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Masha


Active since 2023

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How to add extension to files using MATLAB
I have around 60,000 .pdb files like 1UXC, 1UXA, 3FUS and so on. I need to add an extension of .pdb to each of these files such...

1 year ago | 2 answers | 0

2

answers

Question


Unable to use value of type string as an index
In the code below, I am trying to extract the AtomName, X,Y,Z, resSeq and chainID columns present in the PtnTYR struct array. I ...

1 year ago | 1 answer | 0

1

answer

Question


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.Mo...

1 year ago | 1 answer | 0

1

answer

Question


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 fo...

1 year ago | 1 answer | 0

1

answer

Question


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 at...

1 year ago | 1 answer | 0

1

answer

Question


Index in position 1 is invalid. Array indices must be positive integers or logical values?
In the following code I encounter the problem in the last line. How to rectify this? The integer value is positive , i.e., i=1:3...

2 years ago | 2 answers | 0

2

answers

Question


How to extract the atomic coordinates of a specific amino acid from a pdb file
Hello, Is it possible in Matlab bioinformatics tool, to extract the coordinates of a specific amino acid like lysine and store i...

2 years ago | 1 answer | 0

1

answer

Question


Is there any separate activation procedure for MATLAB online?
I am new to MATLAB and I just activated MATLAB application on my computer. I don't use the software much but I use MATLAB online...

2 years ago | 1 answer | 0

1

answer

Question


How does ismember and assert work in this code?
Previously, I raised a question of how to generate a matrix of only masses; provided that a matrix A is given that contains the ...

2 years ago | 1 answer | 0

1

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Question


I have a list of objects in matrix A and object list and their corresponding masses in matrix B.Howto generate a matrix containing masses of objects present in orderof matrxA
A = ["C"; "A"; "E"; "F"; "I"] B = ["A", 1;"B", 34;"C" 56;"D" 32;"E",11;"F",8;"G", 7;"H",9;"I" 77]

2 years ago | 1 answer | 0

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Question


Is there any built-in code in MATLAB that calculates phi-psi angles in pdb file as the bio.pdb module in biopython does?
Bio.pdb module in biopython helps in calculating the dihedral angles (phi-psi angles) for poly_index, poly in enumerate(polypep...

2 years ago | 1 answer | 0

1

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Question


I would like to extract x,y,z coordinates of any 3 atoms from a pdb file. How to rectify this error and make it generalized?
ubq=getpdb('1UBQ'); for n=[1,2,3] Q(n)=[ubq.Model.Atom(n).X, ubq.Model.Atom(n).Y, ubq.Model.Atom(n).Z] end

2 years ago | 1 answer | 0

1

answer

Question


How to rectify "arrays have incompatible sizes for this operation error" in this code: (Bioinformatics-related)
ubq=getpdb('1UBQ') for i=1:1000 if ubq.Model.Atom(i).AtomName == 'CA' b=[ubq.Model.Atom(i).X,ubq.Model.Atom(i).Y,...

2 years ago | 1 answer | 0

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