Hi Enrico,
I don't see how you could get that error.  I couldn't reproduce it myself.  I would need some kind of recipe for how you get it to occur.  A separate problem is that the averaging in the script isn't really right.  Line 21 of the script should be changed from:

weight = window + 1 + abs(i-j)

to:

weight = window + 1 - abs(i-j)

i.e. change the "+ abs(...)" to "- abs(...)". I have corrected the script on the Scripts page.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab


On Nov 14, 2023, at 6:31 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

update: i've just opened closed chimera-x and reloaded my pdb and
everything works as expected. probably there is a bug somewhere ..

Il giorno mar 14 nov 2023 alle ore 14:56 Enrico Martinez
<jmsstarlight@gmail.com> ha scritto:

Dear Chimera-X users.

I am trying to record a md trajectory loaded as multi-pdb file:

open ./stripped_traj2.pdb coordsets true

I have the issue with smooth-md script (enclosed), which produces the
following error:

open smooth_md_chX.py
open /home/test/Bureau/MOVIE_CHIMERAX\/smooth_md_chX.pyTraceback (most
recent call last):
File "/home/test/Bureau/MOVIE_CHIMERAX\/smooth_md_chX.py", line 23, in <module>
avg += weight * coord_sets[j]
ValueError: operands could not be broadcast together with shapes
(6120,3) (6112,3) (6120,3)

Should something be fixed in the script in order that I could observe
the MD movie with smooth details ?

Thank you in advance

Enrico
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