MATLAB Examples

# CONECT_atom.m

• This function prints the CONECT records sometimes used in pdb files
• Tested 15/04/2017
• Please report bugs to michael.holmboe@umu.se

## Examples

• CONECT_atom(atom,Box_dim,1.25,2.25)
```function CONECT_atom(atom,Box_dim,short_r,long_r) ```
```% short_r=1.25; % long_r=2.25; nAtoms=size(atom,2); atom=bond_angle_atom(atom,Box_dim,short_r,long_r); B=[Bond_index(:,1:2); Bond_index(:,2) Bond_index(:,1)]; b1=sortrows(B); filename='conect'; fid = fopen(strcat(filename,'.pdb'), 'wt'); for i=1:max(b1(:,1)) ind=find(b1(:,1)==i); b2=b1(ind,2); fprintf(fid,'CONECT%5i%5i%5i%5i%5i%5i%5i',[i;b2]); fprintf(fid,'\r\n'); end fprintf(fid,'MASTER %5i%5i%5i%5i%5i%5i%5i%5i%5i%5i%5i%5i\r\n',[0 0 0 0 0 0 0 0 nAtoms 0 i 0]); fprintf(fid,'END'); fclose(fid); % % % COLUMNS DATA TYPE FIELD DEFINITION % % % --------------------------------------------------------------------------------- % % % 1 - 6 Record name "CONECT" % % % 7 - 11 Integer serial Atom serial number % % % 12 - 16 Integer serial Serial number of bonded atom % % % 17 - 21 Integer serial Serial number of bonded atom % % % 22 - 26 Integer serial Serial number of bonded atom % % % 27 - 31 Integer serial Serial number of bonded atom %%%%% We do not use these below... % % % 32 - 36 Integer serial Serial number of hydrogen bonded atom % % % 37 - 41 Integer serial Serial number of hydrogen bonded atom % % % 42 - 46 Integer serial Serial number of salt bridged atom % % % 47 - 51 Integer serial Serial number of hydrogen bonded atom % % % 52 - 56 Integer serial Serial number of hydrogen bonded atom % % % 57 - 61 Integer serial Serial number of salt bridged atom % % % COLUMNS DATA TYPE FIELD DEFINITION % % % ---------------------------------------------------------------------------------- % % % 1 - 6 Record name "MASTER" % % % 11 - 15 Integer numRemark Number of REMARK records % % % 16 - 20 Integer "0" % % % 21 - 25 Integer numHet Number of HET records % % % 26 - 30 Integer numHelix Number of HELIX records % % % 31 - 35 Integer numSheet Number of SHEET records % % % 36 - 40 Integer numTurn deprecated % % % 41 - 45 Integer numSite Number of SITE records % % % 46 - 50 Integer numXform Number of coordinate transformation % % % records (ORIGX+SCALE+MTRIX) % % % 51 - 55 Integer numCoord Number of atomic coordinate records % % % records (ATOM+HETATM) % % % 56 - 60 Integer numTer Number of TER records % % % 61 - 65 Integer numConect Number of CONECT records % % % 66 - 70 Integer numSeq Number of SEQRES records % % % MASTER 0 0 0 0 0 0 0 0 1808 0 1808 0 ```