On 3/8/11 5:44 PM, Cale Dakwar wrote: > > Hello all, > > For any given structure in the PDB, I want to identify all the > Histidine ND1 atoms. I then want to consider these atoms in pairs, > measure the distance in Angstroms between the ND1 atoms in each pair, > and compile these distances (along with residue numbers of the pair) > in a table. I then want to repeat this procedure for each unique > structure in the PDB and generate a table containing all occurrences > of HisND1 pairs with their corresponding separation distance. Amongst > other things, I want e.g. generate a histogram from this table and > determine e.g. the shortest HisND1 pair distance observed and the > structure in which this happens. Does anyone have any suggestions for > any tools I might be able to use to perform this search?
You'll have to more-or-less write something to do this yourself, as others have suggested. Ideally you should use some kind of library that gives you a more usable version of the PDB files, rather than have to parse the PDB files yourself. Something like PROSS, Phenix iotbx.pdb, pdb-tools (all Python), or ParsePDB (Perl) should make your life easier. If you don't already have a local mirror of RCSB, you'll need that too. Some info on that process is here: http://www.wwpdb.org/downloads.html If you are only interested in a small subset of all PDBs, and you can identify that subset based exclusively on sequence comparisons, then you can do searches on the per-chain FASTA entries for all PDBs which are available in this file: ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt Hope that helps, Ian
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