Software:nest Documentation

From Honiglab_public

Using nest:

Usage: nest -seed num -fast num  -tune num -log str -opt num -nopt num  -out num file.pir
-fast     fast mode.from 0-5; default is 3.with 5 fastest
-tune     alignment tuning, from 0-3; defautl is 0.
          0,no alignment tuning
          1,remove gaps in secondary strucutre
          2,remove zig-zag gaps  plus -tune 1;
          3,remove terminal gaps plus -tune 2;
-opt      refine mode, from 0-4; default is 1.with 4 thorough refinement
          0, no minimization at all;
          1, remove atom clashes; 
          2, refine in insertion and deletion regions, usually loop regions; 
          3, refine in all loop regions;
          4, refine in all loop and secondary regions
-out      output mode, from 0-2, defautl is 0. with 2 all intermediate output
          0, only final structures written down;
          1, intermediate structures also outputted;
          2, more intermediate output
-seed     set seed number, defautl is 18120.
-nopt     number of rounds of refinement.default is 1.
-log      log file.default is standard screen output
file.pir  pir alignment file

Go Back

---

nest is supported by a funding from the National Science Foundation Grant # DBI-9904841

Developed in the Honig Lab