pdb files with multiple coordinates

[lvelve0901]

Hi, xiangjun,

I have some pdb files from crystal structures which have multiple coordinates for certain atoms and when I do 3DNA to analyze it, what is the exact result, is it average result?

Best,
Honglue

[xiangjun]

Hi Honglue,

By default, programs in 3DNA (DSSR and SNAP as well) take the alternative atomic positions 'A' or '1' if present (i.e. other than space ' ') into consideration. See the configure file $X3DNA/config/misc_3dna.par:

Code: [Select]

# Section 2: alternative location in ATOM or HETATM records
#   default to A or 1 (A1), and ' ' is always added
<alt_list>A1</alt_list>

You can change the default by directly editing the misc_3dna.par file for global effects, or more conveniently by specifying the -alt_list option from the command line on a case-by-case basis. E.g., -alt_list=B if you want to analyze the other alternative positions ('B' as in your sample PDB file). See the documentation on PDB "Coordinate File Description" at http://deposit.rcsb.org/adit/docs/pdb_atom_format.html on the alternate location indicator.

HTH,

Xiang-Jun