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Questions and answers => General discussions (Q&As) => Topic started by: lvelve0901 on January 06, 2017, 04:56:56 pm

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Title: pdb files with multiple coordinates
Post by: lvelve0901 on January 06, 2017, 04:56:56 pm

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

Title: Re: pdb files with multiple coordinates
Post by: xiangjun on January 06, 2017, 05:23:14 pm

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

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University