Rolf, three questions: 1) Can you run the same analysis, restricting your search to ATOM records? I'm guessing (hoping) that a lot of these are HETATM.
2) Is there a way to detect that a file is remediated? For example, in a remark? 3) Can I do this sort of search myself online? Bob Rolf Huehne wrote: >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 > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 ------------------------------------------------------------------------- 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
