Re: [IMP-users] accuracy and get_average_distance_wrt_reference_structure()

[Julian <>]

I downloaded ftp://salilab.org/tutorials/imp/rnapolii/analysis.tar.gz from the tutorial and ran that against the native.rmf3 in the data directory from git

So, my guess is analysis.tar.gz was created from an earlier version that might have had a slightly different representation defined.Â

Either way, you answered my question.

Thanks,

Julian

On Tue, Oct 4, 2016 at 3:49 PM, Ben Webb <" target="_blank">> wrote:

On 09/15/2016 03:37 PM, Julian wrote:

While playing around with the tutorial, I noticed that the accuracy
calculation errors out:

...

_IMP_kernel.ValueException: Number of children doesn't match the number
of representation nodes at Rpb1. They are 4 and 3 respectively. [2, 8,
1432, 1585] vs [Beads(representation, n3), Rpb1_Res:1(representation,
n9), Rpb1_Res:10(representation, n1433)]

By "playing around", I take it you changed something fundamental? This shouldn't happen if you just run the tutorial as-is.

As far as I understand this is because the representation details in the
native.rmf3 do not exactly match those of the modeled system.

Right, the representation has to match otherwise the (rather simplistic) script cannot determine which pairs of particles correspond in the two models. This isn't something we've worried too much about since usually we don't know the "right answer" anyway. If for some reason you wanted to compare different representations, first you'd have to figure out how to map one onto the other. In *some* cases this is straightforward (e.g. it's pretty easy to coarse grain an atomic model).

    Ben
--
" target="_blank">Â Â Â Â Â Â Â Â Â Â Â https://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
    - Sir Arthur Conan Doyle
_______________________________________________
IMP-users mailing list
" target="_blank">
https://salilab.org/mailman/listinfo/imp-users