> Hello Toni > Your PDB file is malformed. Correct.
> Atom names must be left-aligned to column > 14: > ATOM 1 N GLY 1 4.794 -0.966 -4.193 1.00 99.00 > ATOM 2 CA GLY 1 3.792 0.001 -4.433 1.00 99.00 > ATOM 3 C GLY 1 2.880 0.006 -3.283 1.00 99.00 > ATOM 4 O GLY 1 2.357 -1.002 -2.940 1.00 99.00 It appears to be left-aligned, but in fact it is not. The element symbol must be right-aligned in a two character column at 13 and 14. For single character element symbols there is a space in column 13. The 'A' in an alpha carbon is a separate column. Jmol's rules are compliant with the PDB spec and are more strict than RasMol/Chime. Following the rules allows one to distinguish between calcium and an alpha carbon. An alpha carbon followed by a calcium: ATOM 2 CA GLY 1 3.792 0.001 -4.433 1.00 99.00 ATOM 3 CA UNK 1 5.792 1.001 -5.433 1.00 99.00 The PDB spec is: * Six characters (columns) are reserved for atom names, assigned as follows. COLUMN VALUE ----------------------------------------------------------------------- 13 - 14 Chemical symbol - right justified, except for hydrogen atoms 15 Remoteness indicator (alphabetic) 16 Branch designator (numeric) 77 - 78 Element symbol, right-justified Jmol will use columns 77 & 78 if it contains a valid element symbol ... this is recommended. Miguel ------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel?cmd=lnk&kid3432&bid#0486&dat1642 _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
