August 16, 2004

科學 :: convpdb.pl

One of my collection of handy tools playing with PDB data format is convpdb from Scripps. It can do:

  1. Simple Alignment
    2. I use this to match short sequences.
  2. Renumbering
    3. Saves you some time. However, this one might be better.
  3. Conversion
    4. You can convert between Brookhaven, AMBER and Charmm. At least this is much better than my way. However it still can't do MSI PDB conversion and you might want to use this.

Ray asked me how to get the sequence of the PDB and get the one-letter codes in the dumbest way.
It turns out this fortran program can do the magic http://www.ccp4.ac.uk/dist/src/pdbset.f. My way is kinda crap, I use RasMol's 'show sequence' and paste the sequence to those web service. ^^;

By mjhsieh at August 16, 2004 03:41 AM | Monthly Archives