Index in position 2 exceeds array bounds

I am trying to find the centre of mass of (sidechain of) tyrosine residues in a protein. I extracted the coordinates and then found the mass of the atoms in the following code. But while trying to find the X coordinate of centre of mass, I had this error show up

% Starting from pdb file
uxc = getpdb('1UXC'); 
No_of_residues = uxc.Sequence.NumOfResidues

No_of_residues = 65

isTYR = ({uxc.Model.Atom.resName} == "TYR"); 
uxcTYR = uxc.Model.Atom(isTYR)  % Extracts particulars of only TYR

uxcTYR = 1×63 struct array with fields:
    AtomSerNo
    AtomName
    altLoc
    resName
    chainID
    resSeq
    iCode
    X
    Y
    Z
    occupancy
    tempFactor
    segID
    element
    charge
    AtomNameStruct

%Extracting sidechain coordinates:
uxcTYRt = struct2table(uxcTYR)

uxcTYRt = 63×16 table
    AtomSerNo    AtomName      altLoc      resName    chainID    resSeq      iCode         X         Y         Z       occupancy    tempFactor     segID      element    charge    AtomNameStruct
    _________    ________    __________    _______    _______    ______    __________    ______    ______    ______    _________    __________    ________    _______    ______    ______________

       277       {'N'  }     {0×0 char}    {'TYR'}     {'A'}       19      {0×0 char}     0.363    -2.991      -2.5        1           4.78       {'    '}     {'N'}     {'  '}      1×1 struct  
       278       {'CA' }     {0×0 char}    {'TYR'}     {'A'}       19      {0×0 char}     0.582    -4.369    -1.965        1            4.8       {'    '}     {'C'}     {'  '}      1×1 struct  
       279       {'C'  }     {0×0 char}    {'TYR'}     {'A'}       19      {0×0 char}     -0.04    -4.407    -0.575        1           2.45       {'    '}     {'C'}     {'  '}      1×1 struct  
       280       {'O'  }     {0×0 char}    {'TYR'}     {'A'}       19      {0×0 char}    -0.797    -5.299    -0.238        1            2.8       {'    '}     {'O'}     {'  '}      1×1 struct  
       281       {'CB' }     {0×0 char}    {'TYR'}     {'A'}       19      {0×0 char}     2.085    -4.607     -1.81        1           5.31       {'    '}     {'C'}     {'  '}      1×1 struct  
       282       {'CG' }     {0×0 char}    {'TYR'}     {'A'}       19      {0×0 char}     2.817    -4.625     -3.14        1            4.9       {'    '}     {'C'}     {'  '}      1×1 struct  
       283       {'CD1'}     {0×0 char}    {'TYR'}     {'A'}       19      {0×0 char}     2.135    -4.505    -4.363        1           4.99       {'    '}     {'C'}     {'  '}      1×1 struct  
       284       {'CD2'}     {0×0 char}    {'TYR'}     {'A'}       19      {0×0 char}     4.208    -4.767    -3.146        1           5.42       {'    '}     {'C'}     {'  '}      1×1 struct  
       285       {'CE1'}     {0×0 char}    {'TYR'}     {'A'}       19      {0×0 char}      2.83    -4.527    -5.574        1           2.66       {'    '}     {'C'}     {'  '}      1×1 struct  
       286       {'CE2'}     {0×0 char}    {'TYR'}     {'A'}       19      {0×0 char}     4.906    -4.789    -4.358        1           2.93       {'    '}     {'C'}     {'  '}      1×1 struct  
       287       {'CZ' }     {0×0 char}    {'TYR'}     {'A'}       19      {0×0 char}      4.22    -4.669    -5.574        1            2.4       {'    '}     {'C'}     {'  '}      1×1 struct  
       288       {'OH' }     {0×0 char}    {'TYR'}     {'A'}       19      {0×0 char}     4.906    -4.693     -6.77        1           2.22       {'    '}     {'O'}     {'  '}      1×1 struct  
       289       {'H'  }     {0×0 char}    {'TYR'}     {'A'}       19      {0×0 char}     1.161    -2.485    -2.762        1              0       {'    '}     {'H'}     {'  '}      1×1 struct  
       290       {'HA' }     {0×0 char}    {'TYR'}     {'A'}       19      {0×0 char}     0.151    -5.119    -2.608        1              0       {'    '}     {'H'}     {'  '}      1×1 struct  
       291       {'HB2'}     {0×0 char}    {'TYR'}     {'A'}       19      {0×0 char}      2.49    -3.839    -1.168        1              0       {'    '}     {'H'}     {'  '}      1×1 struct  
       292       {'HB3'}     {0×0 char}    {'TYR'}     {'A'}       19      {0×0 char}     2.211    -5.547    -1.313        1              0       {'    '}     {'H'}     {'  '}      1×1 struct  

atomName=string(uxcTYRt.AtomName); %converting the column AtomName to string array;
REQtyr=uxcTYRt(ismember(atomName,[ "CB","CG","CD1","CD2","CE1","CE2","CZ","OH","HB2","HB3","HD1","HD2","HE1","HE2"]),["AtomName" "resSeq" "X" "Y" "Z"])

