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LePingKYXK / PDB_cleaner

A Python 3 script for cleaning up the PDB file
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PDB_cleaner

A Python3 script to clean up the PDB file

Most of time, the PDB files are complicated, which have lots of redundant information as shown below.

The simplest way is to delete the ANISOU lines.

Since PDBSlicer could not deal with non-standard residues, the simplest way is to delete them.

The bold font lines indicate the discontinuous sequence numbers (223 ...empty... 237) due to the missing residues. We called this case as sequence gap. It is a very serious problem because the Ramachandran subunit is defined by three adjacent residues. It is immpossible to directly choose residue number series (222, 223, 237) and (2233, 237, 238) as the members of the Ramachandran subunit. The solution is that treat the peptide as segments, e.g. from beginning to residue number 223, then from residue number 237 to the end. If the PDB file has more than one gap, we divide it into several segments based on the locations of the gaps. Note: the discontinuous sequence number between different chains also treated as 'gap', just because it is easy for programming.

Improvement (Nov. 16, 2017) In the printing and report format, the chain ID was added aside to the sequence number, e.g. ('A:223', 'A:237'). Previously, only the sequence numbers between gap(s) were showed.

In this case (5DXX.pdb), there are three different types of the alternative locations, A, B, and C high-lighted with the bold font. However, they distribute with irregular way. For instance, in sequence 61, A and B appeared, whereas in sequence 268, B and C emerged. As a result, it is impossible to simply use the pdb_info[(pdb_info.Alt_Loc == ' ') | (pdb_info.Alt_Loc == 'A')] because that would delete all B and C labeled atoms in sequence 268!

Improvement or Debug (Sep. 04, 2017) By using pandas df.groupby() on the ['Seq_Num', 'ChainID'] columns, we can focus on each specific residue and keep the first alternative location, no matter the first one is 'A' or 'B' or 'C'. The code is show as following

    #### delete the redundant alternate locations, only keep the first apperance
    if altloc:
        groups = pdb_info.groupby(['Seq_Num', 'ChainID'], sort=False)
        pdb_info = groups.apply(lambda x:
                                x.drop_duplicates(subset=["AtomTyp"],
                                                  keep='first')
                                if len(groups['Alt_Loc']) >= 2 else x)

Improvement (Nov. 16, 2017) In this case, I added a new option in my PDB_cleaner script enabling the users to choose whether remove all hydrogen atoms or not.

Improvement (Dec. 13, 2017) Modified the script by using 'Element' (at column 76:78 in PDB file) as the condition.

(previously, I used pdb_info.ResName.str.startswith("H"), which is slower).

Some of the PDB files contains ligands/solvents (e.g. 1HQ2.pdb, which contains MG, CL, ACT, APC, PH2, HOH). Those information is listed below the last TER line of the protein chains. Here, only parts of them are shown as an example.

