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21
22
23 """Module for creating PDB records.
24
25 This module currently used the PDB format version 3.30 from July, 2011 U{http://www.wwpdb.org/documentation/file-format/format33/v3.3.html}.
26 """
27
28
29 from textwrap import wrap
30
31
32 from lib.errors import RelaxError
33
34
36 """Handle the funky PDB atom name alignment.
37
38 From the PDB format documents:
39
40 - "Alignment of one-letter atom name such as C starts at column 14, while two-letter atom name such as FE starts at column 13."
41
42
43 @param name: The atom name.
44 @type name: str or None
45 @return: The whitespace padded and PDB formatted atom name. This will be exactly 4 characters.
46 @rtype: str
47 """
48
49
50 if name == None:
51 name = " "
52
53
54 if len(name) == 1:
55 name = " %s " % name
56
57
58 elif len(name) == 2:
59 name = "%s " % name
60
61
62 elif len(name) == 3:
63 name = "%s " % name
64
65
66 return name
67
68
70 """Auxiliary function for handling values of None.
71
72 @param value: The value to convert.
73 @type value: anything
74 @return: If the value is None, then an empty string. Otherwise the original value is returned.
75 @rtype: anything
76 """
77
78
79 if value == None:
80 return ''
81
82
83 return value
84
85
86 -def _handle_text(text):
87 """Auxiliary function for handling text values.
88
89 This will convert None to empty strings and make sure everything is capitalised.
90
91
92 @param text: The text to convert.
93 @type text: anything
94 @return: If the text is None, then an empty string. All text will be capitalised.
95 @rtype: anything
96 """
97
98
99 if text == None:
100 return ''
101
102
103 return text.upper()
104
105
107 """Check that the record is ok.
108
109 @param record: The PDB record as text.
110 @type record: str
111 @raises RelaxError: If the record is not exactly 80 characters long.
112 """
113
114
115 if len(record) != 80:
116 if len(record) < 80:
117 raise RelaxError("The PDB record '%s' is too short." % record)
118 else:
119 raise RelaxError("The PDB record '%s' is too long." % record)
120
121
122 if 'nan' in record:
123 raise RelaxError("The PDB record '%s' contains NaN values." % record)
124
125
126 -def atom(file, serial='', name='', alt_loc='', res_name='', chain_id='', res_seq='', icode='', x='', y='', z='', occupancy=1.0, temp_factor=0.0, element='', charge=''):
127 """Generate the ATOM record.
128
129 The following is the PDB v3.3 documentation U{http://www.wwpdb.org/documentation/file-format/format33/sect9.html#ATOM}.
130
131 ATOM
132 ====
133
134 Overview
135 --------
136
137 The ATOM records present the atomic coordinates for standard amino acids and nucleotides. They also present the occupancy and temperature factor for each atom. Non-polymer chemical coordinates use the HETATM record type. The element symbol is always present on each ATOM record; charge is optional.
138
139 Changes in ATOM/HETATM records result from the standardization atom and residue nomenclature. This nomenclature is described in the Chemical Component Dictionary (U{ftp://ftp.wwpdb.org/pub/pdb/data/monomers}).
140
141
142 Record Format
143 -------------
144
145 The format is::
146 __________________________________________________________________________________________
147 | | | | |
148 | Columns | Data type | Field | Definition |
149 |_________|______________|______________|________________________________________________|
150 | | | | |
151 | 1 - 6 | Record name | "ATOM" | |
152 | 7 - 11 | Integer | serial | Atom serial number. |
153 | 13 - 16 | Atom | name | Atom name. |
154 | 17 | Character | altLoc | Alternate location indicator. |
155 | 18 - 20 | Residue name | resName | Residue name. |
156 | 22 | Character | chainID | Chain identifier. |
157 | 23 - 26 | Integer | resSeq | Residue sequence number. |
158 | 27 | AChar | iCode | Code for insertion of residues. |
159 | 31 - 38 | Real(8.3) | x | Orthogonal coordinates for X in Angstroms. |
160 | 39 - 46 | Real(8.3) | y | Orthogonal coordinates for Y in Angstroms. |
161 | 47 - 54 | Real(8.3) | z | Orthogonal coordinates for Z in Angstroms. |
162 | 55 - 60 | Real(6.2) | occupancy | Occupancy. |
163 | 61 - 66 | Real(6.2) | tempFactor | Temperature factor. |
164 | 77 - 78 | LString(2) | element | Element symbol, right-justified. |
165 | 79 - 80 | LString(2) | charge | Charge on the atom. |
166 |_________|______________|______________|________________________________________________|
167
168
169 Details
170 -------
171
172 ATOM records for proteins are listed from amino to carboxyl terminus.
173
174 Nucleic acid residues are listed from the 5' to the 3' terminus.
175
176 Alignment of one-letter atom name such as C starts at column 14, while two-letter atom name such as FE starts at column 13.
177
178 Atom nomenclature begins with atom type.
179
180 No ordering is specified for polysaccharides.
181
182 Non-blank alphanumerical character is used for chain identifier.
183
184 The list of ATOM records in a chain is terminated by a TER record.
185
186 If more than one model is present in the entry, each model is delimited by MODEL and ENDMDL records.
187
188 AltLoc is the place holder to indicate alternate conformation. The alternate conformation can be in the entire polymer chain, or several residues or partial residue (several atoms within one residue). If an atom is provided in more than one position, then a non-blank alternate location indicator must be used for each of the atomic positions. Within a residue, all atoms that are associated with each other in a given conformation are assigned the same alternate position indicator. There are two ways of representing alternate conformation- either at atom level or at residue level (see examples).
189
190 For atoms that are in alternate sites indicated by the alternate site indicator, sorting of atoms in the ATOM/HETATM list uses the following general rules:
191
192 - In the simple case that involves a few atoms or a few residues with alternate sites, the coordinates occur one after the other in the entry.
193 - In the case of a large heterogen groups which are disordered, the atoms for each conformer are listed together.
194
195 Alphabet letters are commonly used for insertion code. The insertion code is used when two residues have the same numbering. The combination of residue numbering and insertion code defines the unique residue.
196
197 If the depositor provides the data, then the isotropic B value is given for the temperature factor.
198
199 If there are neither isotropic B values from the depositor, nor anisotropic temperature factors in ANISOU, then the default value of 0.0 is used for the temperature factor.
200
201 Columns 79 - 80 indicate any charge on the atom, e.g., 2+, 1-. In most cases, these are blank.
202
203 For refinements with program REFMAC prior 5.5.0042 which use TLS refinement, the values of B may include only the TLS contribution to the isotropic temperature factor rather than the full isotropic value.
204
205
206 Verification/Validation/Value Authority Control
207 -----------------------------------------------
208
209 The ATOM/HETATM records are checked for PDB file format, sequence information, and packing.
210
211
212 Relationships to Other Record Types
213 -----------------------------------
214
215 The ATOM records are compared to the corresponding sequence database. Sequence discrepancies appear in the SEQADV record. Missing atoms are annotated in the remarks. HETATM records are formatted in the same way as ATOM records. The sequence implied by ATOM records must be identical to that given in SEQRES, with the exception that residues that have no coordinates, e.g., due to disorder, must appear in SEQRES.
