<p>OK, tried to figure out a way using Biopython library, I believe there are tens of faster ways, having <code>1lkk_pdb_test.pdb</code> as input :</p>
<pre><code>ATOM      1  N   LEU A 122      49.672   7.391  11.364  1.00 20.16           N  
ANISOU    1  N   LEU A 122     2561   2767   2050    670   -700     42       N  
ATOM      2  CA  LEU A 122      50.030   7.561  12.734  1.00 20.25           C  
ANISOU    2  CA  LEU A 122     2020   3335   2058   -226   -571    629       C  
ATOM      3  C   LEU A 122      48.886   7.480  13.726  1.00 16.62           C  
ANISOU    3  C   LEU A 122     1863   2277   1944   -333   -710    706       C  
ATOM      4  O   LEU A 122      47.816   8.070  13.517  1.00 15.23           O  
ANISOU    4  O   LEU A 122     2132   1556   1887   -122   -845    184       O  
ATOM      5  CB  LEU A 122      51.116   8.488  13.074  1.00 21.98           C  
ANISOU    5  CB  LEU A 122     1769   3688   2587   -148   -358    491       C  
ATOM      6  CG  LEU A 122      51.381   8.978  14.477  1.00 22.50           C  
ANISOU    6  CG  LEU A 122     2191   3459   2586   -263   -523    565       C  
ATOM      7  CD1 LEU A 122      52.229   8.017  15.285  1.00 23.90           C  
ANISOU    7  CD1 LEU A 122     2795   3452   2500   -216   -104    138       C  
ATOM      8  CD2 LEU A 122      51.959  10.377  14.502  1.00 26.42           C  
ANISOU    8  CD2 LEU A 122     3125   3322   3222    375   -323    398       C  
ATOM      9  H1  LEU A 122      48.995   6.786  11.300  1.00 30.24           H  
ANISOU    9  H1  LEU A 122     3829   3829   3829      0      0      0       H  
ATOM     10  H2  LEU A 122      49.399   8.188  11.020  1.00 30.24           H  
ANISOU   10  H2  LEU A 122     3829   3829   3829      0      0      0       H  
ATOM     11  H3  LEU A 122      50.392   7.090  10.897  1.00 30.24           H  
ANISOU   11  H3  LEU A 122     3829   3829   3829      0      0      0       H  
ATOM     12  HA  LEU A 122      50.481   6.686  12.910  1.00 24.30           H  
ANISOU   12  HA  LEU A 122     3077   3077   3077      0      0      0       H  
ATOM     13  HB2 LEU A 122      51.955   8.066  12.760  1.00 26.37           H  
ANISOU   13  HB2 LEU A 122     3339   3339   3339      0      0      0       H  
ATOM     14  HB3 LEU A 122      50.982   9.295  12.515  1.00 26.37           H  
ANISOU   14  HB3 LEU A 122     3339   3339   3339      0      0      0       H  
ATOM     15  HG  LEU A 122      50.493   9.028  14.933  1.00 27.00           H  
ANISOU   15  HG  LEU A 122     3419   3419   3419      0      0      0       H  
ATOM     16 HD11 LEU A 122      51.771   7.153  15.351  1.00 35.85           H  
ANISOU   16 HD11 LEU A 122     4540   4540   4540      0      0      0       H  
ATOM     17 HD12 LEU A 122      53.095   7.895  14.844  1.00 35.85           H  
ANISOU   17 HD12 LEU A 122     4540   4540   4540      0      0      0       H  
ATOM     18 HD13 LEU A 122      52.368   8.382  16.184  1.00 35.85           H  
ANISOU   18 HD13 LEU A 122     4540   4540   4540      0      0      0       H  
ATOM     19 HD21 LEU A 122      52.806  10.390  14.010  1.00 39.63           H  
ANISOU   19 HD21 LEU A 122     5019   5019   5019      0      0      0       H  
ATOM     20 HD22 LEU A 122      51.327  10.999  14.083  1.00 39.63           H  
ANISOU   20 HD22 LEU A 122     5019   5019   5019      0      0      0       H  
ATOM     21 HD23 LEU A 122      52.116  10.649  15.431  1.00 39.63           H  
ANISOU   21 HD23 LEU A 122     5019   5019   5019      0      0      0       H  
ATOM     22  N   GLU A 123      49.124   6.750  14.812  1.00 14.09           N  
ANISOU   22  N   GLU A 123     1166   1937   2055   -326   -424    468       N  
ATOM     23  CA  GLU A 123      48.215   6.514  15.890  1.00 12.65           C  
ANISOU   23  CA  GLU A 123     1143   1584   1903   -273   -331    -29       C  
ATOM     24  C   GLU A 123      46.790   6.330  15.399  1.00 10.88           C  
ANISOU   24  C   GLU A 123     1138   1238   1605   -155   -376    -53       C  
ATOM     25  O   GLU A 123      45.875   7.059  15.809  1.00 10.93           O  
ANISOU   25  O   GLU A 123     1300   1048   1652     37   -173   -144       O  
ATOM     26  CB  GLU A 123      48.256   7.537  17.028  1.00 14.54           C  
ANISOU   26  CB  GLU A 123     1615   1778   1930   -299   -450   -280       C  
ATOM     27  CG  GLU A 123      47.696   6.998  18.341  1.00 19.07           C  
ANISOU   27  CG  GLU A 123     2450   2721   1808   -148   -132   -221       C  
ATOM     28  CD  GLU A 123      47.620   7.948  19.490  1.00 21.48           C  
ANISOU   28  CD  GLU A 123     3199   2805   1858    113    106      6       C  
ATOM     29  OE1 GLU A 123      47.461   9.187  19.266  1.00 25.80           O  
ANISOU   29  OE1 GLU A 123     4100   2736   2608   1002   -257     -4       O  
ATOM     30  OE2 GLU A 123      47.491   7.497  20.672  1.00 22.45           O  
ANISOU   30  OE2 GLU A 123     3024   3373   1819    545    690    367       O  
ATOM     31  H   GLU A 123      49.919   6.375  14.873  1.00 16.91           H  
ANISOU   31  H   GLU A 123     2141   2141   2141      0      0      0       H  
ATOM     32  HA  GLU A 123      48.484   5.640  16.294  1.00 15.18           H  
ANISOU   32  HA  GLU A 123     1922   1922   1922      0      0      0       H  
ATOM     33  HB2 GLU A 123      49.194   7.821  17.171  1.00 17.45           H  
ANISOU   33  HB2 GLU A 123     2210   2210   2210      0      0      0       H  
ATOM     34  HB3 GLU A 123      47.737   8.336  16.761  1.00 17.45           H  
ANISOU   34  HB3 GLU A 123     2210   2210   2210      0      0      0       H  
ATOM     35  HG2 GLU A 123      46.784   6.654  18.167  1.00 22.88           H  
ANISOU   35  HG2 GLU A 123     2897   2897   2897      0      0      0       H  
ATOM     36  HG3 GLU A 123      48.252   6.227  18.618  1.00 22.88           H  
ANISOU   36  HG3 GLU A 123     2897   2897   2897      0      0      0       H  
ATOM     37  N   PRO A 124      46.576   5.340  14.522  1.00  9.86           N  
ANISOU   37  N   PRO A 124      893   1140   1575     13   -285      8       N  
ATOM     38  CA  PRO A 124      45.182   5.138  14.041  1.00  8.89           C  
ANISOU   38  CA  PRO A 124      875   1151   1229     -6   -227     93       C  
ATOM     39  C   PRO A 124      44.244   4.845  15.208  1.00  8.67           C  
ANISOU   39  C   PRO A 124      858   1071   1245    -81   -189    -53       C  
ATOM     40  O   PRO A 124      44.593   4.143  16.165  1.00  8.98           O  
ANISOU   40  O   PRO A 124     1088   1065   1134    -47   -410    127       O  
ATOM     41  CB  PRO A 124      45.309   3.946  13.121  1.00  9.41           C  
ANISOU   41  CB  PRO A 124     1048   1085   1312     99     -1    -37       C  
ATOM     42  CG  PRO A 124      46.555   3.221  13.556  1.00  9.55           C  
ANISOU   42  CG  PRO A 124     1054   1161   1282     62   -243      6       C  
ATOM     43  CD  PRO A 124      47.489   4.326  13.988  1.00 10.06           C  
ANISOU   43  CD  PRO A 124      911   1179   1591    122   -319   -125       C  
ATOM     44  HA  PRO A 124      44.868   5.939  13.533  1.00 10.67           H  
ANISOU   44  HA  PRO A 124     1351   1351   1351      0      0      0       H  
ATOM     45  HB2 PRO A 124      44.517   3.357  13.204  1.00 11.29           H  
ANISOU   45  HB2 PRO A 124     1429   1429   1429      0      0      0       H  
ATOM     46  HB3 PRO A 124      45.388   4.241  12.180  1.00 11.29           H  
ANISOU   46  HB3 PRO A 124     1429   1429   1429      0      0      0       H  
ATOM     47  HG2 PRO A 124      46.363   2.605  14.307  1.00 11.46           H  
ANISOU   47  HG2 PRO A 124     1451   1451   1451      0      0      0       H  
ATOM     48  HG3 PRO A 124      46.943   2.702  12.807  1.00 11.46           H  
ANISOU   48  HG3 PRO A 124     1451   1451   1451      0      0      0       H  
ATOM     49  HD2 PRO A 124      48.119   4.010  14.683  1.00 12.07           H  
ANISOU   49  HD2 PRO A 124     1528   1528   1528      0      0      0       H  
ATOM     50  HD3 PRO A 124      48.005   4.678  13.220  1.00 12.07           H  
ANISOU   50  HD3 PRO A 124     1528   1528   1528      0      0      0       H  
END                                                                             

