Re: Smooth-MD script for a trajectory visualisation
Hello Eric, Just one extra question about the Smooth-MD script :-) Would it be possible to extend the idea of different smooth windows on different selections within the same model id (besides the version that we discussed applying for several different models).. For example, I have a complex system composed of membrane protein bound to a ligand embedded in explicit water and lipids. So, I divided all the components according to three different selections, which I would like smooth differently, in the following way: 1) protein & ligand (protein | :LIG) --> smooth with 5 windows 2) lipids according to amber naming (:PC,PE,PS, OL,PA) smooth with 6 windows 3) water and ions (:WAT|:NA*|:Cl*) smooth with 7 windows Would it be possible to do such tricky things using the same script? Many thanks in advance ! Enrico Il giorno sab 19 ott 2024 alle ore 02:55 Eric Pettersen <pett@cgl.ucsf.edu> ha scritto:
Hi Enrico, Our servers have been down this week, so this is my first opportunity to respond. So one possible approach is to change the "window = 10" line to:
window_by_id = { (1,): 5, (2,): 10 }
and change the 'if/continue' statement just inside the loop to:
try: window = window_by_id[s.id] except KeyError: continue
The 'id' attribute of a model is a tuple of the model ID numbers, so for model #1 it would be (1,), for model #2.2.1 it would be (2,2,1), etc. So the try/except clause skips all models other than the ones you explicitly put in the window_by_id dictionary.
--Eric
On Oct 11, 2024, at 1:32 PM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Hello Eric,
I have an extra question about the Smooth MD script: I modified it abit to apply the smoth effect only on a model with the name "ottimo.pdb" so that it will affect only one selected model ( in the case when there are several models in the same session ..) Here is this version enclosed.
Could you suggest how it could be further modified to affect e.g. 2 models via 2 different smooth windows e.g. smooth the model with the id 1 window=5 and smooth the model with the id 2 with window2=10 ?
Many thanks for help!
Enrico
Il giorno ven 8 dic 2023 alle ore 16:10 Enrico Martinez < jmsstarlight@gmail.com> ha scritto:
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 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
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Well, yes, but you would have to have a good knowledge of numpy operations, since the coordinate sets are numpy arrays. Your structure model will have an ‘atoms’ attribute that returns an “Atoms" instance that contains the structure’s atoms in coordinate-set order. The Atoms instance has ‘residues.names’ and ’structure_categories’ attributes that return numpy arrays of those values that can in turn be used in masking operations to assemble the smoothed coordinates in piecemeal fashion. Not really for the faint of heart. —Eric
On Oct 26, 2024, at 3:03 PM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Hello Eric,
Just one extra question about the Smooth-MD script :-)
Would it be possible to extend the idea of different smooth windows on different selections within the same model id (besides the version that we discussed applying for several different models).. For example, I have a complex system composed of membrane protein bound to a ligand embedded in explicit water and lipids. So, I divided all the components according to three different selections, which I would like smooth differently, in the following way:
1) protein & ligand (protein | :LIG) --> smooth with 5 windows 2) lipids according to amber naming (:PC,PE,PS, OL,PA) smooth with 6 windows 3) water and ions (:WAT|:NA*|:Cl*) smooth with 7 windows
Would it be possible to do such tricky things using the same script?
Many thanks in advance !
Enrico
Il giorno sab 19 ott 2024 alle ore 02:55 Eric Pettersen <pett@cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> ha scritto:
Hi Enrico, Our servers have been down this week, so this is my first opportunity to respond. So one possible approach is to change the "window = 10" line to:
window_by_id = { (1,): 5, (2,): 10 }
and change the 'if/continue' statement just inside the loop to:
try: window = window_by_id[s.id <http://s.id/>] except KeyError: continue
The 'id' attribute of a model is a tuple of the model ID numbers, so for model #1 it would be (1,), for model #2.2.1 it would be (2,2,1), etc. So the try/except clause skips all models other than the ones you explicitly put in the window_by_id dictionary.
--Eric
On Oct 11, 2024, at 1:32 PM, Enrico Martinez <jmsstarlight@gmail.com <mailto:jmsstarlight@gmail.com>> wrote:
Hello Eric,
I have an extra question about the Smooth MD script: I modified it abit to apply the smoth effect only on a model with the name "ottimo.pdb" so that it will affect only one selected model ( in the case when there are several models in the same session ..) Here is this version enclosed.
