Intermediate dot indexing produced a comma-separated list with 34 values, but it must produce a single value when followed by subsequent indexing operations

% Starting from pdb file
Proteinname='1UXD';
uxd = getpdb(Proteinname); 
No_of_residues = uxd.Sequence.NumOfResidues;
uxd.Model.Atom.resName

Intermediate dot '.' indexing produced a comma-separated list with 34 values, but it must produce a single value when followed by subsequent indexing operations.

isTYR = ({uxd.Model.Atom.resName} == "TYR")
uxdTYR = uxd.Model.Atom(isTYR)

In the above code, I am trying to extract the details of only the tyrosine residues from the protein '1UXD'. I am guessing the error is due to the presence of many models of the same protein in the pdb file which might have caused the output to be a comma separated list. I am in need of only the first model's tyrosine (TYR) details.. There is a possibility to handle this by turning the output into a cell array and extracting the first output which corresponds to the first model but I am uncertain of how to approach the code for this. Can anyone help :) Thankyou!

Answer 1

[Stephen23]

The documentation

https://www.mathworks.com/help/bioinfo/ref/getpdb.html#bq5gvma-2

states the the MODEL field can be a structure array. Your code does not take that into account.

"I am in need of only the first model's tyrosine (TYR) details"

If you only want the first model, then just use indexing into that array:

uxd.Model(1).Atom.resName

For more information:

https://www.mathworks.com/matlabcentral/answers/1656435-tutorial-comma-separated-lists-and-how-to-use-them

https://www.mathworks.com/help/matlab/matlab_prog/comma-separated-lists.html

[Masha]

Thank you! :)