How to extract matrix values of a different column that correspond to a value in another column?

In the matrix uxcLYS generated, I want to extract only the x,y,z column values that corresponds to 'CB','CG','CD','CE' in the atom name column. How to do it?

uxc = getpdb('1UXC'); 
No_of_residues = uxc.Sequence.NumOfResidues

No_of_residues = 65

isLYS = ({uxc.Model.Atom.resName} == "LYS"); 
uxcLYS = uxc.Model.Atom(isLYS)  

uxcLYS = 1×110 struct array with fields:
    AtomSerNo
    AtomName
    altLoc
    resName
    chainID
    resSeq
    iCode
    X
    Y
    Z
    occupancy
    tempFactor
    segID
    element
    charge
    AtomNameStruct

Answer 1

[Venkat Siddarth]

Hi @Masha,

I understand that you are trying to extract specifc columns corresponding to few atom names in the above structure.This can be achieved as follows

%Given Code
uxc = getpdb('1UXC'); 
No_of_residues = uxc.Sequence.NumOfResidues

No_of_residues = 65

isLYS = ({uxc.Model.Atom.resName} == "LYS"); 
uxcLYS = uxc.Model.Atom(isLYS)  

uxcLYS = 1×110 struct array with fields:
    AtomSerNo
    AtomName
    altLoc
    resName
    chainID
    resSeq
    iCode
    X
    Y
    Z
    occupancy
    tempFactor
    segID
    element
    charge
    AtomNameStruct

Since uxc is a structure element,for easy access we can convert this to table as follows:

%Structure to Table
req=struct2table(uxc.Model.Atom)

req = 808×16 table
    AtomSerNo    AtomName      altLoc      resName    chainID    resSeq      iCode         X         Y         Z       occupancy    tempFactor     segID      element    charge    AtomNameStruct
    _________    ________    __________    _______    _______    ______    __________    ______    ______    ______    _________    __________    ________    _______    ______    ______________

        1        {'N'  }     {0×0 char}    {'MET'}     {'A'}       1       {0×0 char}    -7.262    10.686    -0.473        1           2.83       {'    '}     {'N'}     {'  '}      1×1 struct  
        2        {'CA' }     {0×0 char}    {'MET'}     {'A'}       1       {0×0 char}    -6.548     9.453    -0.028        1           2.26       {'    '}     {'C'}     {'  '}      1×1 struct  
        3        {'C'  }     {0×0 char}    {'MET'}     {'A'}       1       {0×0 char}    -6.298     8.511     -1.22        1           2.42       {'    '}     {'C'}     {'  '}      1×1 struct  
        4        {'O'  }     {0×0 char}    {'MET'}     {'A'}       1       {0×0 char}    -6.779     7.395    -1.261        1           2.69       {'    '}     {'O'}     {'  '}      1×1 struct  
        5        {'CB' }     {0×0 char}    {'MET'}     {'A'}       1       {0×0 char}    -7.347     8.762     1.091        1           2.33       {'    '}     {'C'}     {'  '}      1×1 struct  
        6        {'CG' }     {0×0 char}    {'MET'}     {'A'}       1       {0×0 char}    -6.383     8.091     2.075        1           2.33       {'    '}     {'C'}     {'  '}      1×1 struct  
        7        {'SD' }     {0×0 char}    {'MET'}     {'A'}       1       {0×0 char}    -5.381     9.359     2.895        1           2.65       {'    '}     {'S'}     {'  '}      1×1 struct  
        8        {'CE' }     {0×0 char}    {'MET'}     {'A'}       1       {0×0 char}    -3.746     8.634     2.608        1            2.5       {'    '}     {'C'}     {'  '}      1×1 struct  
        9        {'H1' }     {0×0 char}    {'MET'}     {'A'}       1       {0×0 char}    -8.171    10.434    -0.913        1              0       {'    '}     {'H'}     {'  '}      1×1 struct  
       10        {'H2' }     {0×0 char}    {'MET'}     {'A'}       1       {0×0 char}    -7.432    11.306     0.344        1              0       {'    '}     {'H'}     {'  '}      1×1 struct  
       11        {'H3' }     {0×0 char}    {'MET'}     {'A'}       1       {0×0 char}    -6.673    11.197    -1.162        1              0       {'    '}     {'H'}     {'  '}      1×1 struct  
       12        {'HA' }     {0×0 char}    {'MET'}     {'A'}       1       {0×0 char}    -5.586     9.751     0.363        1              0       {'    '}     {'H'}     {'  '}      1×1 struct  
       13        {'HB2'}     {0×0 char}    {'MET'}     {'A'}       1       {0×0 char}    -7.941     9.495     1.616        1              0       {'    '}     {'H'}     {'  '}      1×1 struct  
       14        {'HB3'}     {0×0 char}    {'MET'}     {'A'}       1       {0×0 char}    -7.997     8.012     0.665        1              0       {'    '}     {'H'}     {'  '}      1×1 struct  
       15        {'HG2'}     {0×0 char}    {'MET'}     {'A'}       1       {0×0 char}    -6.951     7.545     2.815        1              0       {'    '}     {'H'}     {'  '}      1×1 struct  
       16        {'HG3'}     {0×0 char}    {'MET'}     {'A'}       1       {0×0 char}     -5.74     7.407     1.542        1              0       {'    '}     {'H'}     {'  '}      1×1 struct  

After this we will apply the required constraints;

%converting the column AtomName to string array;
atomName=string(req.AtomName);
%Applying the constraints
ans=req(ismember(atomName,[ "CB","CG","CD","CE"]),["AtomName" "X" "Y" "Z"])

ans = 97×4 table
    AtomName      X         Y         Z   
    ________    ______    ______    ______

     {'CB'}     -7.347     8.762     1.091
     {'CG'}     -6.383     8.091     2.075
     {'CE'}     -3.746     8.634     2.608
     {'CB'}     -4.843      9.06    -4.571
     {'CG'}     -6.097     9.739    -5.137
     {'CD'}     -5.812     11.22    -5.419
     {'CE'}     -6.311    11.618    -6.815
     {'CB'}     -2.636     4.331    -5.025
     {'CG'}     -2.609     2.871    -4.565
     {'CB'}       0.29     8.746    -5.728
     {'CG'}      1.741     8.974    -6.172
     {'CB'}     -1.262    10.625    -1.019
     {'CG'}     -2.558     9.887    -0.698
     {'CD'}     -3.654    10.922    -0.415
     {'CB'}     -1.304     5.303     0.301
     {'CB'}      3.205     5.265    -2.502

I hope this resolves your query.

Thanks,

Venkat Siddarth V

[Masha]

Thank you!