216
217
218 Example
219 -------
220
221 Example 1::
222
223 1 2 3 4 5 6 7 8
224 12345678901234567890123456789012345678901234567890123456789012345678901234567890
225 ATOM 32 N AARG A -3 11.281 86.699 94.383 0.50 35.88 N
226 ATOM 33 N BARG A -3 11.296 86.721 94.521 0.50 35.60 N
227 ATOM 34 CA AARG A -3 12.353 85.696 94.456 0.50 36.67 C
228 ATOM 35 CA BARG A -3 12.333 85.862 95.041 0.50 36.42 C
229 ATOM 36 C AARG A -3 13.559 86.257 95.222 0.50 37.37 C
230 ATOM 37 C BARG A -3 12.759 86.530 96.365 0.50 36.39 C
231 ATOM 38 O AARG A -3 13.753 87.471 95.270 0.50 37.74 O
232 ATOM 39 O BARG A -3 12.924 87.757 96.420 0.50 37.26 O
233 ATOM 40 CB AARG A -3 12.774 85.306 93.039 0.50 37.25 C
234 ATOM 41 CB BARG A -3 13.428 85.746 93.980 0.50 36.60 C
235 ATOM 42 CG AARG A -3 11.754 84.432 92.321 0.50 38.44 C
236 ATOM 43 CG BARG A -3 12.866 85.172 92.651 0.50 37.31 C
237 ATOM 44 CD AARG A -3 11.698 84.678 90.815 0.50 38.51 C
238 ATOM 45 CD BARG A -3 13.374 85.886 91.406 0.50 37.66 C
239 ATOM 46 NE AARG A -3 12.984 84.447 90.163 0.50 39.94 N
240 ATOM 47 NE BARG A -3 12.644 85.487 90.195 0.50 38.24 N
241 ATOM 48 CZ AARG A -3 13.202 84.534 88.850 0.50 40.03 C
242 ATOM 49 CZ BARG A -3 13.114 85.582 88.947 0.50 39.55 C
243 ATOM 50 NH1AARG A -3 12.218 84.840 88.007 0.50 40.76 N
244 ATOM 51 NH1BARG A -3 14.338 86.056 88.706 0.50 40.23 N
245 ATOM 52 NH2AARG A -3 14.421 84.308 88.373 0.50 40.45 N
246
247 Example 2::
248
249 1 2 3 4 5 6 7 8
250 12345678901234567890123456789012345678901234567890123456789012345678901234567890
251 ATOM 32 N AARG A -3 11.281 86.699 94.383 0.50 35.88 N
252 ATOM 33 CA AARG A -3 12.353 85.696 94.456 0.50 36.67 C
253 ATOM 34 C AARG A -3 13.559 86.257 95.222 0.50 37.37 C
254 ATOM 35 O AARG A -3 13.753 87.471 95.270 0.50 37.74 O
255 ATOM 36 CB AARG A -3 12.774 85.306 93.039 0.50 37.25 C
256 ATOM 37 CG AARG A -3 11.754 84.432 92.321 0.50 38.44 C
257 ATOM 38 CD AARG A -3 11.698 84.678 90.815 0.50 38.51 C
258 ATOM 39 NE AARG A -3 12.984 84.447 90.163 0.50 39.94 N
259 ATOM 40 CZ AARG A -3 13.202 84.534 88.850 0.50 40.03 C
260 ATOM 41 NH1AARG A -3 12.218 84.840 88.007 0.50 40.76 N
261 ATOM 42 NH2AARG A -3 14.421 84.308 88.373 0.50 40.45 N
262 ATOM 43 N BARG A -3 11.296 86.721 94.521 0.50 35.60 N
263 ATOM 44 CA BARG A -3 12.333 85.862 95.041 0.50 36.42 C
264 ATOM 45 C BARG A -3 12.759 86.530 96.365 0.50 36.39 C
265 ATOM 46 O BARG A -3 12.924 87.757 96.420 0.50 37.26 O
266 ATOM 47 CB BARG A -3 13.428 85.746 93.980 0.50 36.60 C
267 ATOM 48 CG BARG A -3 12.866 85.172 92.651 0.50 37.31 C
268 ATOM 49 CD BARG A -3 13.374 85.886 91.406 0.50 37.66 C
269 ATOM 50 NE BARG A -3 12.644 85.487 90.195 0.50 38.24 N
270 ATOM 51 CZ BARG A -3 13.114 85.582 88.947 0.50 39.55 C
271 ATOM 52 NH1BARG A -3 14.338 86.056 88.706 0.50 40.23 N
272
273
274 @param file: The file to write the record to.
275 @type file: file object
276 @keyword serial: The atom serial number.
277 @type serial: int
278 @keyword name: The atom name.
279 @type name: str
280 @keyword alt_loc: The alternate location indicator.
281 @type alt_loc: str
282 @keyword res_name: The residue name.
283 @type res_name: str
284 @keyword chain_id: The chain identifier.
285 @type chain_id: str
286 @keyword res_seq: The sequence number.
287 @type res_seq: int
288 @keyword icode: The insertion code.
289 @type icode: str
290 @keyword x: Orthogonal coordinates for X in Angstroms.
291 @type x: float
292 @keyword y: Orthogonal coordinates for Y in Angstroms.
293 @type y: float
294 @keyword z: Orthogonal coordinates for Z in Angstroms.
295 @type z: float
296 @keyword occupancy: Occupancy.
297 @type occupancy: float
298 @keyword temp_factor: Temperature factor.
299 @type temp_factor: float
300 @keyword element: Element symbol.
301 @type element: str
302 @keyword charge: Charge on the atom.
303 @type charge: int
304 """
305
306
307 pdb_min = -999.999
308 pdb_max = 9999.999
309 coord = [x, y, z]
310 for i in range(3):
311 if coord[i] != '' and coord[i] < pdb_min:
312 coord[i] = pdb_min
313 if coord[i] != '' and coord[i] > pdb_max:
314 coord[i] = pdb_max
315
316
317 text = "%-6s%5s %-4s%1s%3s %1s%4s%1s %8.3f%8.3f%8.3f%6.2f%6.2f %2s%2s" % (
318 'ATOM',
319 _handle_none(serial),
320 _handle_atom_name(name),
321 _handle_none(alt_loc),
322 _handle_none(res_name),
323 _handle_none(chain_id),
324 _handle_none(res_seq),
325 _handle_none(icode),
326 _handle_none(coord[0]),
327 _handle_none(coord[1]),
328 _handle_none(coord[2]),
329 _handle_none(occupancy),
330 _handle_none(temp_factor),
331 _handle_none(element),
332 _handle_none(charge)
333 )
334
335
336 _record_validate(text)
337
338
339 file.write(text)
340 file.write('\n')
341
342
343 -def conect(file, serial='', bonded1='', bonded2='', bonded3='', bonded4=''):
344 """Generate the CONECT record.
345
346 The following is the PDB v3.3 documentation U{http://www.wwpdb.org/documentation/file-format/format33/sect10.html#CONECT}.
347
348 CONECT
349 ======
350
351 Overview
352 --------
353
354 The CONECT records specify connectivity between atoms for which coordinates are supplied. The connectivity is described using the atom serial number as shown in the entry. CONECT records are mandatory for HET groups (excluding water) and for other bonds not specified in the standard residue connectivity table. These records are generated automatically.
355
356 Record Format
357 -------------
358
359 The format is::
360 ______________________________________________________________________________________________
361 | | | | |
362 | Columns | Data type | Field | Definition |
363 |_________|______________|______________|____________________________________________________|
364 | | | | |
365 | 1 - 6 | Record name | "CONECT" | |
366 | 7 - 11 | Integer | serial | Atom serial number |
367 | 12 - 16 | Integer | serial | Serial number of bonded atom |
368 | 17 - 21 | Integer | serial | Serial number of bonded atom |
369 | 22 - 26 | Integer | serial | Serial number of bonded atom |
370 | 27 - 31 | Integer | serial | Serial number of bonded atom |
371 |_________|______________|______________|____________________________________________________|
372
373
374 Details
375 -------
376
377 CONECT records are present for:
378
379 - Intra-residue connectivity within non-standard (HET) residues (excluding water).
380 - Inter-residue connectivity of HET groups to standard groups (including water) or to other HET groups.
381 - Disulfide bridges specified in the SSBOND records have corresponding records.
382
383 No differentiation is made between atoms with delocalized charges (excess negative or positive charge).
384
385 Atoms specified in the CONECT records have the same numbers as given in the coordinate section.
386
387 All atoms connected to the atom with serial number in columns 7 - 11 are listed in the remaining fields of the record.
388
389 If more than four fields are required for non-hydrogen and non-salt bridges, a second CONECT record with the same atom serial number in columns 7 - 11 will be used.
390
391 These CONECT records occur in increasing order of the atom serial numbers they carry in columns 7 - 11. The target-atom serial numbers carried on these records also occur in increasing order.
392
393 The connectivity list given here is redundant in that each bond indicated is given twice, once with each of the two atoms involved specified in columns 7 - 11.
394
395 For hydrogen bonds, when the hydrogen atom is present in the coordinates, a CONECT record between the hydrogen atom and its acceptor atom is generated.
396
397 For NMR entries, CONECT records for one model are generated describing heterogen connectivity and others for LINK records assuming that all models are homogeneous models.
398
399
400 Verification/Validation/Value Authority Control
401 -----------------------------------------------
402
403 Connectivity is checked for unusual bond lengths.
404
405
406 Relationships to Other Record Types
407 -----------------------------------
408
409 CONECT records must be present in an entry that contains either non-standard groups or disulfide bonds.
410
411
412 Example
413 -------
414
415 Example 1::
416
417 1 2 3 4 5 6 7 8
418 12345678901234567890123456789012345678901234567890123456789012345678901234567890
419 CONECT 1179 746 1184 1195 1203
420 CONECT 1179 1211 1222
421 CONECT 1021 544 1017 1020 1022
422
423
424 Known Problems
425 --------------
426
427 CONECT records involving atoms for which the coordinates are not present in the entry (e.g., symmetry-generated) are not given.
428
429 CONECT records involving atoms for which the coordinates are missing due to disorder, are also not provided.
430
431
432 @param file: The file to write the record to.
433 @type file: file object
434 @keyword serial: The atom serial number.
435 @type serial: int
436 @keyword bonded1: The serial number of the bonded atom.
437 @type bonded1: int
438 @keyword bonded2: The serial number of the bonded atom.
439 @type bonded2: int
440 @keyword bonded3: The serial number of the bonded atom.
441 @type bonded3: int
442 @keyword bonded4: The serial number of the bonded atom.
