How to use pdbsuperpose without .Sequence field?

I created a pdb from XYZ coordinates using the function mat2pdb (<http://www.mathworks.com/matlabcentral/fileexchange/42957-read-and-write-pdb-files-using-matlab/content/mat2pdb.m)>. This function does not create a .Sequence field. The matlab function pdbsuperpose.m seems to require this field to do the alignment. I was wondering if there was a solution where I could conduct superposition without the sequence field. I am not working with a protein structure.

Error: Reference to non-existent field 'Sequence'. Error in pdbsuperpose (line 133) chainList1 = {pdbStruct1.Sequence.ChainID}; % all chains

Answer 1

[Yuebin Zhou]

You may want to use getpdb function to first retrieve protein structure data from Protein Data Bank (PDB) database, then you should be able to use pdbsuperpose to process it.

Please check the links below:

http://www.mathworks.com/help/bioinfo/ref/pdbsuperpose.html#zmw57dd0e122773

http://www.mathworks.com/help/bioinfo/ref/getpdb.html

Answer 2

[Steven]

I believe I found a solution. In my case I only had x, y, z coordinates for the structure. It was not a protein structure. However, I wanted to view the x,y,z coordinates with molviewer. Thus there was no corresponding pdb accession associated with the molecule I was interested in. In fact, the structure I was interested in was a chromosome 3D model. The answer was to conduct the alignment on the x, y, z using procrustes analysis (<http://www.mathworks.com/help/stats/procrustes.html>) then convert that aligned structures to pdb using mat2pdb (<http://www.mathworks.com/matlabcentral/fileexchange/42957-read-and-write-pdb-files-using-matlab/content/mat2pdb.m)>. Finally the pdb formatted x,y,z coordinates could be viewed with molviewer from within matlab.

[OLUWATOSIN OLUWADARE]

Can you please explain what you mean by "conduct the alignment on the x, y, z using procrustes analysis ". I know procustes function only take 2 arguments as input. I am also tring to do this but I get the error too. Thanks.