The following commands for MOLMOL are not perfect enough to do all work I'd like to do. My purpose is calculating the distance of some particular pairs, for example, NH(i), NH(i+1), HA(i), NH(i+1)…that's a way to evaluate the NOE constraints and the proteins structure you want to compare. I know you could say the software running structure calculation does this function well, but sometimes, I don't do calculation, I just want to get the distance list…
Here is the commands (using 2GB1, res 41-56 as examples)
CalcDist 5 1 1 0 1 0 0 'selected' 'selected'
and you will get a window like this:
41 GLY H 42 GLU H 60 (2.68..3.80)
41 GLY H 55 THR H 3 (4.97..4.99)
42 GLU H 55 THR H 60 (3.32..3.58)
42 GLU H 56 GLU H 26 (4.80..4.99)
It doesn't fit my request, but at least generate enough data I want to see. I set 5A as the upper boundary, all H to H distances which are shorter than 5A will return in the window. For the above data, 3 of 60 structure of 2GB1 has 41G NH to 55T NH distance closer than others, and the distance range is 3.32 to 3.58 A.