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
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
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
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
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
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
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
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