Hi Tim, a non-ccp4 solution (since you haven't gotten any suggestion yet)..
1) Get atom selection of atoms involved into ion coordination: phenix.metal_coordination model.pdb 2) Using atom selection from above extract portion of PDB that contains atoms in question: phenix.pdb_atom_selection model.pdb "atom_selection_string_here" --write-pdb-file="partial.pdb" 3) Get average B: phenix.pdbtools partial.pdb model_statistics=true Remark: steps 2)-3) can be done in one go: phenix.b_factor_statistics model.pdb selection="atom_selection_string_here" If this is of general interest I can wrap 1)-3) into one command. Good luck, Pavel On Thu, Jan 23, 2014 at 4:36 AM, Tim Gruene <t...@shelx.uni-ac.gwdg.de> wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Dear all, > > could anyone suggest a way to get the average B-factor from a PDB-file > of those atoms a specific ion binds to (e.g. as judged by header LINK > records or a distance interval)? > > I would like to get this number for all K-ions from a set of > PDB-files, and I hope there is a quicker way than using coot to click > on the surrounding atoms and transfer the numbers into a chart. > > Best, > Tim > > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.12 (GNU/Linux) > Comment: Using GnuPG with Icedove - http://www.enigmail.net/ > > iD8DBQFS4QziUxlJ7aRr7hoRAtlAAKCei/Ehfg71Xir3pkvWvTQg93YwEQCePFM6 > 2kPFPJw8aZySVYnLaQCjKR4= > =q9pT > -----END PGP SIGNATURE----- >