TER    1288      TRP A 158                                                      
HETATM 1289 MG    MG A 161      -2.797   1.884  19.740  1.00  6.70          MG  
ANISOU 1289 MG    MG A 161     1097    971    478     15    338    -47      MG  
HETATM 1290 MG    MG A 162      -5.869   3.399  19.011  1.00  7.19          MG  
ANISOU 1290 MG    MG A 162      855   1269    610    165    324   -165      MG  
HETATM 1291 CL    CL A 163     -16.840 -10.191  19.213  1.00 15.49          CL  
ANISOU 1291 CL    CL A 163     2248   1922   1713    -61    398      8      CL  
HETATM 1292  C   ACT A 164      -6.064  -1.027  24.199  1.00 37.58           C  
ANISOU 1292  C   ACT A 164     7931   1868   4482    143  -3066   -290       C  
HETATM 1293  O   ACT A 164      -6.343  -1.714  23.182  1.00 14.54           O  
ANISOU 1293  O   ACT A 164     1249   1159   3116    -81    364     -9       O  
HETATM 1294  OXT ACT A 164      -6.052   0.230  24.235  1.00 21.94           O  
ANISOU 1294  OXT ACT A 164     2886   1823   3627     17   -396   -183       O  
HETATM 1295  CH3 ACT A 164      -5.715  -1.844  25.481  1.00 22.07           C  
ANISOU 1295  CH3 ACT A 164     2913   2265   3206   1466    -77   -427       C  
...
HETATM 1308  PG  APC A 171      -7.079   2.750  21.870  1.00  6.88           P  
ANISOU 1308  PG  APC A 171      911    790    915     71    401   -193       P  
HETATM 1309  O1G APC A 171      -6.616   1.344  22.152  1.00  9.60           O  
ANISOU 1309  O1G APC A 171      871    835   1940    100    305    -71       O  
HETATM 1310  O2G APC A 171      -8.226   3.192  22.715  1.00  6.03           O  
ANISOU 1310  O2G APC A 171      938    744    609     31    592     49       O  
HETATM 1311  O3G APC A 171      -7.294   3.042  20.400  1.00  7.08           O  
ANISOU 1311  O3G APC A 171      758   1522    408     29    337   -202       O  
HETATM 1312  PB  APC A 171      -4.370   3.764  21.854  1.00  6.31           P  
ANISOU 1312  PB  APC A 171      909   1010    479     80    206    -23       P  
HETATM 1313  O1B APC A 171      -4.334   3.108  20.508  1.00  6.48           O  
ANISOU 1313  O1B APC A 171     1088    961    411    197    230    187       O  
HETATM 1314  O2B APC A 171      -3.797   5.194  21.941  1.00  8.43           O  
ANISOU 1314  O2B APC A 171     1093    812   1296   -168    237    134       O  
HETATM 1315  O3B APC A 171      -5.859   3.729  22.378  1.00  6.62           O  
ANISOU 1315  O3B APC A 171      943    913    661     23    285    -98       O  
HETATM 1316  PA  APC A 171      -1.763   2.605  22.706  1.00  6.54           P  
ANISOU 1316  PA  APC A 171      934    931    619    -41    125    -54       P  
HETATM 1317  O1A APC A 171      -1.570   2.627  21.218  1.00  6.39           O  
ANISOU 1317  O1A APC A 171     1032    863    534   -110     85    176       O  
HETATM 1318  O2A APC A 171      -1.020   3.644  23.495  1.00  7.30           O  
ANISOU 1318  O2A APC A 171     1040    900    833   -144    100   -132       O  
HETATM 1319  C3A APC A 171      -3.506   2.689  22.980  1.00  6.45           C  
ANISOU 1319  C3A APC A 171     1048    908    494    -10     50   -250       C  
HETATM 1320  O5' APC A 171      -1.282   1.138  23.187  1.00  7.04           O  
ANISOU 1320  O5' APC A 171     1051    899    726     99    216    199       O  
HETATM 1321  C5' APC A 171      -1.316   0.838  24.562  1.00  6.44           C  
ANISOU 1321  C5' APC A 171     1106    788    551     17    188     29       C  
HETATM 1322  C4' APC A 171      -1.315  -0.661  24.737  1.00  6.29           C  
ANISOU 1322  C4' APC A 171     1058   1000    331    -50    125    -50       C  
HETATM 1323  O4' APC A 171      -2.428  -1.236  24.248  1.00  6.72           O  
ANISOU 1323  O4' APC A 171     1097    794    660   -168     83   -206       O  
HETATM 1324  C3' APC A 171      -0.144  -1.406  24.035  1.00  5.09           C  
ANISOU 1324  C3' APC A 171      840    635    461    114   -260    152       C  
HETATM 1325  O3' APC A 171       1.112  -1.294  24.673  1.00  8.26           O  
ANISOU 1325  O3' APC A 171      951   1232    954    -47   -388     51       O  
HETATM 1326  C2' APC A 171      -0.589  -2.790  23.968  1.00  6.71           C  
ANISOU 1326  C2' APC A 171      899    800    850   -297    285    216       C  
HETATM 1327  O2' APC A 171      -0.030  -3.702  24.840  1.00  7.41           O  
ANISOU 1327  O2' APC A 171     1086    962    766     50    -20    387       O  
HETATM 1328  C1' APC A 171      -2.056  -2.689  24.271  1.00  6.78           C  
ANISOU 1328  C1' APC A 171      966   1005    607     69    -51    -28       C  
HETATM 1329  N9  APC A 171      -3.025  -3.347  23.426  1.00  6.15           N  
ANISOU 1329  N9  APC A 171      878   1013    448    -50      4    190       N  
HETATM 1330  C8  APC A 171      -4.109  -4.250  23.860  1.00  5.38           C  
ANISOU 1330  C8  APC A 171      963    639    442    128    139   -256       C  
HETATM 1331  N7  APC A 171      -4.834  -4.707  22.964  1.00  6.53           N  
ANISOU 1331  N7  APC A 171     1035    948    498     64    114   -303       N  
HETATM 1332  C5  APC A 171      -4.263  -4.110  21.750  1.00  6.10           C  
ANISOU 1332  C5  APC A 171      827    920    570     95     98    -94       C  
HETATM 1333  C6  APC A 171      -4.711  -4.298  20.433  1.00  6.59           C  
ANISOU 1333  C6  APC A 171      929    875    698    -65    341   -235       C  
HETATM 1334  N6  APC A 171      -5.694  -5.022  20.065  1.00  5.61           N  
ANISOU 1334  N6  APC A 171     1039    448    646    -77    172     -3       N  
HETATM 1335  N1  APC A 171      -3.967  -3.599  19.483  1.00  5.96           N  
ANISOU 1335  N1  APC A 171      967    811    486    -27    349    -21       N  
HETATM 1336  C2  APC A 171      -2.985  -2.876  19.852  1.00  6.29           C  
ANISOU 1336  C2  APC A 171      770    937    683     62    -16    219       C  
HETATM 1337  N3  APC A 171      -2.475  -2.631  21.110  1.00  7.13           N  
ANISOU 1337  N3  APC A 171     1440    715    552    -17    159     88       N  
HETATM 1338  C4  APC A 171      -3.227  -3.343  22.105  1.00  5.85           C  
ANISOU 1338  C4  APC A 171      888    820    514     95    -85    145       C  
HETATM 1339  N1  PH2 A 181      -7.610   6.951  18.003  1.00  6.05           N  
ANISOU 1339  N1  PH2 A 181     1052    952    296    -94     78   -172       N  
HETATM 1340  C2  PH2 A 181      -7.491   7.106  19.276  1.00  6.24           C  
ANISOU 1340  C2  PH2 A 181      751   1399    220     93    132     13       C  
HETATM 1341  C3  PH2 A 181      -8.350   8.309  19.918  1.00 12.59           C  
ANISOU 1341  C3  PH2 A 181     2656   1496    632   1012   -233   -450       C  
HETATM 1342  N4  PH2 A 181      -9.107   9.037  19.073  1.00  8.47           N  
ANISOU 1342  N4  PH2 A 181     1999    603    614     77    272     74       N  
HETATM 1343  N5  PH2 A 181      -9.913   9.531  16.981  1.00  6.33           N  
ANISOU 1343  N5  PH2 A 181      859    710    836   -209    210    247       N  
HETATM 1344  C6  PH2 A 181     -10.042   9.367  15.609  1.00  6.17           C  
ANISOU 1344  C6  PH2 A 181     1209    401    734    -75    256    195       C  
HETATM 1345  N6  PH2 A 181     -10.760  10.085  14.925  1.00  7.94           N  
ANISOU 1345  N6  PH2 A 181     1288    739    992    607    231     -6       N  
HETATM 1346  N7  PH2 A 181      -9.294   8.335  15.116  1.00  6.20           N  
ANISOU 1346  N7  PH2 A 181     1142    360    855     36     21    218       N  
HETATM 1347  C8  PH2 A 181      -8.506   7.520  15.753  1.00  5.42           C  
ANISOU 1347  C8  PH2 A 181      958    690    411     48    430    -24       C  
HETATM 1348  O8  PH2 A 181      -7.860   6.607  15.236  1.00  6.00           O  
ANISOU 1348  O8  PH2 A 181      592   1089    600    260     34   -140       O  
HETATM 1349  C9  PH2 A 181      -8.445   7.773  17.143  1.00  6.49           C  
ANISOU 1349  C9  PH2 A 181      857   1146    461    217     -8    -87       C  
HETATM 1350  C10 PH2 A 181      -9.183   8.808  17.707  1.00  6.03           C  
ANISOU 1350  C10 PH2 A 181     1024    777    489     36    384      5       C  
HETATM 1351  C11 PH2 A 181      -6.690   6.344  20.210  1.00  7.41           C  
ANISOU 1351  C11 PH2 A 181     1201   1148    469    155   -176    -66       C  
HETATM 1352  O4  PH2 A 181      -5.798   5.476  19.528  1.00  8.32           O  
ANISOU 1352  O4  PH2 A 181     1571    989    601    322    507   -127       O  
HETATM 1353  O   HOH A 201      -1.216   0.760  18.974  1.00  7.10           O  
ANISOU 1353  O   HOH A 201     1048   1158    492    106     60    -57       O  
HETATM 1354  O   HOH A 202     -10.274 -11.677  16.318  1.00  6.62           O  
ANISOU 1354  O   HOH A 202      865    817    835    -50    295    115       O  
HETATM 1355  O   HOH A 203      -7.887   3.653  14.884  1.00  8.89           O  
ANISOU 1355  O   HOH A 203     1091   1226   1061   -110    356    -28       O

