blast two protein by pdb id

Question

[iamsmor]

Hello everyone I am trying to blast two protein (PDB ID:6UFO, 4XMB) each other using python. I read guideline but ı am not condifident user for python programme. I need help for this process. I will be greatful for any kind of little help. Thank you.

[Pierre Lindenbaum]

why python when you can use a shell script ?

[iamsmor]

because ı followed guidline for NCBI blast. Btw ı got only similarity results by script of python.I used blast search tool and get some list of protein but ı dont know how ı can connect results to pubchem compount (by e-link)

Answer 1

[Asaf]

The easiest way would be to use NCBI BLAST web interface, where you can simply check the box next to "Align two or more sequences" and just give the accession IDs as input: pdb|6UFO|A and pdb|4XMB|A (A is the chain)

[iamsmor]

thank you ı used web interface already but ı could not set elink for puchem compounds.

[Asaf]

I didn't understand how it's related to your post. Can you please elaborate?