How to use pdbsuperpose without .Sequence field?

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Steven
Steven 2015-12-3
编辑： OLUWATOSIN OLUWADARE 2016-8-25
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

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回答（2 个）

Yuebin Zhou
Yuebin Zhou 2015-12-7
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
Steven
Steven 2015-12-7
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.
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OLUWATOSIN OLUWADARE
OLUWATOSIN OLUWADARE 2016-8-25
编辑：OLUWATOSIN OLUWADARE 2016-8-25
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.

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