How do I overwrite the 7th, 8th and 9th column of the text file with new values? What can I use?

ATOM      1  N   ASN A   1      12.844  -5.008 -17.071  1.00  0.00           N  
ATOM      2  CA  ASN A   1      12.377  -4.399 -15.793  1.00  0.00           C  
ATOM      3  C   ASN A   1      12.631  -2.888 -15.803  1.00  0.00           C

Depends on the kind of updates you are making; are they for the entire file or only parts of the file? If for the entire file, read the file line by line and write out the modified line to a new file. If the updates are targeted updates and only for selective lines in the entire text file, look into the RandomAccessFile class though I must say it's a bit tricky to get right.