Windows

The Win32 version has been added in the download area: http://www.ccp4.ac.uk/download/#os=windows Apologies for the long delay. On behalf of the CCP4 group Marcin Wojdyr -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of th

[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

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 fro

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, Ju

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 Laborat

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

[ccp4bb] references on application of broad specificity of enzyme

Dear All, I have a transferase, which is showing broad specificity for both the substrates (nucleotides) in our organism of interest, but is highly specific in other organisms. Are there any references showing the applications of (bi-substrate) proteins with such broad specificity towards nucleo