Index in position 2 exceeds array bounds

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Masha
Masha 2023-3-16
评论： Masha 2023-3-16
Ran in:
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.

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采纳的回答

David Hill
David Hill 2023-3-16
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
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