443 @type bonded4: int
444 """
445
446
447 text = "%-6s%5s%5s%5s%5s%5s%49s" % (
448 'CONECT',
449 _handle_none(serial),
450 _handle_none(bonded1),
451 _handle_none(bonded2),
452 _handle_none(bonded3),
453 _handle_none(bonded4),
454 ''
455 )
456
457
458 _record_validate(text)
459
460
461 file.write(text)
462 file.write('\n')
463
464
466 """Generate the END record.
467
468 The following is the PDB v3.3 documentation U{http://www.wwpdb.org/documentation/file-format/format33/sect11.html#END}.
469
470 END
471 ===
472
473 Overview
474 --------
475
476 The END record marks the end of the PDB file.
477
478
479 Record Format
480 -------------
481
482 The format is::
483 ______________________________________________________________________________________________
484 | | | | |
485 | Columns | Data type | Field | Definition |
486 |_________|______________|______________|____________________________________________________|
487 | | | | |
488 | 1 - 6 | Record name | "END " | |
489 |_________|______________|______________|____________________________________________________|
490
491
492 Details
493 -------
494
495 END is the final record of a coordinate entry.
496
497
498 Verification/Validation/Value Authority Control
499 -----------------------------------------------
500
501 END must appear in every coordinate entry.
502
503
504 Relationships to Other Record Types
505 -----------------------------------
506
507 This is the final record in the entry.
508
509
510 Example
511 -------
512
513 Example 1::
514
515 1 2 3 4 5 6 7 8
516 12345678901234567890123456789012345678901234567890123456789012345678901234567890
517 END
518
519
520 @param file: The file to write the record to.
521 @type file: file object
522 """
523
524
525 text = "END" + ' '*77
526
527
528 _record_validate(text)
529
530
531 file.write(text)
532 file.write('\n')
533
534
536 """Generate the ENDMDL record.
537
538 The following is the PDB v3.3 documentation U{http://www.wwpdb.org/documentation/file-format/format33/v3.3.html}.
539
540 ENDMDL
541 ======
542
543 Overview
544 --------
545
546 The ENDMDL records are paired with MODEL records to group individual structures found in a coordinate entry.
547
548
549 Record Format
550 -------------
551
552 The format is::
553 ______________________________________________________________________________________________
554 | | | | |
555 | Columns | Data type | Field | Definition |
556 |_________|______________|______________|____________________________________________________|
557 | | | | |
558 | 1 - 6 | Record name | "ENDMDL" | |
559 |_________|______________|______________|____________________________________________________|
560
561
562 Details
563 -------
564
565 MODEL/ENDMDL records are used only when more than one structure is presented in the entry, as is often the case with NMR entries.
566
567 All the models in a multi-model entry must represent the same structure.
568
569 Every MODEL record has an associated ENDMDL record.
570
571
572 Verification/Validation/Value Authority Control
573 -----------------------------------------------
574
575 Entries with multiple structures in the NUMMDL record are checked for corresponding pairs of MODEL/ ENDMDL records, and for consecutively numbered models.
576
577
578 Relationships to Other Record Types
579 -----------------------------------
580
581 There must be a corresponding MODEL record.
582
583 In the case of an NMR entry, the NUMMDL record states the number of model structures that are present in the individual entry.
584
585
586 Example
587 -------
588
589 Example 1::
590
591 1 2 3 4 5 6 7 8
592 12345678901234567890123456789012345678901234567890123456789012345678901234567890
593 ...
594 ...
595 ATOM 14550 1HG GLU 122 -14.364 14.787 -14.258 1.00 0.00 H
596 ATOM 14551 2HG GLU 122 -13.794 13.738 -12.961 1.00 0.00 H
597 TER 14552 GLU 122
598 ENDMDL
599 MODEL 9
600 ATOM 14553 N SER 1 -28.280 1.567 12.004 1.00 0.00 N
601 ATOM 14554 CA SER 1 -27.749 0.392 11.256 1.00 0.00 C
602 ...
603 ...
604 ATOM 16369 1HG GLU 122 -3.757 18.546 -8.439 1.00 0.00 H
605 ATOM 16370 2HG GLU 122 -3.066 17.166 -7.584 1.00 0.00 H
606 TER 16371 GLU 122
607 ENDMDL
608
609
610 @param file: The file to write the record to.
611 @type file: file object
612 """
613
614
615 text = 'ENDMDL' + ' '*74
616
617
618 _record_validate(text)
619
620
621 file.write(text)
622 file.write('\n')
623
624
735
736
737 -def helix(file, ser_num='', helix_id='', init_res_name='', init_chain_id='', init_seq_num='', init_icode='', end_res_name='', end_chain_id='', end_seq_num='', end_icode='', helix_class='', comment='', length=''):
738 """Generate the HELIX record.
739
740 The following is the PDB v3.3 documentation U{http://www.wwpdb.org/documentation/file-format/format33/sect5.html#HELIX}.
741
742 HELIX
743 =====
744
745 Overview
746 --------
747
748 HELIX records are used to identify the position of helices in the molecule. Helices are named, numbered, and classified by type. The residues where the helix begins and ends are noted, as well as the total length.
749
750
751 Record Format
752 -------------
753
754 The format is::
755 ______________________________________________________________________________________________
756 | | | | |
757 | Columns | Data type | Field | Definition |
758 |_________|______________|______________|____________________________________________________|
759 | | | | |
760 | 1 - 6 | Record name | "HELIX " | |
761 | 8 - 10 | Integer | serNum | Serial number of the helix. This starts at 1 and |
762 | | | | increases incrementally. |
763 | 12 - 14 | LString(3) | helixID | Helix identifier. In addition to a serial number, |
764 | | | | each helix is given an alphanumeric character |
765 | | | | helix identifier. |
766 | 16 - 18 | Residue name | initResName | Name of the initial residue. |
767 | 20 | Character | initChainID | Chain identifier for the chain containing this |
768 | | | | helix. |
769 | 22 - 25 | Integer | initSeqNum | Sequence number of the initial residue. |
770 | 26 | AChar | initICode | Insertion code of the initial residue. |
771 | 28 - 30 | Residue name | endResName | Name of the terminal residue of the helix. |
772 | 32 | Character | endChainID | Chain identifier for the chain containing this |
773 | | | | helix. |
774 | 34 - 37 | Integer | endSeqNum | Sequence number of the terminal residue. |
775 | 38 | AChar | endICode | Insertion code of the terminal residue. |
776 | 39 - 40 | Integer | helixClass | Helix class (see below). |
777 | 41 - 70 | String | comment | Comment about this helix. |
778 | 72 - 76 | Integer | length | Length of this helix. |
779 |_________|______________|______________|____________________________________________________|
780
781
782 Details
783 -------
784
785 Additional HELIX records with different serial numbers and identifiers occur if more than one helix is present.
786
787 The initial residue of the helix is the N-terminal residue.
788
789 Helices are classified as follows::
790
791 _____________________________________________________
792 | | CLASS NUMBER |
793 | TYPE OF HELIX | (COLUMNS 39 - 40) |
794 |_______________________________|___________________|
795 | | |
796 | Right-handed alpha (default) | 1 |
797 | Right-handed omega | 2 |
798 | Right-handed pi | 3 |
799 | Right-handed gamma | 4 |
800 | Right-handed 3 - 10 | 5 |
801 | Left-handed alpha | 6 |
802 | Left-handed omega | 7 |
803 | Left-handed gamma | 8 |
804 | 2 - 7 ribbon/helix | 9 |
805 | Polyproline | 10 |
806 |_______________________________|___________________|
807
808
809 Relationships to Other Record Types
810 -----------------------------------
811
812 There may be related information in the REMARKs.
813
814
815 Example
816 -------
817
818 Example 1::
819
820 1 2 3 4 5 6 7 8
821 12345678901234567890123456789012345678901234567890123456789012345678901234567890
822 HELIX 1 HA GLY A 86 GLY A 94 1 9
823 HELIX 2 HB GLY B 86 GLY B 94 1 9
824
825 HELIX 21 21 PRO J 385 LEU J 388 5 4
826 HELIX 22 22 PHE J 397 PHE J 402 5 6
827
828
829 @param file: The file to write the record to.
830 @type file: file object
831 @keyword ser_num: The helix serial number
832 @type ser_num: int
833 @keyword helix_id: The helix identifier
834 @type helix_id: str
835 @keyword init_res_name: The name of the initial residue
836 @type init_res_name: str
837 @keyword init_chain_id: The chain identifier
838 @type init_chain_id: str
839 @keyword init_seq_num: The sequence number of the initial residue
840 @type init_seq_num: int
841 @keyword init_icode: The insertion code of the initial residue
842 @type init_icode: str
843 @keyword end_res_name: The name of the terminal residue
844 @type end_res_name: str
845 @keyword end_chain_id: The chain identifier
846 @type end_chain_id: str
847 @keyword end_seq_num: The sequence number of the terminal residue
848 @type end_seq_num: int
849 @keyword end_icode: The insertion code of the terminal residue
850 @type end_icode: str
851 @keyword helix_class: The helix class
852 @type helix_class: int
853 @keyword comment: The comment
854 @type comment: str
855 @keyword length: The helix length.