Could you suggest how it could be further modified to affect e.g. 2 models via 2 different smooth windows e.g. smooth the model with the id 1 window=5 and smooth the model with the id 2 with window2=10 ?
Many thanks for help!
Enrico
Il giorno ven 8 dic 2023 alle ore 16:10 Enrico Martinez <jmsstarlight@gmail.com <mailto:jmsstarlight@gmail.com>> ha scritto:
Thank you very much Eric !
Cheers
Enrico
Le mer. 6 déc. 2023 à 19:02, Eric Pettersen <pett@cgl.ucsf.edu <mailto: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 <mailto: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 <mailto: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 Lab > > >> On Dec 5, 2023, at 7:13 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto:chimerax-users@cgl.ucsf.edu> >>>>> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto: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 <mailto:chimerax-users@cgl.ucsf.edu> >>>> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto: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 <mailto:chimerax-users@cgl.ucsf.edu> >> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto: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 <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
I actually thought that it could be like this ! That's why I found a more easy way to apply smoothness on the separate models. Well, I hope that one day the things will be more simple for non-python experts :-) Anyway, it could be cool to have a short example of the script demonstrating how to apply just two different smooth windows w.g. on WATER and on the rest of the system :-) Yours sincerely Enrico Il giorno lun 28 ott 2024 alle ore 20:13 Eric Pettersen <pett@cgl.ucsf.edu> ha scritto:
Well, yes, but you would have to have a good knowledge of numpy operations, since the coordinate sets are numpy arrays. Your structure model will have an ‘atoms’ attribute that returns an “Atoms" instance that contains the structure’s atoms in coordinate-set order. The Atoms instance has ‘residues.names’ and ’structure_categories’ attributes that return numpy arrays of those values that can in turn be used in masking operations to assemble the smoothed coordinates in piecemeal fashion. Not really for the faint of heart.
—Eric
On Oct 26, 2024, at 3:03 PM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Hello Eric,
Just one extra question about the Smooth-MD script :-)
Would it be possible to extend the idea of different smooth windows on different selections within the same model id (besides the version that we discussed applying for several different models).. For example, I have a complex system composed of membrane protein bound to a ligand embedded in explicit water and lipids. So, I divided all the components according to three different selections, which I would like smooth differently, in the following way:
1) protein & ligand (protein | :LIG) --> smooth with 5 windows 2) lipids according to amber naming (:PC,PE,PS, OL,PA) smooth with 6 windows 3) water and ions (:WAT|:NA*|:Cl*) smooth with 7 windows
Would it be possible to do such tricky things using the same script?
Many thanks in advance !
Enrico
Il giorno sab 19 ott 2024 alle ore 02:55 Eric Pettersen <pett@cgl.ucsf.edu> ha scritto:
Hi Enrico, Our servers have been down this week, so this is my first opportunity to respond. So one possible approach is to change the "window = 10" line to:
window_by_id = { (1,): 5, (2,): 10 }
and change the 'if/continue' statement just inside the loop to:
try: window = window_by_id[s.id] except KeyError: continue
The 'id' attribute of a model is a tuple of the model ID numbers, so for model #1 it would be (1,), for model #2.2.1 it would be (2,2,1), etc. So the try/except clause skips all models other than the ones you explicitly put in the window_by_id dictionary.
--Eric
On Oct 11, 2024, at 1:32 PM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Hello Eric,
I have an extra question about the Smooth MD script: I modified it abit to apply the smoth effect only on a model with the name "ottimo.pdb" so that it will affect only one selected model ( in the case when there are several models in the same session ..) Here is this version enclosed.
Could you suggest how it could be further modified to affect e.g. 2 models via 2 different smooth windows e.g. smooth the model with the id 1 window=5 and smooth the model with the id 2 with window2=10 ?
Many thanks for help!
Enrico
Il giorno ven 8 dic 2023 alle ore 16:10 Enrico Martinez < jmsstarlight@gmail.com> ha scritto:
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 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/
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participants (2)
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Enrico Martinez -
Eric Pettersen