OK, I've done some more research as promised on atom name changes in PDB. Strikingly enough, I cannot find any document on the wwPDB site simply listing these changes. These are my conclusions:
On 15 Oct 2007 at 14:10, Bob Hanson wrote: > Please check also the following if you can: > > > "H5T", // 45 - 5' terminus hydrogen which replaces P + O1P + O2P > > "O5T", // 46 - 5' terminus oxygen which replaces P + O1P + O2P can't find these two (maybe because that's not standard residue); they are bound to have changed, though (see H3T below) > > "O4'", // 49 - sugar ring 4' oxygen ... not present in +T ... > > maybe others This is OK, no change (in fact, it was O4* before, now O4') > > "O2'", // 50 - sugar 2' oxygen, unique to RNA OK, O2' in all ribonucleotide residues > // nucleic acid backbone hydrogens > // > "1H5'", // 51 - first equivalent H on sugar 5' carbon > "2H5'", // 52 - second equivalent H on sugar 5' carbon These were 1H5* and 2H5*, now are H5 prime and H5 prime prime > "H4'", // 53 - H on sugar ring 4' carbon > "H3'", // 54 - H on sugar ring 3' carbon No change here, just * to prime > "1H2'", // 55 - first equivalent H on sugar ring 2' carbon > "2H2'", // 56 - second equivalent H on sugar ring 2' carbon These were 1H2*, 2H2*, now are H2 prime and H2 prime prime > "2HO'", // 57 - H on sugar 2' oxygen, unique to RNA Changes from 2HO* to HO2 prime > "H1'", // 58 - H on sugar ring 1' carbon No change, just * to prime > "H3T", // 59 - 3' terminus hydrogen Changes to HO3 prime For anyone interested, I am pasting below the full list of changes. ------------- Changes of atom names in PDB v.3 interpreted from reading http://www.ebi.ac.uk/~henrick/newpdb/standard_geometry.cif "r500.f is a program which reads PDB V3 format data files and produces V3 validation records based standard geometries described in [1-2]. This Fortran 77 program requires supporting the supporting libraries standard_geometry.cif and symop.lib" A) Summarized: 1) In all deoxyribo- and ribo-nucleotides: - Asterisk changes to prime (after O5, C5, C4, O4, C3, O3, C2, C1, H3, H4, H1; O2 ribo only) - O1P to OP1 - O2P to OP2 - O3P to OP3 - 2HOP to HOP2 - 3HOP to HOP3 - H3T to HO3' - 1H5* to H5' - 2H5* to H5'' 2) Only in deoxyribonucleotides: - 1H2* to H2' - 2H2* to H2'' 3) Only in ribonucleotides: - H2* to H2' - 2HO* to HO2' 4) Nucleotide-specific: A and DA: - 1H6 to H61 - 2H6 to H62 C and DC: - 1H4 to H41 - 2H4 to H42 G and DG: - 1H2 to H21 - 2H2 to H22 T and DT: - C5M to C7 - 1H5M to H71 - 2H5M to H72 - 3H5M to H73 B) Detailed: old new in: O5* O5' DA A C5* C5' DA A C4* C4' DA A O4* O4' DA A C3* C3' DA A O3* O3' DA A C2* C2' DA A C1* C1' DA A O2* O2' A C G U T I O1P OP1 DA A DC C DG G DU U DT T DI I O2P OP2 DA A DC C DG G DU U DT T DI I O3P OP3 DA A DC C DG G DU U DT T DI I 3HOP HOP3 DA A DC C DG G DU U DT T DI I 2HOP HOP2 DA A DC C DG G DU U DT T DI I 1H5* H5' DA A DC C DG G DU U DT T DI I 2H5* H5'' DA A DC C DG G DU U DT T DI I H4* H4' DA A DC C DG G DU U DT T DI I H3* H3' DA A DC C DG G DU U DT T DI I H3T HO3' DA A DC C DG G DU U DT T DI I H1* H1' DA A DC C DG G DU U DT T DI I 1H2* H2' DA DC DG DU DT T DI 2H2* H2'' DA DC DG DU DT DI H2* H2' A C G U I 2HO* HO2' A C G U T I 1H6 H61 DA A 2H6 H62 DA A 1H4 H41 DC C 2H4 H42 DC C 1H2 H21 DG G 2H2 H22 DG G C5M C7 DT T 1H5M H71 DT T 2H5M H72 DT T 3H5M H73 DT T Note: I think 1H2* to H2' in T is wrong, should be H2* to H2' as in other ribonucleotides ------------------------------------------------------------------------- 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