856 @type length: int
857 """
858
859
860 text = "%-6s %3s %3s %3s %1s %4s%1s %3s %1s %4s%1s%2s%30s %5s " % (
861 'HELIX',
862 _handle_none(ser_num),
863 _handle_none(helix_id),
864 _handle_none(init_res_name),
865 _handle_none(init_chain_id),
866 _handle_none(init_seq_num),
867 _handle_none(init_icode),
868 _handle_none(end_res_name),
869 _handle_none(end_chain_id),
870 _handle_none(end_seq_num),
871 _handle_none(end_icode),
872 _handle_none(helix_class),
873 _handle_none(comment),
874 _handle_none(length)
875 )
876
877
878 _record_validate(text)
879
880
881 file.write(text)
882 file.write('\n')
883
884
885 -def het(file, het_id='', chain_id='', seq_num='', icode='', num_het_atoms='', text=''):
886 """Generate the HET record.
887
888 The following is the PDB v3.3 documentation U{http://www.wwpdb.org/documentation/file-format/format33/sect4.html#HET}.
889
890 HET
891 ===
892
893 Overview
894 --------
895
896 HET records are used to describe non-standard residues, such as prosthetic groups, inhibitors, solvent molecules, and ions for which coordinates are supplied. Groups are considered HET if they are not part of a biological polymer described in SEQRES and considered to be a molecule bound to the polymer, or they are a chemical species that constitute part of a biological polymer and is not one of the following:
897
898 - standard amino acids, or
899 - standard nucleic acids (C, G, A, U, I, DC, DG, DA, DU, DT and DI), or
900 - unknown amino acid (UNK) or nucleic acid (N) where UNK and N are used to indicate the unknown residue name.
901
902 HET records also describe chemical components for which the chemical identity is unknown, in which case the group is assigned the hetID UNL (Unknown Ligand).
903
904 The heterogen section of a PDB formatted file contains the complete description of non-standard residues in the entry.
905
906
907 Record Format
908 -------------
909
910 The format is::
911 ______________________________________________________________________________________________
912 | | | | |
913 | Columns | Data type | Field | Definition |
914 |_________|______________|______________|____________________________________________________|
915 | | | | |
916 | 1 - 6 | Record name | "HET " | |
917 | 8 - 10 | LString(3) | hetID | Het identifier, right-justified. |
918 | 13 | Character | ChainID | Chain identifier. |
919 | 14 - 17 | Integer | seqNum | Sequence number. |
920 | 18 | AChar | iCode | Insertion code. |
921 | 21 - 25 | Integer | numHetAtoms | Number of HETATM records for the group present in |
922 | | | | the entry. |
923 | 31 - 70 | String | text | Text describing Het group. |
924 |_________|______________|______________|____________________________________________________|
925
926
927 Details
928 -------
929
930 Each HET group is assigned a hetID of not more than three (3) alphanumeric characters. The sequence number, chain identifier, insertion code, and number of coordinate records are given for each occurrence of the HET group in the entry. The chemical name of the HET group is given in the HETNAM record and synonyms for the chemical name are given in the HETSYN records, see U{ftp://ftp.wwpdb.org/pub/pdb/data/monomers}.
931
932 There is a separate HET record for each occurrence of the HET group in an entry.
933
934 A particular HET group is represented in the PDB archive with a unique hetID.
935
936 PDB entries do not have HET records for water molecules, deuterated water, or methanol (when used as solvent).
937
938 Unknown atoms or ions will be represented as UNX with the chemical formula X1. Unknown ligands are UNL; unknown amino acids are UNK.
939
940
941 Verification/Validation/Value Authority Control
942 -----------------------------------------------
943
944 For each het group that appears in the entry, the wwPDB checks that the corresponding HET, HETNAM, HETSYN, FORMUL, HETATM, and CONECT records appear, if applicable. The HET record is generated automatically using the Chemical Component Dictionary and information from the HETATM records.
945
946 Each unique hetID represents a unique molecule.
947
948
949 Relationships to Other Record Types
950 -----------------------------------
951
952 For each het group that appears in the entry, there must be corresponding HET, HETNAM, HETSYN, FORMUL,HETATM, and CONECT records. LINK records may also be created.
953
954
955 Example
956 -------
957
958 Example 1::
959
960 1 2 3 4 5 6 7 8
961 12345678901234567890123456789012345678901234567890123456789012345678901234567890
962 HET TRS B 975 8
963
964 HET UDP A1457 25
965 HET B3P A1458 19
966
967 HET NAG Y 3 15
968 HET FUC Y 4 10
969 HET NON Y 5 12
970 HET UNK A 161 1
971
972
973 @param file: The file to write the record to.
974 @type file: file object
975 @keyword het_id: The Het identifier.
976 @type het_id: str
977 @keyword chain_id: The chain identifier.
978 @type chain_id: str
979 @keyword seq_num: The sequence number.
980 @type seq_num: int
981 @keyword icode: The insertion code.
982 @type icode: str
983 @keyword num_het_atoms: The number of HETATM records for the group present in the entry.
984 @type num_het_atoms: int
985 @keyword text: Text describing the Het group.
986 @type text: str
987 """
988
989
990 text = "%-6s %3s %1s%4s%1s %5s %-40s%10s" % (
991 'HET',
992 _handle_none(het_id),
993 _handle_none(chain_id),
994 _handle_none(seq_num),
995 _handle_none(icode),
996 _handle_none(num_het_atoms),
997 _handle_text(text),
998 ''
999 )
1000
1001
1002 _record_validate(text)
1003
1004
1005 file.write(text)
1006 file.write('\n')
1007
1008
1009 -def hetatm(file, serial='', name='', alt_loc='', res_name='', chain_id='', res_seq='', icode='', x='', y='', z='', occupancy=1.0, temp_factor=0.0, element='', charge=''):
1010 """Generate the HETATM record.
1011
1012 The following is the PDB v3.3 documentation U{http://www.wwpdb.org/documentation/file-format/format33/sect9.html#HETATM}.
1013
1014 HETATM
1015 ======
1016
1017 Overview
1018 --------
1019
1020 Non-polymer or other "non-standard" chemical coordinates, such as water molecules or atoms presented in HET groups use the HETATM record type. They also present the occupancy and temperature factor for each atom. The ATOM records present the atomic coordinates for standard residues. The element symbol is always present on each HETATM record; charge is optional.
1021
1022 Changes in ATOM/HETATM records will require standardization in atom and residue nomenclature. This nomenclature is described in the Chemical Component Dictionary, U{ftp://ftp.wwpdb.org/pub/pdb/data/monomers}.
1023
1024
1025 Record Format
1026 -------------
1027
1028 The format is::
1029 ______________________________________________________________________________________________
1030 | | | | |
1031 | Columns | Data type | Field | Definition |
1032 |_________|______________|______________|____________________________________________________|
1033 | | | | |
1034 | 1 - 6 | Record name | "HETATM" | |
1035 | 7 - 11 | Integer | serial | Atom serial number. |
1036 | 13 - 16 | Atom | name | Atom name. |
1037 | 17 | Character | altLoc | Alternate location indicator. |
1038 | 18 - 20 | Residue name | resName | Residue name. |
1039 | 22 | Character | chainID | Chain identifier. |
1040 | 23 - 26 | Integer | resSeq | Residue sequence number. |
1041 | 27 | AChar | iCode | Code for insertion of residues. |
1042 | 31 - 38 | Real(8.3) | x | Orthogonal coordinates for X. |
1043 | 39 - 46 | Real(8.3) | y | Orthogonal coordinates for Y. |
1044 | 47 - 54 | Real(8.3) | z | Orthogonal coordinates for Z. |
1045 | 55 - 60 | Real(6.2) | occupancy | Occupancy. |
1046 | 61 - 66 | Real(6.2) | tempFactor | Temperature factor. |
1047 | 77 - 78 | LString(2) | element | Element symbol; right-justified. |
1048 | 79 - 80 | LString(2) | charge | Charge on the atom. |
1049 |_________|______________|______________|____________________________________________________|
1050
1051
1052 Details
1053 -------
1054
1055 The x, y, z coordinates are in Angstrom units.
1056
1057 No ordering is specified for polysaccharides.
1058
1059 See the HET section of this document regarding naming of heterogens. See the Chemical Component Dictionary for residue names, formulas, and topology of the HET groups that have appeared so far in the PDB (see U{ftp://ftp.wwpdb.org/pub/pdb/data/monomers}).
1060
1061 If the depositor provides the data, then the isotropic B value is given for the temperature factor.
1062
1063 If there are neither isotropic B values provided by the depositor, nor anisotropic temperature factors in ANISOU, then the default value of 0.0 is used for the temperature factor.