Improvement (Dec. 13, 2017) PDB_cleaner is able to report them in the final report.txt file.

Modules required

How to run this script

This script can be run in both Linux and Windows system. The command is shown below,

$python pdb_cleaner.py

Then, the program will ask you to specified the directory that the PDB files located, and how to deal with multiple chains (keep all the chains or just one of them).

If you choose "one", the program will choose the longest chain in the PDB file (if all chains have the same length, the first chain will be kept).

  1. Collect all the PDB files in the given directory;

  2. In each PDB file, check the following items:

    2.1 ligands;

    2.2. alternate locations;

    2.3. non-standard amino acid residues;

    2.4. negative sequence numbers (less important);

    2.5. sequence gaps;

    2.6. insertion code;

    2.7. multiple chains;

    2.8. hydrogen atoms;

    2.9. to do: missing atoms;

    2.10. to do: keep ligands/solvents or not. Currently, all ligands/solvents are removed.

  3. Clean the PDB files if the aforementioned items exist, with following options if protein has multiple chains;

    3.1. remove hydrogein, if the user specified "y";

    3.2. keep all chains if the user specified "all";

    3.3. keep the longest chain (or the 1st chain, if all chains have the same length), if the user specified "one".

  4. Save the cleaned PDB files one by one;

  5. Save the summary report.