[ccp4bb] Job opportunity: Scientist Position in the X-ray Crystallography Center at St. Jude

Dear all, The Biomolecular X-ray Crystallography Center at St. Jude Children's Research Hospital is seeking a motivated scientist to provide a central service-l

Re: [ccp4bb] SMILES from PDB records (HELP-21524)

Dear Doeke, Here is the process we recommend: For now you can get the entire collection of ligand definitions at http://www.wwpdb.org/data/ccd, using the file https://files.wwpdb.org/pub/pdb/data/monomers/components.cif.gz From there you would parse the SMILES from _pdbx_chem_comp_descriptor

Re: [ccp4bb] SMILES from PDB records

components.cif file from https://www.wwpdb.org/data/ccd has SMILES strings for all monomers in the PDB. Best, Marcin On Fri, Sep 13, 2024 at 5:28 PM Hekstra, Doeke Romke wrote: > > Hi, > > > > Does anyone have experience (or scripts!) to extract ligand SMILES from > macromolecular PDB records

Re: [ccp4bb] SMILES from PDB records

I have used this web site to generate SMILES strings from PDB coordinates. You need to strictly examine the output to ensure that you get the proper chirality, bond order and correct number of hydrogens, and if there are discrepancies you may have to edit the string. Diana

[ccp4bb] SMILES from PDB records

Hi, Does anyone have experience (or scripts!) to extract ligand SMILES from macromolecular PDB records using the PDB data API or from a library of PDB or mmCIF files? We would greatly appreciate any pointers to get us started. Thank you, Doeke = Doeke Hekstra Assistant Professor of Molecu

[ccp4bb] Opening: RCSB PDB Director and Tenured Professor of Chemistry and Chemical Biology

Rutgers, The State University of New Jersey (New Brunswick, NJ, USA) invites applications for a distinguished scientist, focused on 3D structures of biological macromolecules, to be appointed to the tenured rank of Professor. This role will include directorship of the Research Collaboratory for