1064
1065 Insertion codes and element naming are fully described in the ATOM section of this document.
1066
1067
1068 Verification/Validation/Value Authority Control
1069 -----------------------------------------------
1070
1071 Processing programs check ATOM/HETATM records for PDB file format, sequence information, and packing.
1072
1073
1074 Relationships to Other Record Types
1075 -----------------------------------
1076
1077 HETATM records must have corresponding HET, HETNAM, FORMUL and CONECT records, except for waters.
1078
1079
1080 Example
1081 -------
1082
1083 Example 1::
1084
1085 1 2 3 4 5 6 7 8
1086 12345678901234567890123456789012345678901234567890123456789012345678901234567890
1087 HETATM 8237 MG MG A1001 13.872 -2.555 -29.045 1.00 27.36 MG
1088
1089 HETATM 3835 FE HEM A 1 17.140 3.115 15.066 1.00 14.14 FE
1090 HETATM 8238 S SO4 A2001 10.885 -15.746 -14.404 1.00 47.84 S
1091 HETATM 8239 O1 SO4 A2001 11.191 -14.833 -15.531 1.00 50.12 O
1092 HETATM 8240 O2 SO4 A2001 9.576 -16.338 -14.706 1.00 48.55 O
1093 HETATM 8241 O3 SO4 A2001 11.995 -16.703 -14.431 1.00 49.88 O
1094 HETATM 8242 O4 SO4 A2001 10.932 -15.073 -13.100 1.00 49.91 O
1095
1096
1097 @param file: The file to write the record to.
1098 @type file: file object
1099 @keyword serial: The atom serial number.
1100 @type serial: int
1101 @keyword name: The atom name.
1102 @type name: str
1103 @keyword alt_loc: The alternate location indicator.
1104 @type alt_loc: str
1105 @keyword res_name: The residue name.
1106 @type res_name: str
1107 @keyword chain_id: The chain identifier.
1108 @type chain_id: str
1109 @keyword res_seq: The sequence number.
1110 @type res_seq: int
1111 @keyword icode: The insertion code.
1112 @type icode: str
1113 @keyword x: Orthogonal coordinates for X in Angstroms.
1114 @type x: float
1115 @keyword y: Orthogonal coordinates for Y in Angstroms.
1116 @type y: float
1117 @keyword z: Orthogonal coordinates for Z in Angstroms.
1118 @type z: float
1119 @keyword occupancy: Occupancy.
1120 @type occupancy: float
1121 @keyword temp_factor: Temperature factor.
1122 @type temp_factor: float
1123 @keyword element: Element symbol.
1124 @type element: str
1125 @keyword charge: Charge on the atom.
1126 @type charge: int
1127 """
1128
1129
1130 pdb_min = -999.999
1131 pdb_max = 9999.999
1132 coord = [x, y, z]
1133 for i in range(3):
1134 if coord[i] != '' and coord[i] < pdb_min:
1135 coord[i] = pdb_min
1136 if coord[i] != '' and coord[i] > pdb_max:
1137 coord[i] = pdb_max
1138
1139
1140 text = "%-6s%5s %4s%1s%3s %1s%4s%1s %8.3f%8.3f%8.3f%6.2f%6.2f %2s%2s" % (
1141 'HETATM',
1142 _handle_none(serial),
1143 _handle_none(name),
1144 _handle_none(alt_loc),
1145 _handle_none(res_name),
1146 _handle_none(chain_id),
1147 _handle_none(res_seq),
1148 _handle_none(icode),
1149 _handle_none(coord[0]),
1150 _handle_none(coord[1]),
1151 _handle_none(coord[2]),
1152 _handle_none(occupancy),
1153 _handle_none(temp_factor),
1154 _handle_none(element),
1155 _handle_none(charge)
1156 )
1157
1158
1159 _record_validate(text)
1160
1161
1162 file.write(text)
1163 file.write('\n')
1164
1165
1166 -def hetnam(file, continuation='', het_id='', text=''):
1167 """Generate the HETNAM record.
1168
1169 The following is the PDB v3.3 documentation U{http://www.wwpdb.org/documentation/file-format/format33/sect4.html#HETNAM}.
1170
1171 HETNAM
1172 ======
1173
1174 Overview
1175 --------
1176
1177 This record gives the chemical name of the compound with the given hetID.
1178
1179
1180 Record Format
1181 -------------
1182
1183 The format is::
1184 ______________________________________________________________________________________________
1185 | | | | |
1186 | Columns | Data type | Field | Definition |
1187 |_________|______________|______________|____________________________________________________|
1188 | | | | |
1189 | 1 - 6 | Record name | "HETNAM" | |
1190 | 9 - 10 | Continuation | continuation | Allows concatenation of multiple records. |
1191 | 12 - 14 | LString(3) | hetID | Het identifier, right-justified. |
1192 | 16 - 70 | String | text | Chemical name. |
1193 |_________|______________|______________|____________________________________________________|
1194
1195
1196 Details
1197 -------
1198
1199 Each hetID is assigned a unique chemical name for the HETNAM record, see U{ftp://ftp.wwpdb.org/pub/pdb/data/monomers}.
1200
1201 Other names for the group are given on HETSYN records.
1202
1203 PDB entries follow IUPAC/IUB naming conventions to describe groups systematically.
1204
1205 The special character "~" is used to indicate superscript in a heterogen name. For example: N6 will be listed in the HETNAM section as N~6~, with the ~ character indicating both the start and end of the superscript in the name, e.g.:
1206
1207 - N-(BENZYLSULFONYL)SERYL-N~1~-{4-[AMINO(IMINO)METHYL]BENZYL}GLYCINAMIDE
1208
1209 Continuation of chemical names onto subsequent records is allowed.
1210
1211 Only one HETNAM record is included for a given hetID, even if the same hetID appears on more than one HET record.
1212
1213
1214 Verification/Validation/Value Authority Control
1215 -----------------------------------------------
1216
1217 For each het group that appears in the entry, the corresponding HET, HETNAM, FORMUL, HETATM, and CONECT records must appear. The HETNAM record is generated automatically using the Chemical Component Dictionary and information from HETATM records.
1218
1219
1220 Relationships to Other Record Types
1221 -----------------------------------
1222
1223 For each het group that appears in the entry, there must be corresponding HET, HETNAM, FORMUL, HETATM, and CONECT records. HETSYN and LINK records may also be created.
1224
1225
1226 Example
1227 -------
1228
1229 Example 1::
1230
1231 1 2 3 4 5 6 7 8
1232 12345678901234567890123456789012345678901234567890123456789012345678901234567890
1233 HETNAM NAG N-ACETYL-D-GLUCOSAMINE
1234 HETNAM SAD BETA-METHYLENE SELENAZOLE-4-CARBOXAMIDE ADENINE
1235 HETNAM 2 SAD DINUCLEOTIDE
1236
1237 HETNAM UDP URIDINE-5'-DIPHOSPHATE
1238
1239 HETNAM UNX UNKNOWN ATOM OR ION
1240 HETNAM UNL UNKNOWN LIGAND
1241
1242 HETNAM B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-
1243 HETNAM 2 B3P PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
1244
1245
1246 @param file: The file to write the record to.
1247 @type file: file object
1248 @keyword continuation: Allows concatenation of multiple records.
1249 @type continuation: int
1250 @keyword het_id: The Het identifier.
1251 @type het_id: str
1252 @keyword text: The chemical name.
1253 @type text: str
1254 """
1255
1256
1257 text = "%-6s %2s %3s %-55s%10s" % (
1258 'HETNAM',
1259 _handle_none(continuation),
1260 _handle_none(het_id),
1261 _handle_text(text),
1262 ''
1263 )
1264
1265
1266 _record_validate(text)
1267
1268
1269 file.write(text)
1270 file.write('\n')
1271
1272
1273 -def master(file, num_remark=0, num_het=0, num_helix=0, num_sheet=0, num_turn=0, num_site=0, num_xform=0, num_coord=0, num_ter=0, num_conect=0, num_seq=0):
1274 """Generate the MASTER record.
1275
1276 The following is the PDB v3.3 documentation U{http://www.wwpdb.org/documentation/file-format/format33/sect11.html#MASTER}.
1277
1278 MASTER
1279 ======
1280
1281 Overview
1282 --------
1283
1284 The MASTER record is a control record for bookkeeping. It lists the number of lines in the coordinate entry or file for selected record types. MASTER records only the first model when there are multiple models in the coordinates.