</code></pre>
<p>my code is:</p>
<pre><code>import Bio

from Bio.PDB import PDBParser


print('imported Biopython module vesion : ' , Bio.__version__)


parser = PDBParser (QUIET = True)

structure = parser.get_structure('test',  '1lkk_pdb_test.pdb')


atoms = structure.get_atoms()
    

coordz = []

for i in [i for i in atoms]:
    
    if i.get_id() == 'HA' :
     
        print(i.get_parent(), i.get_parent().id, i, i.coord)
        
        coordz.append(i.coord)        

print('coordz list : ')

for i in coordz :
    print(i , type(i))


</code></pre>
<p>output:</p>
<pre><code>imported Biopython module vesion :  1.80
imported Biopython module vesion :  1.80
&lt;Residue LEU het=  resseq=122 icode= &gt; (' ', 122, ' ') &lt;Atom HA&gt; [50.481  6.686 12.91 ]
&lt;Residue GLU het=  resseq=123 icode= &gt; (' ', 123, ' ') &lt;Atom HA&gt; [48.484  5.64  16.294]
&lt;Residue PRO het=  resseq=124 icode= &gt; (' ', 124, ' ') &lt;Atom HA&gt; [44.868  5.939 13.533]
coordz list : 
[50.481  6.686 12.91 ] &lt;class 'numpy.ndarray'&gt;
[48.484  5.64  16.294] &lt;class 'numpy.ndarray'&gt;
[44.868  5.939 13.533] &lt;class 'numpy.ndarray'&gt;
</code></pre>
<p>as per the reason <code>HA</code> represent Cα hydrogen, please refer to _</p>
<blockquote>
<p>Westbrook, John D et al. “The chemical component dictionary: complete descriptions of constituent molecules
in experimentally determined 3D macromolecules in the Protein Data Bank.”
Bioinformatics (Oxford, England) vol. 31,8 (2015): 1274-8. doi:10.1093/bioinformatics/btu789</p>
</blockquote>
<p><a href="https://httpswww.ncbi.nlm.nih.govpmcarticlesPMC4393513pdfbtu789.pdf" rel="nofollow noreferrer">httpswww.ncbi.nlm.nih.govpmcarticlesPMC4393513pdfbtu789.pdf</a></p>
<p><a href="https://www.wwpdb.org/data/ccd" rel="nofollow noreferrer">Chemical Component Dictionary</a></p>
<p>as explamples pages for Leucine links to :</p>
<p><a href="https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/LEU" rel="nofollow noreferrer">https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/LEU</a></p>
<p>and <a href="http://ligand-expo.rcsb.org/reports/L/LEU/LEU_D3L3.gif" rel="nofollow noreferrer">http://ligand-expo.rcsb.org/reports/L/LEU/LEU_D3L3.gif</a></p>
<p>lot of trouble to find a diagram:</p>
<p><a href="https://i.sstatic.net/6e28A.gif" rel="nofollow noreferrer"><img src="https://i.sstatic.net/6e28A.gif" alt="enter image description here" /></a></p>
<p>Just loop over all your proteins in a similar way and store the coords as you need/wish, remember coordinates are retrieved as numpy arrays.</p>

