Errors while analyzing pdb file

Hello, I have obtained a .pdb file from RASPA-2.0 for modelling argon, and I am trying to open it in MATLAB and analyze it using pdbdistplot. I first attempted to open it using pdbread, but when I entered in the file name--while it was in the current directory--the following error message appeared:

Incorrect number of right hand side elements in dot name assignment. Missing [] around left hand side is a likely cause. Error in pdbread (line 1085) PDB_struct.Model.Atom = TmpAtomStruct;

I then attempted to analyze the .pdb file without opening it using pdbread, using pdbdistplot, but I got the following error:

Error using pdbdistplot (line 50) The input should be a structure of data, a PDB file, or a valid PDB ID.

I've never had to use this software before, so I'm not sure where I'm screwing up. If anyone could provide feedback and advice, it would be greatly appreciated. Thank you.

Answer 1

[Csaba]

PDB stands for "Protein Data Bank" and a pdb file from this data bank has - as a main part - coordinates for each atom in a protein. It has a specific format with all other useful information for that protein.

I do not know RASTA, but from the internet I learned that it is has nothing to do with proteins. So the name (extension) of the files is just coincidental.

I think that is the reason Matlab does not recognize it.

Answer 2

[Sebastian Doniach]

trying to analyze structure of a pdb file created by molecular dynamics

I enter tst_pdb0 =

    'file://Users/sebastiandoniach/work/xfel/protein_states/models_for_seb_2/Gi-GDP-AlF_semiopen_0'
error msg
pdbstr0=pdbread('tst_pdb0');
Error using pdbread (line 78)
File does not exist or does not contain valid PDB data.