Re: [PyMOL] script to write down distances ligand-protein: need feedback

[Andrea Spitaleri]

>   HBA = cmd.distance('HBA', '(lig and acc)','(active and don)', 3.2)
yes thanks for the trick. However, I edited my script to:
DistOutput.write(" %14s  %14s %8s %8s\n"%("donor","acceptor","hba","hbd"))
DistOutput.write(" %14s  %14s %8.3f %8.3f\n"%(Don,Acc,HBA,HBD))
but I cannot figure out the meaning of the output:
complex_1
          donor        acceptor      hba      hbd
            260             271    2.536   -1.000
complex_2
          donor        acceptor      hba      hbd
            391             409    2.489   -1.000
complex_3
          donor        acceptor      hba      hbd
            522             547    2.512   -1.000
complex_4
          donor        acceptor      hba      hbd
            653             685    2.456   -1.000
what the numbers under donor and acceptor are?

> 
>   atoms_Don = cmd.index('don')
> 

I tried also this option and it works fine (more or less) excet that
it takes a lot time to calculate all the distance (quite weird on my
dual-cpu 3Gz intel)
this is the loop used:
   for donor in atoms_Don:
            for acceptor in atoms_Acc:
                di = cmd.get_distance("%s`%d"%donor,"%s`%d"%acceptor)
                DistOutput.write("%8s %8s %8.3f\n"%(donor,acceptor,di))

thanks

Regards

andrea