CC BY-SA 4.0
2022-12-26T17:25:59.563Z
2022-12-26T17:51:00.200Z
2022-12-26T17:51:00.200Z
pippo1980
<p>I would import the PDB into the molecular dynamics package GROMACS and use the built-in utilities to calculate the centroid (<a href="https://manual.gromacs.org/current/onlinehelp/gmx-rms.html" rel="nofollow noreferrer">https://manual.gromacs.org/current/onlinehelp/gmx-rms.html</a>).  This is much simpler than trying to write your own utility for this.  Other pre-written calculations to perform on your PDB files:
<a href="https://manual.gromacs.org/current/user-guide/cmdline.html" rel="nofollow noreferrer">https://manual.gromacs.org/current/user-guide/cmdline.html</a></p>

CC BY-SA 4.0
2022-12-28T18:53:57.207Z
2022-12-28T18:53:57.207Z
Guy Francis Mongelli
<p>I am trying to extract the hydrogen atoms attached to the Ca carbon in N no. of proteins. I would be needing the coordinates to calculate its centroid. How should I do it in python ?</p>

<python><proteins><protein-structure><pdb>
How can I get the coordinates of Hydrogen atoms attached to alpha-carbon?
# How can I get the coordinates of Hydrogen atoms attached to alpha-carbon?

(Asked by: username_0 on 2022-12-24)

I am trying to extract the hydrogen atoms attached to the Ca carbon in N no. of proteins. I would be needing the coordinates to calculate its centroid. How should I do it in python ?

