All against all structure alignments

Question

[Baby Bioinformatician]

Dear Biostars,

I am working on a small project on protein sequence-structure relationships. I would like to perform all-against-all structural alignments for some proteins I obtained from PDB. For this, I have been trying the TMalign command below but with no success. My PDB files are named as pdbxxxx.pdb.

$ TMalign -dir chain_folder/ chain_list -outfmt 2

Any comments on what I am doing wrong or suggestions on another program I could use for the same purpose are highly appreciated.

Answer 1

[Mensur Dlakic]

Tough to tell what the problem is without knowing the error message you received, the content of your PDB directory, and at least couple of lines from the chain list. The instructions for running this seem clear to me:

-dir     Perform all-against-all alignment among the list of PDB
         chains listed by 'chain_list' under 'chain_folder'. Note
         that the slash is necessary.
         $ TMalign -dir chain_folder/ chain_list

Let's say you have a directory /home/baby/PDB that contains those PDB files. Change into that directory and type:

find . -maxdepth 1 -name "pdb*.pdb" | sort | xargs -i basename {} > chain_list

Finally:

TMalign -dir /home/baby/PDB/ chain_list -outfmt 2

To make the screen formatting easier to read, ans assuming you are inside the directory with PDB files, and your chain list is there as well:

TMalign -dir ./ chain_list -outfmt 2

[Baby Bioinformatician]

Thank you very much. This worked for me. I had not prepared the chain_folder and the cahin_list correctly.