1285
1286
1287 Record Format
1288 -------------
1289
1290 The format is::
1291 ______________________________________________________________________________________________
1292 | | | | |
1293 | Columns | Data type | Field | Definition |
1294 |_________|______________|______________|____________________________________________________|
1295 | | | | |
1296 | 1 - 6 | Record name | "MASTER" | |
1297 | 11 - 15 | Integer | numRemark | Number of REMARK records |
1298 | 16 - 20 | Integer | "0" | |
1299 | 21 - 25 | Integer | numHet | Number of HET records |
1300 | 26 - 30 | Integer | numHelix | Number of HELIX records |
1301 | 31 - 35 | Integer | numSheet | Number of SHEET records |
1302 | 36 - 40 | Integer | numTurn | deprecated |
1303 | 41 - 45 | Integer | numSite | Number of SITE records |
1304 | 46 - 50 | Integer | numXform | Number of coordinate transformation records |
1305 | | | | (ORIGX+SCALE+MTRIX) |
1306 | 51 - 55 | Integer | numCoord | Number of atomic coordinate records (ATOM+HETATM) |
1307 | 56 - 60 | Integer | numTer | Number of TER records |
1308 | 61 - 65 | Integer | numConect | Number of CONECT records |
1309 | 66 - 70 | Integer | numSeq | Number of SEQRES records |
1310 |_________|______________|______________|____________________________________________________|
1311
1312
1313 Details
1314 -------
1315
1316 MASTER gives checksums of the number of records in the entry, for selected record types.
1317
1318 MASTER records only the first model when there are multiple models in the coordinates.
1319
1320
1321 Verification/Validation/Value Authority Control
1322 -----------------------------------------------
1323
1324 The MASTER line is automatically generated.
1325
1326
1327 Relationships to Other Record Types
1328 -----------------------------------
1329
1330 MASTER presents a checksum of the lines present for each of the record types listed above.
1331
1332
1333 Example
1334 -------
1335
1336 Example 1::
1337
1338 1 2 3 4 5 6 7 8
1339 12345678901234567890123456789012345678901234567890123456789012345678901234567890
1340 MASTER 40 0 0 0 0 0 0 6 2930 2 0 29
1341
1342
1343 @param file: The file to write the record to.
1344 @type file: file object
1345 @keyword num_remark: The number of REMARK records.
1346 @type num_remark: int
1347 @keyword num_het: The number of HET records.
1348 @type num_het: int
1349 @keyword num_helix: The number of HELIX records.
1350 @type num_helix: int
1351 @keyword num_sheet: The number of SHEET records.
1352 @type num_sheet: int
1353 @keyword num_turn: Depreciated.
1354 @type num_turn: int
1355 @keyword num_site: The number of SITE records.
1356 @type num_site: int
1357 @keyword num_xform: The number of coordinate transformation records (ORIGX+SCALE+MTRIX).
1358 @type num_xform: int
1359 @keyword num_coord: The number of atomic coordinate records (ATOM+HETATM).
1360 @type num_coord: int
1361 @keyword num_ter: The number of TER records.
1362 @type num_ter: int
1363 @keyword num_conect: The number of CONECT records.
1364 @type num_conect: int
1365 @keyword num_seq The number of SEQRES records.
1366 @type num_seq int
1367 """
1368
1369
1370 text = "%-6s %5s%5s%5s%5s%5s%5s%5s%5s%5s%5s%5s%5s%10s" % (
1371 'MASTER',
1372 _handle_none(num_remark),
1373 0,
1374 _handle_none(num_het),
1375 _handle_none(num_helix),
1376 _handle_none(num_sheet),
1377 _handle_none(num_turn),
1378 _handle_none(num_site),
1379 _handle_none(num_xform),
1380 _handle_none(num_coord),
1381 _handle_none(num_ter),
1382 _handle_none(num_conect),
1383 _handle_none(num_seq),
1384 ''
1385 )
1386
1387
1388 _record_validate(text)
1389
1390
1391 file.write(text)
1392 file.write('\n')
1393
1394
1395 -def model(file, serial=''):
1396 """Generate the MODEL record.
1397
1398 The following is the PDB v3.3 documentation U{http://www.wwpdb.org/documentation/file-format/format33/sect9.html#MODEL}.
1399
1400 MODEL
1401 =====
1402
1403 Overview
1404 --------
1405
1406 The MODEL record specifies the model serial number when multiple models of the same structure are presented in a single coordinate entry, as is often the case with structures determined by NMR.
1407
1408
1409 Record Format
1410 -------------
1411
1412 The format is::
1413 ______________________________________________________________________________________________
1414 | | | | |
1415 | Columns | Data type | Field | Definition |
1416 |_________|______________|______________|____________________________________________________|
1417 | | | | |
1418 | 1 - 6 | Record name | "MODEL " | |
1419 | 11 - 14 | Integer | serial | Model serial number. |
1420 |_________|______________|______________|____________________________________________________|
1421
1422
1423 Details
1424 -------
1425
1426 This record is used only when more than one model appears in an entry. Generally, it is employed mainly for NMR structures. The chemical connectivity should be the same for each model. ATOM, HETATM, ANISOU, and TER records for each model structure and are interspersed as needed between MODEL and ENDMDL records.
1427
1428 The numbering of models is sequential, beginning with 1.
1429
1430 All models in a deposition should be superimposed in an appropriate author determined manner and only one superposition method should be used. Structures from different experiments, or different domains of a structure should not be superimposed and deposited as models of a deposition.
1431
1432 All models in an NMR ensemble should be homogeneous - each model should have the exact same atoms (hydrogen and heavy atoms), sequence and chemistry.
1433
1434 All models in an NMR entry should have hydrogen atoms.
1435
1436 Deposition of minimized average structure must be accompanied with ensemble and must be homogeneous with ensemble.
1437
1438 A model cannot have more than 99,999 atoms. Where the entry does not contain an ensemble of models, then the entry cannot have more than 99,999 atoms. Entries that go beyond this atom limit must be split into multiple entries, each containing no more than the limits specified above.
1439
1440
1441 Verification/Validation/Value Authority Control
1442 -----------------------------------------------
1443
1444 Entries with multiple models in the NUMMDL record are checked for corresponding pairs of MODEL/ ENDMDL records, and for consecutively numbered models.
1445
1446
1447 Relationships to Other Record Types
1448 -----------------------------------
1449
1450 Each MODEL must have a corresponding ENDMDL record.
1451
1452
1453 Examples
1454 --------
1455
1456 Example 1::
1457
1458 1 2 3 4 5 6 7 8
1459 12345678901234567890123456789012345678901234567890123456789012345678901234567890
1460 MODEL 1
1461 ATOM 1 N ALA A 1 11.104 6.134 -6.504 1.00 0.00 N
1462 ATOM 2 CA ALA A 1 11.639 6.071 -5.147 1.00 0.00 C
1463 ...
1464 ...
1465 ...
1466 ATOM 293 1HG GLU A 18 -14.861 -4.847 0.361 1.00 0.00 H
1467 ATOM 294 2HG GLU A 18 -13.518 -3.769 0.084 1.00 0.00 H
1468 TER 295 GLU A 18
1469 ENDMDL
1470 MODEL 2
1471 ATOM 296 N ALA A 1 10.883 6.779 -6.464 1.00 0.00 N
1472 ATOM 297 CA ALA A 1 11.451 6.531 -5.142 1.00 0.00 C
1473 ...
1474 ...
1475 ATOM 588 1HG GLU A 18 -13.363 -4.163 -2.372 1.00 0.00 H
1476 ATOM 589 2HG GLU A 18 -12.634 -3.023 -3.475 1.00 0.00 H
1477 TER 590 GLU A 18
1478 ENDMDL
1479
1480 Example 2::
1481
1482 1 2 3 4 5 6 7 8
1483 12345678901234567890123456789012345678901234567890123456789012345678901234567890
1484 MODEL 1
1485 ATOM 1 N AALA A 1 72.883 57.697 56.410 0.50 83.80 N
1486 ATOM 2 CA AALA A 1 73.796 56.531 56.644 0.50 84.78 C
1487 ATOM 3 C AALA A 1 74.549 56.551 57.997 0.50 85.05 C
1488 ATOM 4 O AALA A 1 73.951 56.413 59.075 0.50 84.77 O
1489 ...
1490 ...
1491 ...
1492 HETATM37900 O AHOH 490 -24.915 147.513 36.413 0.50 41.86 O
1493 HETATM37901 O AHOH 491 -28.699 130.471 22.248 0.50 36.06 O
1494 HETATM37902 O AHOH 492 -33.309 184.488 26.176 0.50 15.00 O
1495 ENDMDL
1496 MODEL 2
1497 ATOM 1 N BALA A 1 72.883 57.697 56.410 0.50 83.80 N
1498 ATOM 2 CA BALA A 1 73.796 56.531 56.644 0.50 84.78 C
1499 ATOM 3 C BALA A 1 74.549 56.551 57.997 0.50 85.05 C
1500 ATOM 4 O BALA A 1 73.951 56.413 59.075 0.50 84.77 O
1501 ATOM 5 CB BALA A 1 74.804 56.369 55.453 0.50 84.29 C
1502 ATOM 6 N BASP A 2 75.872 56.703 57.905 0.50 85.59 N
1503 ATOM 7 CA BASP A 2 76.801 56.651 59.048 0.50 85.67 C
1504 ATOM 8 C BASP A 2 76.283 57.361 60.309 0.50 84.80 C
1505 ...
1506
1507
1508 @param file: The file to write the record to.
1509 @type file: file object
1510 @keyword serial: The model serial number.
1511 @type serial: int
1512 """
1513
1514
1515 text = "%-6s %4i%66s" % (
1516 'MODEL',
1517 _handle_none(serial),
1518 ''
1519 )
1520
1521
1522 _record_validate(text)
1523
1524
1525 file.write(text)
1526 file.write('\n')
1527
1528
1530 """Generate the REMARK record.
1531
1532 The following is the PDB v3.3 documentation U{http://www.wwpdb.org/documentation/file-format/format33/remarks.html}.