**Tags:** python, proteins, protein-structure, pdb

---

## 2 answers

### Answer by username_1 on 2022-12-26. Score: 2

OK, tried to figure out a way using Biopython library, I believe there are tens of faster ways, having 1lkk_pdb_test.pdb as input :
ATOM      1  N   LEU A 122      49.672   7.391  11.364  1.00 20.16           N  
ANISOU    1  N   LEU A 122     2561   2767   2050    670   -700     42       N  
ATOM      2  CA  LEU A 122      50.030   7.561  12.734  1.00 20.25           C  
ANISOU    2  CA  LEU A 122     2020   3335   2058   -226   -571    629       C  
ATOM      3  C   LEU A 122      48.886   7.480  13.726  1.00 16.62           C  
ANISOU    3  C   LEU A 122     1863   2277   1944   -333   -710    706       C  
ATOM      4  O   LEU A 122      47.816   8.070  13.517  1.00 15.23           O  
ANISOU    4  O   LEU A 122     2132   1556   1887   -122   -845    184       O  
ATOM      5  CB  LEU A 122      51.116   8.488  13.074  1.00 21.98           C  
ANISOU    5  CB  LEU A 122     1769   3688   2587   -148   -358    491       C  
ATOM      6  CG  LEU A 122      51.381   8.978  14.477  1.00 22.50           C  
ANISOU    6  CG  LEU A 122     2191   3459   2586   -263   -523    565       C  
ATOM      7  CD1 LEU A 122      52.229   8.017  15.285  1.00 23.90           C  
ANISOU    7  CD1 LEU A 122     2795   3452   2500   -216   -104    138       C  
ATOM      8  CD2 LEU A 122      51.959  10.377  14.502  1.00 26.42           C  
ANISOU    8  CD2 LEU A 122     3125   3322   3222    375   -323    398       C  
ATOM      9  H1  LEU A 122      48.995   6.786  11.300  1.00 30.24           H  
ANISOU    9  H1  LEU A 122     3829   3829   3829      0      0      0       H  
ATOM     10  H2  LEU A 122      49.399   8.188  11.020  1.00 30.24           H  
ANISOU   10  H2  LEU A 122     3829   3829   3829      0      0      0       H  
ATOM     11  H3  LEU A 122      50.392   7.090  10.897  1.00 30.24           H  
ANISOU   11  H3  LEU A 122     3829   3829   3829      0      0      0       H  
ATOM     12  HA  LEU A 122      50.481   6.686  12.910  1.00 24.30           H  
ANISOU   12  HA  LEU A 122     3077   3077   3077      0      0      0       H  
ATOM     13  HB2 LEU A 122      51.955   8.066  12.760  1.00 26.37           H  
ANISOU   13  HB2 LEU A 122     3339   3339   3339      0      0      0       H  
ATOM     14  HB3 LEU A 122      50.982   9.295  12.515  1.00 26.37           H  
ANISOU   14  HB3 LEU A 122     3339   3339   3339      0      0      0       H  
ATOM     15  HG  LEU A 122      50.493   9.028  14.933  1.00 27.00           H  
ANISOU   15  HG  LEU A 122     3419   3419   3419      0      0      0       H  
ATOM     16 HD11 LEU A 122      51.771   7.153  15.351  1.00 35.85           H  
ANISOU   16 HD11 LEU A 122     4540   4540   4540      0      0      0       H  
ATOM     17 HD12 LEU A 122      53.095   7.895  14.844  1.00 35.85           H  
ANISOU   17 HD12 LEU A 122     4540   4540   4540      0      0      0       H  
ATOM     18 HD13 LEU A 122      52.368   8.382  16.184  1.00 35.85           H  
ANISOU   18 HD13 LEU A 122     4540   4540   4540      0      0      0       H  
ATOM     19 HD21 LEU A 122      52.806  10.390  14.010  1.00 39.63           H  
ANISOU   19 HD21 LEU A 122     5019   5019   5019      0      0      0       H  
ATOM     20 HD22 LEU A 122      51.327  10.999  14.083  1.00 39.63           H  
ANISOU   20 HD22 LEU A 122     5019   5019   5019      0      0      0       H  
ATOM     21 HD23 LEU A 122      52.116  10.649  15.431  1.00 39.63           H  
ANISOU   21 HD23 LEU A 122     5019   5019   5019      0      0      0       H  
ATOM     22  N   GLU A 123      49.124   6.750  14.812  1.00 14.09           N  
ANISOU   22  N   GLU A 123     1166   1937   2055   -326   -424    468       N  
ATOM     23  CA  GLU A 123      48.215   6.514  15.890  1.00 12.65           C  
ANISOU   23  CA  GLU A 123     1143   1584   1903   -273   -331    -29       C  
ATOM     24  C   GLU A 123      46.790   6.330  15.399  1.00 10.88           C  
ANISOU   24  C   GLU A 123     1138   1238   1605   -155   -376    -53       C  
ATOM     25  O   GLU A 123      45.875   7.059  15.809  1.00 10.93           O  
