Smooth-MD script for a trajectory visualisation
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
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
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 https://www.cgl.ucsf.edu/trac/chimera/wiki/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
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
You are welcome.
I don't think there is a "right" value for the window. A larger value will provide more smoothing, while also creating more non-physical geometries for highly mobile parts of the structure. A judgement call really.
--Eric
On Nov 15, 2023, at 3:33 AM, Enrico Martinez via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
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
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
update: I've just got a crash with md-smooth py script on chimera-x working on a big system with > 1000 frames loaded in a single pdb (with smaller trajectory there is no issues ..)
Enrico
Il giorno mer 15 nov 2023 alle ore 18:53 Eric Pettersen pett@cgl.ucsf.edu ha scritto:
You are welcome.
I don't think there is a "right" value for the window. A larger value will provide more smoothing, while also creating more non-physical geometries for highly mobile parts of the structure. A judgement call really.
--Eric
On Nov 15, 2023, at 3:33 AM, Enrico Martinez via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
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
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Well, the smoothing script temporarily takes about triple the memory use of the baseline trajectory, so I can imagine it crashing for a large trajectory. Do you need 1000 frames? I could change the script to use every Nth frame, which would use a lot less memory...
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Dec 5, 2023, at 7:13 AM, Enrico Martinez via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
update: I've just got a crash with md-smooth py script on chimera-x working on a big system with > 1000 frames loaded in a single pdb (with smaller trajectory there is no issues ..)
Enrico
Il giorno mer 15 nov 2023 alle ore 18:53 Eric Pettersen pett@cgl.ucsf.edu ha scritto:
You are welcome.
I don't think there is a "right" value for the window. A larger value will provide more smoothing, while also creating more non-physical geometries for highly mobile parts of the structure. A judgement call really.
--Eric
On Nov 15, 2023, at 3:33 AM, Enrico Martinez via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
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
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
and generally it would be visually fine with averaging of every N frame ? well it would be interesting to test anyway :-)
Cheers
Enrico
Il giorno mar 5 dic 2023 alle ore 19:30 Eric Pettersen pett@cgl.ucsf.edu ha scritto:
Well, the smoothing script temporarily takes about triple the memory use of the baseline trajectory, so I can imagine it crashing for a large trajectory. Do you need 1000 frames? I could change the script to use every Nth frame, which would use a lot less memory...
--Eric
Eric Pettersen UCSF Computer Graphics LabOn Dec 5, 2023, at 7:13 AM, Enrico Martinez via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
update: I've just got a crash with md-smooth py script on chimera-x working on a big system with > 1000 frames loaded in a single pdb (with smaller trajectory there is no issues ..)
Enrico
Il giorno mer 15 nov 2023 alle ore 18:53 Eric Pettersen pett@cgl.ucsf.edu ha scritto:
You are welcome.
I don't think there is a "right" value for the window. A larger value will provide more smoothing, while also creating more non-physical geometries for highly mobile parts of the structure. A judgement call really.
--Eric
On Nov 15, 2023, at 3:33 AM, Enrico Martinez via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
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
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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Hi Enrico, I have updated the smoothing script on the Scripts https://www.cgl.ucsf.edu/trac/chimera/wiki/Scripts page. If you get a new version, there is a line near the top ("stride = 1") that you can edit to make it use, say, every 5th frame ("stride = 5"). One issue is that the coordinate set slider doesn't properly react to the change in the number of frames. You have to close the slider and open a new one ("coordset slider #1"). I will look into fixing that.
--Eric
On Dec 6, 2023, at 1:34 AM, Enrico Martinez via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
and generally it would be visually fine with averaging of every N frame ? well it would be interesting to test anyway :-)
Cheers
Enrico
Il giorno mar 5 dic 2023 alle ore 19:30 Eric Pettersen pett@cgl.ucsf.edu ha scritto:
Well, the smoothing script temporarily takes about triple the memory use of the baseline trajectory, so I can imagine it crashing for a large trajectory. Do you need 1000 frames? I could change the script to use every Nth frame, which would use a lot less memory...
--Eric
Eric Pettersen UCSF Computer Graphics LabOn Dec 5, 2023, at 7:13 AM, Enrico Martinez via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
update: I've just got a crash with md-smooth py script on chimera-x working on a big system with > 1000 frames loaded in a single pdb (with smaller trajectory there is no issues ..)
Enrico
Il giorno mer 15 nov 2023 alle ore 18:53 Eric Pettersen pett@cgl.ucsf.edu ha scritto:
You are welcome.
I don't think there is a "right" value for the window. A larger value will provide more smoothing, while also creating more non-physical geometries for highly mobile parts of the structure. A judgement call really.
--Eric
On Nov 15, 2023, at 3:33 AM, Enrico Martinez via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
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
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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Thank you very much Eric !
Cheers
Enrico
Le mer. 6 déc. 2023 à 19:02, Eric Pettersen pett@cgl.ucsf.edu a écrit :
Hi Enrico, I have updated the smoothing script on the Scripts https://www.cgl.ucsf.edu/trac/chimera/wiki/Scripts page. If you get a new version, there is a line near the top ("stride = 1") that you can edit to make it use, say, every 5th frame ("stride = 5"). One issue is that the coordinate set slider doesn't properly react to the change in the number of frames. You have to close the slider and open a new one ("coordset slider #1"). I will look into fixing that.
--Eric
On Dec 6, 2023, at 1:34 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
and generally it would be visually fine with averaging of every N frame ? well it would be interesting to test anyway :-)
Cheers
Enrico
Il giorno mar 5 dic 2023 alle ore 19:30 Eric Pettersen pett@cgl.ucsf.edu ha scritto:
Well, the smoothing script temporarily takes about triple the memory use of the baseline trajectory, so I can imagine it crashing for a large trajectory. Do you need 1000 frames? I could change the script to use every Nth frame, which would use a lot less memory...
--Eric
Eric Pettersen UCSF Computer Graphics LabOn Dec 5, 2023, at 7:13 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
update: I've just got a crash with md-smooth py script on chimera-x working on a big system with > 1000 frames loaded in a single pdb (with smaller trajectory there is no issues ..)
Enrico
Il giorno mer 15 nov 2023 alle ore 18:53 Eric Pettersen pett@cgl.ucsf.edu ha scritto:
You are welcome.
I don't think there is a "right" value for the window. A larger value will provide more smoothing, while also creating more non-physical geometries for highly mobile parts of the structure. A judgement call really.
--Eric
On Nov 15, 2023, at 3:33 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
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
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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participants (2)
-
Enrico Martinez -
Eric Pettersen