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Proteins structure commandsBasic commands ls /usr/cbs/databases/pdb/allpdb/ See all pdb files at CBS zcat /usr/cbs/databases/pdb/allpdb/pdb1hge.ent.Z | less Read pdb entry 1hge (press space to go one page down) rasmol /usr/cbs/databases/pdb/allpdb/pdb1hge.ent.Z See structure zcat /usr/cbs/databases/pdb/allpdb/pdb1hge.ent.Z | grep "^ATOM.........CA......A" > tmp.pdb Get C-alpha atoms in A chain rasmol tmp.pdb See selected atoms zcat /usr/cbs/databases/pdb/allpdb/pdb1hge.ent.Z | gawk '{if (/^ATOM/){print $0}}'|head Print atom records using gawk Example of ATOM lines ATOM 1 N GLN A 1 79.647 -9.863 41.673 1.00148.74 1 1HGE 458 ATOM 2 CA GLN A 1 78.339 -9.240 41.704 1.00148.69 1 1HGE 459 ATOM 3 C GLN A 1 77.991 -9.916 43.032 1.00148.41 1 1HGE 460 ATOM 4 O GLN A 1 78.781 -9.726 43.965 1.00148.59 1 1HGE 461 ATOM 5 CB GLN A 1 77.503 -9.741 40.499 1.00148.97 1 1HGE 462 ATOM 6 CG GLN A 1 76.513 -8.726 39.888 1.00149.76 1 1HGE 463 ATOM 7 CD GLN A 1 75.435 -8.146 40.813 1.00150.33 1 1HGE 464 ATOM 8 OE1 GLN A 1 75.584 -8.142 42.032 1.00150.63 1 1HGE 465 ATOM 9 NE2 GLN A 1 74.321 -7.645 40.310 1.00150.73 1 1HGE 466 ATOM 10 1H GLN A 1 80.024 -9.640 42.628 1.00 0.00 1 1HGE 467 ATOM 11 2H GLN A 1 79.526 -10.898 41.695 1.00 0.00 1 1HGE 468 ATOM 12 3H GLN A 1 80.276 -9.535 40.926 1.00 0.00 1 1HGE 469 ATOM 13 1HE2 GLN A 1 73.645 -7.304 40.934 1.00 0.00 1 1HGE 470 ATOM 14 2HE2 GLN A 1 74.181 -7.642 39.340 1.00 0.00 1 1HGE 471 ATOM 15 N ASP A 2 76.904 -10.686 43.115 1.00147.82 1 1HGE 472 ATOM 16 CA ASP A 2 76.637 -11.610 44.215 1.00146.80 1 1HGE 473 ATOM 17 C ASP A 2 77.557 -12.824 43.939 1.00145.99 1 1HGE 474 ATOM 18 O ASP A 2 78.750 -12.654 43.617 1.00146.02 1 1HGE 475 ATOM 19 CB ASP A 2 75.114 -11.872 44.111 1.00146.96 1 1HGE 476 ATOM 20 CG ASP A 2 74.508 -12.974 44.963 1.00147.11 1 1HGE 477 ATOM 21 OD1 ASP A 2 74.477 -12.845 46.180 1.00147.52 1 1HGE 478 ATOM 22 OD2 ASP A 2 74.119 -13.994 44.392 1.00147.01 1 1HGE 479 ATOM 23 H ASP A 2 76.173 -10.542 42.482 1.00 0.00 1 1HGE 480 Format of ATOM lines from http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html COLUMNS DATA TYPE FIELD DEFINITION --------------------------------------------------------------------------------- 1 - 6 Record name "ATOM " 7 - 11 Integer serial Atom serial number. 13 - 16 Atom name Atom name. 17 Character altLoc Alternate location indicator. 18 - 20 Residue name resName Residue name. 22 Character chainID Chain identifier. 23 - 26 Integer resSeq Residue sequence number. 27 AChar iCode Code for insertion of residues. 31 - 38 Real(8.3) x Orthogonal coordinates for X in 39 - 46 Real(8.3) y Orthogonal coordinates for Y in 47 - 54 Real(8.3) z Orthogonal coordinates for Z in 55 - 60 Real(6.2) occupancy Occupancy. 