Bob Hanson wrote: > Angel, we need to know of any more renaming of backbone groups and what > we would refer to as "key atoms" that tell us if something is a > carbohydrate, for instance. So a list of all the old/new atom names > would be wonderful. Maybe Rolf can help us find that. > There are now (temporarily) 3 lists available at the JenaLib server containing atom name changes between pre-remediated and remediated PDB files in PDB format. The comparison is based on atom coordinates of the first model. (Identical coordinates in the old and new file should represent the same atom.) Since there were also coordinate changes the results might not be absolutely complete.
The first list contains all unique atom name changes that were detected (5475), sorted by "ATOM_NAME_OLD, ATOM_NAME_NEW". The second list provides the changes residue name specific (27443), sorted by "RES_NAME_OLD, ATOM_NAME_OLD,ATOM_NAME". In order to allow searching for new residue names the same atom name change is reported several times if the old residue name was changed into different new names. (This is for example the case for the modified nucleic acid residues. They were formerly just named e.g. "+A" but now got specific 3-letter names e.g. "A2M, EDA, A44 ...".) The third list contains the raw data with all atom name changes detected (9327946), sorted by "PDB_ID, RES_NAME_OLD, ATOM_NAME_OLD, ATOM_NUMBER_OLD, ATOM_NAME_NEW". This allows to find examples. In all lists the columns are separated with tabulators and the first line contains the column names (TSV/CSV format). Since the second and third list are quite large (436 KB, 383 MB) they are available as compressed "zip" archives (121 KB, 92 MB). 1) http://www.fli-leibniz.de/ImgLibPDB/tmp/pdb_remediation-atom_name_changes-unique.txt 2) http://www.fli-leibniz.de/ImgLibPDB/tmp/pdb_remediation-atom_name_changes-residue_specific.zip 3) http://www.fli-leibniz.de/ImgLibPDB/tmp/pdb_remediation-atom_name_changes-full.zip Although the documentation at the remediation project site states that all atom names now start with the element symbol, there are still a lot of hydrogen atom names starting with a number). ("Atoms names uniformly begin with their atom type symbol, including hydrogen atoms. Names beginning with numbers and unusual atom names have been changed accordingly.", cited from "http://www.wwpdb.org/documentation/remediation-impacts.pdf";) Regards, Rolf ------------------------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