1533
1534 REMARK
1535 ======
1536
1537 Overview
1538 --------
1539
1540 REMARK records present experimental details, annotations, comments, and information not included in other records. In a number of cases, REMARKs are used to expand the contents of other record types. A new level of structure is being used for some REMARK records. This is expected to facilitate searching and will assist in the conversion to a relational database.
1541
1542 The very first line of every set of REMARK records is used as a spacer to aid in reading::
1543
1544 ______________________________________________________________________________________________
1545 | | | | |
1546 | Columns | Data type | Field | Definition |
1547 |_________|_____________|_____________|______________________________________________________|
1548 | | | | |
1549 | 1 - 6 | Record name | "REMARK" | |
1550 | 8 - 10 | Integer | remarkNum | Remark number. It is not an error for remark n to |
1551 | | | | exist in an entry when remark n-1 does not. |
1552 | 12 - 79 | LString | empty | Left as white space in first line of each new |
1553 | | | | remark. |
1554 |_________|_____________|_____________|______________________________________________________|
1555
1556
1557 @param file: The file to write the record to.
1558 @type file: file object
1559 @keyword num: The remarkNum value.
1560 @type num: int
1561 @keyword remark: The remark.
1562 @type remark: str
1563 """
1564
1565
1566 lines = []
1567
1568
1569 if remark == None:
1570 lines.append("%-6s %3s %-68s " % ("REMARK", num, ''))
1571
1572
1573 else:
1574 for line in wrap(remark, 68):
1575 lines.append("%-6s %3s %-68s " % ("REMARK", num, line.upper()))
1576
1577
1578 for text in lines:
1579
1580 _record_validate(text)
1581
1582
1583 file.write(text)
1584 file.write('\n')
1585
1586
1587 -def sheet(file, strand='', sheet_id='', num_strands='', init_res_name='', init_chain_id='', init_seq_num='', init_icode='', end_res_name='', end_chain_id='', end_seq_num='', end_icode='', sense='', cur_atom='', cur_res_name='', cur_chain_id='', cur_res_seq='', cur_icode='', prev_atom='', prev_res_name='', prev_chain_id='', prev_res_seq='', prev_icode=''):
1588 """Generate the SHEET record.
1589
1590 The following is the PDB v3.3 documentation U{http://www.wwpdb.org/documentation/file-format/format33/sect5.html#SHEET}.
1591
1592 SHEET
1593 =====
1594
1595 Overview
1596 --------
1597
1598 SHEET records are used to identify the position of sheets in the molecule. Sheets are both named and numbered. The residues where the sheet begins and ends are noted.
1599
1600
1601 Record Format
1602 -------------
1603
1604 The format is::
1605 ______________________________________________________________________________________________
1606 | | | | |
1607 | Columns | Data type | Field | Definition |
1608 |_________|______________|______________|____________________________________________________|
1609 | | | | |
1610 | 1 - 6 | Record name | "SHEET " | |
1611 | 8 - 10 | Integer | strand | Strand number which starts at 1 for each strand |
1612 | | | | within a sheet and increases by one. |
1613 | 12 - 14 | LString(3) | sheetID | Sheet identifier. |
1614 | 15 - 16 | Integer | numStrands | Number of strands in sheet. |
1615 | 18 - 20 | Residue name | initResName | Residue name of initial residue. |
1616 | 22 | Character | initChainID | Chain identifier of initial residue in strand. |
1617 | 23 - 26 | Integer | initSeqNum | Sequence number of initial residue in strand. |
1618 | 27 | AChar | initICode | Insertion code of initial residue in strand. |
1619 | 29 - 31 | Residue name | endResName | Residue name of terminal residue. |
1620 | 33 | Character | endChainID | Chain identifier of terminal residue. |
1621 | 34 - 37 | Integer | endSeqNum | Sequence number of terminal residue. |
1622 | 38 | AChar | endICode | Insertion code of terminal residue. |
1623 | 39 - 40 | Integer | sense | Sense of strand with respect to previous strand in |
1624 | | | | the sheet. 0 if first strand, 1 if parallel, and |
1625 | | | | -1 if anti-parallel. |
1626 | 42 - 45 | Atom | curAtom | Registration. Atom name in current strand. |
1627 | 46 - 48 | Residue name | curResName | Registration. Residue name in current strand. |
1628 | 50 | Character | curChainId | Registration. Chain identifier in current strand. |
1629 | 51 - 54 | Integer | curResSeq | Registration. Residue sequence number in current |
1630 | | | | strand. |
1631 | 55 | AChar | curICode | Registration. Insertion code in current strand. |
1632 | 57 - 60 | Atom | prevAtom | Registration. Atom name in previous strand. |
1633 | 61 - 63 | Residue name | prevResName | Registration. Residue name in previous strand. |
1634 | 65 | Character | prevChainId | Registration. Chain identifier in previous strand.|
1635 | 66 - 69 | Integer | prevResSeq | Registration. Residue sequence number in previous |
1636 | | | | strand. |
1637 | 70 | AChar | prevICode | Registration. Insertion code in previous strand. |
1638 |_________|______________|______________|____________________________________________________|
1639
1640
1641 Details
1642 -------
1643
1644 The initial residue for a strand is its N-terminus. Strand registration information is provided in columns 39 - 70. Strands are listed starting with one edge of the sheet and continuing to the spatially adjacent strand.
1645
1646 The sense in columns 39 - 40 indicates whether strand n is parallel (sense = 1) or anti-parallel (sense = -1) to strand n-1. Sense is equal to zero (0) for the first strand of a sheet.
1647
1648 The registration (columns 42 - 70) of strand n to strand n-1 may be specified by one hydrogen bond between each such pair of strands. This is done by providing the hydrogen bonding between the current and previous strands. No register information should be provided for the first strand.
1649
1650 Split strands, or strands with two or more runs of residues from discontinuous parts of the amino acid sequence, are explicitly listed. Detail description can be included in the REMARK 700.
1651
1652
1653 Relationships to Other Record Types
1654 -----------------------------------
1655
1656 If the entry contains bifurcated sheets or beta-barrels, the relevant REMARK 700 records must be provided. See the REMARK section for details.
1657
1658
1659 Examples
1660 --------
1661
1662 Example 1::
1663
1664 1 2 3 4 5 6 7 8
1665 12345678901234567890123456789012345678901234567890123456789012345678901234567890
1666 SHEET 1 A 5 THR A 107 ARG A 110 0
1667 SHEET 2 A 5 ILE A 96 THR A 99 -1 N LYS A 98 O THR A 107
1668 SHEET 3 A 5 ARG A 87 SER A 91 -1 N LEU A 89 O TYR A 97
1669 SHEET 4 A 5 TRP A 71 ASP A 75 -1 N ALA A 74 O ILE A 88
1670 SHEET 5 A 5 GLY A 52 PHE A 56 -1 N PHE A 56 O TRP A 71
1671 SHEET 1 B 5 THR B 107 ARG B 110 0
1672 SHEET 2 B 5 ILE B 96 THR B 99 -1 N LYS B 98 O THR B 107
1673 SHEET 3 B 5 ARG B 87 SER B 91 -1 N LEU B 89 O TYR B 97
1674 SHEET 4 B 5 TRP B 71 ASP B 75 -1 N ALA B 74 O ILE B 88
1675 SHEET 5 B 5 GLY B 52 ILE B 55 -1 N ASP B 54 O GLU B 73
1676
1677 The sheet presented as BS1 below is an eight-stranded beta-barrel. This is represented by a nine-stranded sheet in which the first and last strands are identical::
1678
1679 SHEET 1 BS1 9 VAL 13 ILE 17 0
1680 SHEET 2 BS1 9 ALA 70 ILE 73 1 O TRP 72 N ILE 17
1681 SHEET 3 BS1 9 LYS 127 PHE 132 1 O ILE 129 N ILE 73
1682 SHEET 4 BS1 9 GLY 221 ASP 225 1 O GLY 221 N ILE 130
1683 SHEET 5 BS1 9 VAL 248 GLU 253 1 O PHE 249 N ILE 222
1684 SHEET 6 BS1 9 LEU 276 ASP 278 1 N LEU 277 O GLY 252
1685 SHEET 7 BS1 9 TYR 310 THR 318 1 O VAL 317 N ASP 278
1686 SHEET 8 BS1 9 VAL 351 TYR 356 1 O VAL 351 N THR 318
1687 SHEET 9 BS1 9 VAL 13 ILE 17 1 N VAL 14 O PRO 352
1688
1689 The sheet structure of this example is bifurcated. In order to represent this feature, two sheets are defined. Strands 2 and 3 of BS7 and BS8 are identical::
1690
1691 SHEET 1 BS7 3 HIS 662 THR 665 0
1692 SHEET 2 BS7 3 LYS 639 LYS 648 -1 N PHE 643 O HIS 662
1693 SHEET 3 BS7 3 ASN 596 VAL 600 -1 N TYR 598 O ILE 646
1694 SHEET 1 BS8 3 ASN 653 TRP 656 0
1695 SHEET 2 BS8 3 LYS 639 LYS 648 -1 N LYS 647 O THR 655
1696 SHEET 3 BS8 3 ASN 596 VAL 600 -1 N TYR 598 O ILE 646
1697
1698
1699 @param file: The file to write the record to.