REQtyr = 42×5 table
    AtomName    resSeq      X        Y         Z   
    ________    ______    _____    ______    ______

    {'CB' }       19      2.085    -4.607     -1.81
    {'CG' }       19      2.817    -4.625     -3.14
    {'CD1'}       19      2.135    -4.505    -4.363
    {'CD2'}       19      4.208    -4.767    -3.146
    {'CE1'}       19       2.83    -4.527    -5.574
    {'CE2'}       19      4.906    -4.789    -4.358
    {'CZ' }       19       4.22    -4.669    -5.574
    {'OH' }       19      4.906    -4.693     -6.77
    {'HB2'}       19       2.49    -3.839    -1.168
    {'HB3'}       19      2.211    -5.547    -1.313
    {'HD1'}       19      1.061    -4.394    -4.371
    {'HD2'}       19      4.743    -4.861    -2.212
    {'HE1'}       19       2.29    -4.432    -6.505
    {'HE2'}       19      5.979    -4.898    -4.354
    {'CB' }       28       4.35    -8.133    -3.978
    {'CG' }       28       2.99    -8.068    -4.646

Atom_mass = ["CB", 12.01;"CG", 12.01; "CD1",12.01; "CD2",12.01;"CE1", 12.01;"CE2", 12.01; "CZ", 12.01; "OH", 17.006; "HB2", 1.007; "HB3", 1.007; "HD1", 1.007;"HD2", 1.007; "HE1", 1.007; "HE2", 1.007];
DICTAtom_mass = dictionary(Atom_mass(:,1), Atom_mass(:,2));
sizeTyr = size(REQtyr);
numTyr = sizeTyr(1)/14; %number of tyrosine residues

resSeq = REQtyr.resSeq;
sizeresSeq = size(resSeq);
eresSeq = sizeresSeq(1);

% To extract XYZ coordinates of only the tyrosine residues.
uniq = unique(resSeq)

uniq = 3×1

19 28 47

for i = uniq(1,1):uniq(end,end)
    Tyro1{i} = table2cell(REQtyr(ismember(resSeq,i),["AtomName","X","Y","Z"]));
Tyro{i} = table2struct(REQtyr(ismember(resSeq,i),["AtomName","X","Y","Z"]));
Tyroc{i} = [Tyro{i}.X;Tyro{i}.Y;Tyro{i}.Z];
Tyrocd{i} = Tyroc{i}';
end

% Finding out the mass of each and every atom in the sidechain of the
% tyrosine residue
for i = uniq(1,1):uniq(end,end)
Tyromas{i} = str2double(DICTAtom_mass(Tyro1{i}(:,1)));
Tyromass{i} = [Tyromas{i}];
end

%X coordinate:

for i= uniq(1,1):uniq(end,end)
    TyrocdX{i} = (Tyromass{i}'*Tyrocd{i}(:,1))/sum(Tyromass{i})
end

TyrocdX = 1×19 cell array
    {0×0 double}    {0×0 double}    {0×0 double}    {0×0 double}    {0×0 double}    {0×0 double}    {0×0 double}    {0×0 double}    {0×0 double}    {0×0 double}    {0×0 double}    {0×0 double}    {0×0 double}    {0×0 double}    {0×0 double}    {0×0 double}    {0×0 double}    {0×0 double}    {[3.5566]}

Index in position 2 exceeds array bounds.

Answer 1

[David Hill]

for i = 1:numel(uniq)
    Tyro1{i} = table2cell(REQtyr(ismember(resSeq,uniq(i)),["AtomName","X","Y","Z"]));
    Tyro{i} = table2struct(REQtyr(ismember(resSeq,uniq(i)),["AtomName","X","Y","Z"]));
    Tyroc{i} = [Tyro{i}.X;Tyro{i}.Y;Tyro{i}.Z];
    Tyrocd{i} = Tyroc{i}';
end
% Finding out the mass of each and every atom in the sidechain of the
% tyrosine residue
for i = 1:numel(uniq)
    Tyromas{i} = str2double(DICTAtom_mass(Tyro1{i}(:,1)));
    Tyromass{i} = [Tyromas{i}];
end
%X coordinate:
for i= 1:numel(uniq)
    TyrocdX{i} = (Tyromass{i}'*Tyrocd{i}(:,1))/sum(Tyromass{i})
end

[Masha]

Hello Mr. Hill. Thank you for the response. In your code the value of i goes from 1 to 3. The value of i in my code corresponds to the residue number of tyrosine [19,28,47] So that I would know at the end, for "which" tyrosines i calculated the centre of mass for.

is there a way to fix this?

Or like map the index of i to the residue number of tyrosine?

[Masha]

I chose i values to be 19,28,47 (values of uniq) so it would extract the coordinates that correspond to those values (of residue number) from Tyro{i} using ismember.

So choosing 1,2,3 (1:numel(uniq)) would give me wrong results.

[David Hill]

ismember(resSeq,uniq(i))

[Masha]

Thank you so much!