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Author Topic: pdb files with multiple coordinates  (Read 2270 times)

Offline lvelve0901

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pdb files with multiple coordinates
« 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


Offline xiangjun

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Re: pdb files with multiple coordinates
« Reply #1 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
« Last Edit: January 06, 2017, 05:32:02 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.