1700 @type file: file object
1701 @keyword strand: The strand number.
1702 @type strand: int
1703 @keyword sheet_id: The sheet identifier.
1704 @type sheet_id: str
1705 @keyword num_strands: The number of strands in sheet.
1706 @type num_strands: int
1707 @keyword init_res_name: The residue name of initial residue.
1708 @type init_res_name: str
1709 @keyword init_chain_id: The chain identifier of initial residue in strand.
1710 @type init_chain_id: str
1711 @keyword init_seq_num: The sequence number of initial residue in strand.
1712 @type init_seq_num: int
1713 @keyword init_icode: The insertion code of initial residue in strand.
1714 @type init_icode: str
1715 @keyword end_res_name: The residue name of terminal residue.
1716 @type end_res_name: str
1717 @keyword end_chain_id: The chain identifier of terminal residue.
1718 @type end_chain_id: str
1719 @keyword end_seq_num: The sequence number of terminal residue.
1720 @type end_seq_num: int
1721 @keyword end_icode: The insertion code of terminal residue.
1722 @type end_icode: str
1723 @keyword sense: The sense of strand with respect to previous strand.
1724 @type sense: int
1725 @keyword cur_atom: The atom name in current strand.
1726 @type cur_atom: str
1727 @keyword cur_res_name: The residue name in current strand.
1728 @type cur_res_name: str
1729 @keyword cur_chain_id: The chain identifier in current strand.
1730 @type cur_chain_id: str
1731 @keyword cur_res_seq: The residue sequence number in current strand.
1732 @type cur_res_seq: int
1733 @keyword cur_icode: The insertion code in current strand.
1734 @type cur_icode: str
1735 @keyword prev_atom: The atom name in previous strand.
1736 @type prev_atom: str
1737 @keyword prev_res_name: The residue name in previous strand.
1738 @type prev_res_name: str
1739 @keyword prev_chain_id: The chain identifier in previous strand.
1740 @type prev_chain_id: str
1741 @keyword prev_res_seq: The residue sequence number in previous strand.
1742 @type prev_res_seq: int
1743 @keyword prev_icode: The insertion code in previous strand.
1744 @type prev_icode: str
1745 """
1746
1747
1748 text = "%-6s %3s %3s%2s %3s %1s%4s%1s %3s %1s%4s%1s%2s %4s%3s %1s%4s%1s %4s%3s %1s%4s%1s%10s" % (
1749 'SHEET',
1750 _handle_none(strand),
1751 _handle_none(sheet_id),
1752 _handle_none(num_strands),
1753 _handle_none(init_res_name),
1754 _handle_none(init_chain_id),
1755 _handle_none(init_seq_num),
1756 _handle_none(init_icode),
1757 _handle_none(end_res_name),
1758 _handle_none(end_chain_id),
1759 _handle_none(end_seq_num),
1760 _handle_none(end_icode),
1761 _handle_none(sense),
1762 _handle_atom_name(cur_atom),
1763 _handle_none(cur_res_name),
1764 _handle_none(cur_chain_id),
1765 _handle_none(cur_res_seq),
1766 _handle_none(cur_icode),
1767 _handle_atom_name(prev_atom),
1768 _handle_none(prev_res_name),
1769 _handle_none(prev_chain_id),
1770 _handle_none(prev_res_seq),
1771 _handle_none(prev_icode),
1772 ''
1773 )
1774
1775
1776 _record_validate(text)
1777
1778
1779 file.write(text)
1780 file.write('\n')
1781
1782
1783 -def ter(file, serial='', res_name='', chain_id='', res_seq='', icode=''):
1784 """Generate the TER record.
1785
1786 The following is the PDB v3.3 documentation U{http://www.wwpdb.org/documentation/file-format/format33/sect9.html#TER}.
1787
1788 TER
1789 ===
1790
1791 Overview
1792 --------
1793
1794 The TER record indicates the end of a list of ATOM/HETATM records for a chain.
1795
1796
1797 Record Format
1798 -------------
1799
1800 The format is::
1801 ______________________________________________________________________________________________
1802 | | | | |
1803 | Columns | Data type | Field | Definition |
1804 |_________|______________|______________|____________________________________________________|
1805 | | | | |
1806 | 1 - 6 | Record name | "TER " | |
1807 | 7 - 11 | Integer | serial | Serial number. |
1808 | 18 - 20 | Residue name | resName | Residue name. |
1809 | 22 | Character | chainID | Chain identifier. |
1810 | 23 - 26 | Integer | resSeq | Residue sequence number. |
1811 | 27 | AChar | iCode | Insertion code. |
1812 |_________|______________|______________|____________________________________________________|
1813
1814
1815 Details
1816 -------
1817
1818 Every chain of ATOM/HETATM records presented on SEQRES records is terminated with a TER record.
1819
1820 The TER records occur in the coordinate section of the entry, and indicate the last residue presented for each polypeptide and/or nucleic acid chain for which there are determined coordinates. For proteins, the residue defined on the TER record is the carboxy-terminal residue; for nucleic acids it is the 3'-terminal residue.
1821
1822 For a cyclic molecule, the choice of termini is arbitrary.
1823
1824 Terminal oxygen atoms are presented as OXT for proteins, and as O5' or OP3 for nucleic acids. These atoms are present only if the last residue in the polymer is truly the last residue in the SEQRES.
1825
1826 The TER record has the same residue name, chain identifier, sequence number and insertion code as the terminal residue. The serial number of the TER record is one number greater than the serial number of the ATOM/HETATM preceding the TER.
1827
1828
1829 Verification/Validation/Value Authority Control
1830 -----------------------------------------------
1831
1832 TER must appear at the terminal carboxyl end or 3' end of a chain. For proteins, there is usually a terminal oxygen, labeled OXT. The validation program checks for the occurrence of TER and OXT records.
1833
1834
1835 Relationships to Other Record Types
1836 -----------------------------------
1837
1838 The residue name appearing on the TER record must be the same as the residue name of the immediately preceding ATOM or non-water HETATM record.
1839
1840
1841 Example
1842 -------
1843
1844 Example 1::
1845
1846 1 2 3 4 5 6 7 8
1847 12345678901234567890123456789012345678901234567890123456789012345678901234567890
1848 ATOM 601 N LEU A 75 -17.070 -16.002 2.409 1.00 55.63 N
1849 ATOM 602 CA LEU A 75 -16.343 -16.746 3.444 1.00 55.50 C
1850 ATOM 603 C LEU A 75 -16.499 -18.263 3.300 1.00 55.55 C
1851 ATOM 604 O LEU A 75 -16.645 -18.789 2.195 1.00 55.50 O
1852 ATOM 605 CB LEU A 75 -16.776 -16.283 4.844 1.00 55.51 C
1853 TER 606 LEU A 75
1854 ...
1855 ATOM 1185 O LEU B 75 26.292 -4.310 16.940 1.00 55.45 O
1856 ATOM 1186 CB LEU B 75 23.881 -1.551 16.797 1.00 55.32 C
1857 TER 1187 LEU B 75
1858 HETATM 1188 H2 SRT A1076 -17.263 11.260 28.634 1.00 59.62 H
1859 HETATM 1189 HA SRT A1076 -19.347 11.519 28.341 1.00 59.42 H
1860 HETATM 1190 H3 SRT A1076 -17.157 14.303 28.677 1.00 58.00 H
1861 HETATM 1191 HB SRT A1076 -15.110 13.610 28.816 1.00 57.77 H
1862 HETATM 1192 O1 SRT A1076 -17.028 11.281 31.131 1.00 62.63 O
1863
1864 ATOM 295 HB2 ALA A 18 4.601 -9.393 7.275 1.00 0.00 H
1865 ATOM 296 HB3 ALA A 18 3.340 -9.147 6.043 1.00 0.00 H
1866 TER 297 ALA A 18
1867 ENDMDL
1868
1869
1870 @param file: The file to write the record to.
1871 @type file: file object
1872 @keyword serial: The atom serial number.
1873 @type serial: int
1874 @keyword res_name: The residue name.
1875 @type res_name: str
1876 @keyword chain_id: The chain identifier.
1877 @type chain_id: str
1878 @keyword res_seq: The sequence number.
1879 @type res_seq: int
1880 @keyword icode: The insertion code.
1881 @type icode: str
1882 """
1883
1884
1885 text = "%-6s%5s %3s %1s%4s%1s%53s" % (
1886 'TER',
1887 _handle_none(serial),
1888 _handle_none(res_name),
1889 _handle_none(chain_id),
1890 _handle_none(res_seq),
1891 _handle_none(icode),
1892 ''
1893 )
1894
1895
1896 _record_validate(text)
1897
1898
1899 file.write(text)
1900 file.write('\n')
1901