ANISOU   25  O   GLU A 123     1300   1048   1652     37   -173   -144       O  
ATOM     26  CB  GLU A 123      48.256   7.537  17.028  1.00 14.54           C  
ANISOU   26  CB  GLU A 123     1615   1778   1930   -299   -450   -280       C  
ATOM     27  CG  GLU A 123      47.696   6.998  18.341  1.00 19.07           C  
ANISOU   27  CG  GLU A 123     2450   2721   1808   -148   -132   -221       C  
ATOM     28  CD  GLU A 123      47.620   7.948  19.490  1.00 21.48           C  
ANISOU   28  CD  GLU A 123     3199   2805   1858    113    106      6       C  
ATOM     29  OE1 GLU A 123      47.461   9.187  19.266  1.00 25.80           O  
ANISOU   29  OE1 GLU A 123     4100   2736   2608   1002   -257     -4       O  
ATOM     30  OE2 GLU A 123      47.491   7.497  20.672  1.00 22.45           O  
ANISOU   30  OE2 GLU A 123     3024   3373   1819    545    690    367       O  
ATOM     31  H   GLU A 123      49.919   6.375  14.873  1.00 16.91           H  
ANISOU   31  H   GLU A 123     2141   2141   2141      0      0      0       H  
ATOM     32  HA  GLU A 123      48.484   5.640  16.294  1.00 15.18           H  
ANISOU   32  HA  GLU A 123     1922   1922   1922      0      0      0       H  
ATOM     33  HB2 GLU A 123      49.194   7.821  17.171  1.00 17.45           H  
ANISOU   33  HB2 GLU A 123     2210   2210   2210      0      0      0       H  
ATOM     34  HB3 GLU A 123      47.737   8.336  16.761  1.00 17.45           H  
ANISOU   34  HB3 GLU A 123     2210   2210   2210      0      0      0       H  
ATOM     35  HG2 GLU A 123      46.784   6.654  18.167  1.00 22.88           H  
ANISOU   35  HG2 GLU A 123     2897   2897   2897      0      0      0       H  
ATOM     36  HG3 GLU A 123      48.252   6.227  18.618  1.00 22.88           H  
ANISOU   36  HG3 GLU A 123     2897   2897   2897      0      0      0       H  
ATOM     37  N   PRO A 124      46.576   5.340  14.522  1.00  9.86           N  
ANISOU   37  N   PRO A 124      893   1140   1575     13   -285      8       N  
ATOM     38  CA  PRO A 124      45.182   5.138  14.041  1.00  8.89           C  
ANISOU   38  CA  PRO A 124      875   1151   1229     -6   -227     93       C  
ATOM     39  C   PRO A 124      44.244   4.845  15.208  1.00  8.67           C  
ANISOU   39  C   PRO A 124      858   1071   1245    -81   -189    -53       C  
ATOM     40  O   PRO A 124      44.593   4.143  16.165  1.00  8.98           O  
ANISOU   40  O   PRO A 124     1088   1065   1134    -47   -410    127       O  
ATOM     41  CB  PRO A 124      45.309   3.946  13.121  1.00  9.41           C  
ANISOU   41  CB  PRO A 124     1048   1085   1312     99     -1    -37       C  
ATOM     42  CG  PRO A 124      46.555   3.221  13.556  1.00  9.55           C  
ANISOU   42  CG  PRO A 124     1054   1161   1282     62   -243      6       C  
ATOM     43  CD  PRO A 124      47.489   4.326  13.988  1.00 10.06           C  
ANISOU   43  CD  PRO A 124      911   1179   1591    122   -319   -125       C  
ATOM     44  HA  PRO A 124      44.868   5.939  13.533  1.00 10.67           H  
ANISOU   44  HA  PRO A 124     1351   1351   1351      0      0      0       H  
ATOM     45  HB2 PRO A 124      44.517   3.357  13.204  1.00 11.29           H  
ANISOU   45  HB2 PRO A 124     1429   1429   1429      0      0      0       H  
ATOM     46  HB3 PRO A 124      45.388   4.241  12.180  1.00 11.29           H  
ANISOU   46  HB3 PRO A 124     1429   1429   1429      0      0      0       H  
ATOM     47  HG2 PRO A 124      46.363   2.605  14.307  1.00 11.46           H  
ANISOU   47  HG2 PRO A 124     1451   1451   1451      0      0      0       H  
ATOM     48  HG3 PRO A 124      46.943   2.702  12.807  1.00 11.46           H  
ANISOU   48  HG3 PRO A 124     1451   1451   1451      0      0      0       H  
ATOM     49  HD2 PRO A 124      48.119   4.010  14.683  1.00 12.07           H  
ANISOU   49  HD2 PRO A 124     1528   1528   1528      0      0      0       H  
ATOM     50  HD3 PRO A 124      48.005   4.678  13.220  1.00 12.07           H  
ANISOU   50  HD3 PRO A 124     1528   1528   1528      0      0      0       H  
END                                                                             


