Hi,
I suppose that these numbers are the atom_ids. It's probably the same
numbers returned by the cmd.index function.
I guess you could test this by typing "select atom260, id 260" and see if
that makes a selection with atom260...
As for the speed question, I have no idea. More of a question for Mr DeLano
:) Calculating pairwise like this is always going to be computationally
expensive, but I don't know ways to speed this up.
gilleain torrance
On 5/7/05 15:17, "Andrea Spitaleri" <andrea.spital...@gmail.com> wrote:
>> 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
>
>
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