My software notes

January 27, 2011

Names of Atoms of Amino acids

Filed under: softwares and scripts,xplor/xplor-nih/cns — kpwu @ 4:03 pm
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I really hate the inconsistent nomenclature of atoms of amino acids between different programs/database. I finished all NOESY assignment on Sparky using PDB nomenclature and the Sparky XPLOR constraint plugin (shortcut xf) doesn’t take care of the differences between XPLOR and PDB. Thus I have to find a table showing me the differences of names between XPLOR and PDB.

I found BMRB provides such table including few programs (XPLOR, DIANA, PDB, BMRB, SYBYL…) and I have extracted the BMRB/PDB/XPLOR/DIANA columns and reorganized the information. The new table I made is saved as PDF and attached.

Snapshot of part of this table is shown here.

Attached PDF: AA_atoms-nomemclature

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