my code is:
import Bio

from Bio.PDB import PDBParser


print('imported Biopython module vesion : ' , Bio.__version__)


parser = PDBParser (QUIET = True)

structure = parser.get_structure('test',  '1lkk_pdb_test.pdb')


atoms = structure.get_atoms()
    

coordz = []

for i in [i for i in atoms]:
    
    if i.get_id() == 'HA' :
     
        print(i.get_parent(), i.get_parent().id, i, i.coord)
        
        coordz.append(i.coord)        

print('coordz list : ')

for i in coordz :
    print(i , type(i))



output:
imported Biopython module vesion :  1.80
imported Biopython module vesion :  1.80
 (' ', 122, ' ')  [50.481  6.686 12.91 ]
 (' ', 123, ' ')  [48.484  5.64  16.294]
 (' ', 124, ' ')  [44.868  5.939 13.533]
coordz list : 
[50.481  6.686 12.91 ] 
[48.484  5.64  16.294] 
[44.868  5.939 13.533] 

as per the reason HA represent Cα hydrogen, please refer to _

Westbrook, John D et al. “The chemical component dictionary: complete descriptions of constituent molecules
in experimentally determined 3D macromolecules in the Protein Data Bank.”
Bioinformatics (Oxford, England) vol. 31,8 (2015): 1274-8. doi:10.1093/bioinformatics/btu789

httpswww.ncbi.nlm.nih.govpmcarticlesPMC4393513pdfbtu789.pdf
Chemical Component Dictionary
as explamples pages for Leucine links to :
https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/LEU
and http://ligand-expo.rcsb.org/reports/L/LEU/LEU_D3L3.gif
lot of trouble to find a diagram:

Just loop over all your proteins in a similar way and store the coords as you need/wish, remember coordinates are retrieved as numpy arrays.


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### Answer by username_2 on 2022-12-28. Score: 1

I would import the PDB into the molecular dynamics package GROMACS and use the built-in utilities to calculate the centroid (<https://manual.gromacs.org/current/onlinehelp/gmx-rms.html>). This is much simpler than trying to write your own utility for this. Other pre-written calculations to perform on your PDB files:
<https://manual.gromacs.org/current/user-guide/cmdline.html>


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