old PDB structure error

Hello all,

I have a pdb file which is not in standard format, I can read it by pdbread function but when I want to convert it to standard form by pdbwrite, I get the error " old PDB structure" . I found this m file : sbpl.net:8080/shared/Brian/quad init load/opt/matlab/toolbox/bioinfo/proteins/private/convertpdbstruct.ma

but when I use it the error " too many arguments" comes up although I just enter the old pdb file's name. Could anyone help me with this problem please?

Thank you in advance.

Answer 1

[arushi]

Hi Haleh,

To address the issue of converting a non-standard PDB file to a standard format using MATLAB, you can follow these steps:

1. Read the non-standard PDB file using pdbread:matlabCopy codepdbStruct = pdbread('non_standard.pdb');
2. Modify the PDB structure to conform to the standard format: This step might involve ensuring that all required fields are present and correctly formatted. You may need to write a custom function to adjust the structure as needed.
3. Write the modified PDB structure using pdbwrite:

            pdbwrite('standard.pdb', pdbStruct);

If you encounter errors such as "old PDB structure" or "too many arguments," it may be due to incorrect or missing fields in the PDB structure.

Hope this helps.