This is how I am doing it right now
- I go to https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome
- Paste query sequence
- Select pdb as database
- Select PSI-BLAST as algorithm
- Run, wait for results and copy paste required data from results
If there is an XML output using url only, I could easily automate the process. How to make such url?