How can I parse alternative atom information in a PDB file?
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6 weeks ago
user366312 ▴ 10

I am trying to parse PDB files.

Say, a PDB file has the following data:

ATOM     33  N  ATHR A   2       4.935 -11.632  15.046  0.74  2.95           N  
ATOM     34  N  BTHR A   2       5.078 -11.406  15.180  0.31  2.78           N  
ATOM     35  CA ATHR A   2       5.757 -11.521  13.850  0.81  3.02           C  
ATOM     36  CA BTHR A   2       5.773 -11.153  13.921  0.20  2.67           C  
ATOM     37  C  ATHR A   2       7.070 -10.839  14.210  0.74  2.82           C  
ATOM     38  C  BTHR A   2       7.155 -10.559  14.193  0.29  1.80           C  
ATOM     39  O  ATHR A   2       7.152  -9.941  15.050  0.80  3.31           O  
ATOM     40  O  BTHR A   2       7.214  -9.641  15.012  0.25  2.41           O  
ATOM     41  CB ATHR A   2       4.976 -10.693  12.813  0.87  5.53           C  
ATOM     42  CB BTHR A   2       4.896 -10.354  12.941  0.25 12.07           C  
ATOM     43  OG1ATHR A   2       4.611  -9.432  13.388  1.00  6.88           O  
ATOM     44  OG1BTHR A   2       3.743 -11.083  12.501  0.25  9.57           O  
ATOM     45  CG2ATHR A   2       3.858 -11.584  12.293  0.75 10.03           C  
ATOM     46  CG2BTHR A   2       5.683  -9.885  11.726  0.27  5.90           C  
ATOM     47  H  ATHR A   2       4.547 -10.814  15.527  0.75  3.44           H  
ATOM     48  H  BTHR A   2       5.510 -10.211  15.754  0.25  2.90           H  
ATOM     49  HA ATHR A   2       5.962 -12.339  13.548  0.75  3.32           H  
ATOM     50  HA BTHR A   2       4.036  -9.929  13.477  0.25  2.86           H  
ATOM     51  HB ATHR A   2       5.648 -10.589  11.938  0.75  5.43           H  
ATOM     52  HB BTHR A   2       4.644  -9.326  13.574  0.25  5.67           H  
ATOM     53  HG1ATHR A   2       5.030  -9.344  14.216  0.75  8.74           H  
ATOM     54  HG1BTHR A   2       3.236 -11.198  13.399  0.25 10.21           H  
ATOM     55 HG21ATHR A   2       4.096 -12.441  11.924  0.75 10.92           H  
ATOM     56 HG21BTHR A   2       6.542  -9.278  12.024  0.25  9.66           H  
ATOM     57 HG22ATHR A   2       3.222 -10.974  11.650  0.75 10.92           H  
ATOM     58 HG22BTHR A   2       5.039  -9.142  11.179  0.25  9.66           H  
ATOM     59 HG23ATHR A   2       3.163 -11.738  13.200  0.75 10.92           H  
ATOM     60 HG23BTHR A   2       5.904 -10.639  11.169  0.25  9.66           H  

We see that there are many alternative atoms in the 2nd residue.

How should I choose the atoms?

Should I just randomly choose one atom from the alternatives? How can my parser learn to differentiate between those two atoms (say, 33 and 34)? Coz, from the parsing point of view, there is no indication that they are related.

How can I parse alternative atom information in a PDB file?

pdb protein • 186 views
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Entering edit mode

It may help your parsing endeavor if you reviewed alternate locations and the columns related to this in the PDB format. Particularly your statement, "from the parsing point of view, there is no indication that they are related", needs reconsidering. See Proteopedia's page on 'Alternate locations' about the 17th column, and also the occupancy value.
That page also describes a way to visualize the alternate conformations of a PDB file using FirstGlance in Jmol. And the information included in FirstGlance about the examples of alternate locations goes beyond the brief coverage on the associated Proteopedia page.
Often the associated publications can have information about the different conformations, too.

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