61 - 66 Real(6.2) tempFactor Temperature factor. 73 - 76 LString(4) segID Segment identifier, left-justified. 77 - 78 LString(2) element Element symbol, right-justified. 79 - 80 LString(2) charge Charge on the atom. Read pdbfile formated and and write it out again zcat /usr/cbs/databases/pdb/allpdb/pdb1hge.ent.Z | gawk '{if (/^ATOM/){ATOM=substr($0,1,6);serial=substr($0,7,4);name=substr($0,13,4);altLoc=substr($0,17,1);resName=substr($0,18,3);chainID=substr($0,22,1);resSeq=substr($0,23,4);iCode=substr($0,27,1);x=substr($0,31,8)*1.0;y=substr($0,39,8)*1.0;z=substr($0,47,8)*1.0;occupancy=substr($0,55,6)*1.0;tempFactor=substr($0,61,6);segID=substr($0,73,4);element=substr($0,77,2);charge=substr($0,79,2); printf("%6s%5d %4s%1s%3s %s%4d%1s %8.3f%8.3f%8.3f%6.2f%6.2f%4s%2s%2s\n",ATOM, serial, name, altLoc, resName, chainID, resSeq, iCode, x, y, z, occupancy, tempFactor, segID, element, charge)}}' > tmp.pdb The oneliner above contains the core: gawk '{if (/^ATOM/){READ_A_LINE; PRINT_A_LINE}}' > tmp.pdb where the read write statements are defined by: READ_A_LINE: ATOM=substr($0,1,6);serial=substr($0,7,4);name=substr($0,13,4);altLoc=substr($0,17,1);resName=substr($0,18,3);chainID=substr($0,22,1);resSeq=substr($0,23,4);iCode=substr($0,27,1);x=substr($0,31,8)*1.0;y=substr($0,39,8)*1.0;z=substr($0,47,8)*1.0;occupancy=substr($0,55,6)*1.0;tempFactor=substr($0,61,6);segID=substr($0,73,4);element=substr($0,77,2);charge=substr($0,79,2) PRINT_A_LINE: printf("%6s%5d %4s%1s%3s %s%4d%1s %8.3f%8.3f%8.3f%6.2f%6.2f%4s%2s%2s\n",ATOM, serial, name, altLoc, resName, chainID, resSeq, iCode, x, y, z, occupancy, tempFactor, segID, element, charge) A version og the onliner with more newlines can be found in pdb2pdb.gawk You can run it using the command: zcat /usr/cbs/databases/pdb/allpdb/pdb1hge.ent.Z | /usr/opt/www/pub/CBS/researchgroups/immunology/intro/Unix/pdb2pdb.gawk Read pdbfile formated and and print out the mirror image of the C-alpha atoms in chain B! - How can you see it is mirrored? pdb1hge.ent.Z | gawk '{if (/^ATOM/){ATOM=substr($0,1,6);serial=substr($0,7,4);name=substr($0,13,4);altLoc=substr($0,17,1);resName=substr($0,18,3);chainID=substr($0,22,1);resSeq=substr($0,23,4);iCode=substr($0,27,1);x=substr($0,31,8)*1.0;y=substr($0,39,8)*1.0;z=substr($0,47,8)*1.0;occupancy=substr($0,55,6)*1.0;tempFactor=substr($0,61,6);segID=substr($0,73,4);element=substr($0,77,2);charge=substr($0,79,2); if (name == " CA "&&chainID=="B") {printf("%6s%5d %4s%1s%3s %s%4d%1s %8.3f%8.3f%8.3f%6.2f%6.2f%4s%2s%2s\n",ATOM, serial, name, altLoc, resName, chainID, resSeq, iCode, x, y, -z, occupancy, tempFactor, segID, element, charge)}}}' > tmp.pdb |
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