Gotcha, thank you very much Eric ! BTW what is the value for the window that should be used ? Does it mean that the higher value would result in smoother dynamics ? Enrico Il giorno mar 14 nov 2023 alle ore 19:47 Eric Pettersen <pett@cgl.ucsf.edu> ha scritto:
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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