About surface representation
Dear ChimeraX users! I am performing visualization of a molecular dynamics trajectory containing a membrane system. I have two questions about surface representation. 1- I've found that the quality of the surface could be mainly controlled using two options gridSpacing and probeRadius so that decreasing the both usually produces better results. Are there other relevant parameters that could improve the quality of the surface ? 2- Setting different degrees of transparency of different selections. In the case when the lipids in the modelled membrane are splitted into two parts (according to the amber force field) I tried to colour the heads and tails differently setting different degree of transparency, using # first color the entire membrane in blue color ~protein blue surface transparency 40 # color only the headgroups in red setting less transparency color :PC red surface transparency 80 This looks as expected only in the current frame. However, when I start to play a trajectory using coordset, the both selections become equally transparent (setting to 40). Is it possible to control this in a more flexible way ? Thank you very much in advance Best regards Enrico
I will try to answer #1: As I understand it, gridSpacing is really the only "quality" setting for surfaces. Decreasing the probeRadius doesn't change the quality of a solvent-excluded surface, it just changes the shape of surface to include smaller crevices. The figure in the "surface" manual page shows how the probe radius affects the shape of the solvent-excluded surface: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html> Surface calculation parameters are explained here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#options> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#parameters> As explained in the link above, the "resolution" option does not apply to a solvent-excluded surface, but instead changes the calculation to a Gaussian surface. Gaussian surfaces do not use the atomic VDW radii or probe radius, but instead the specified "resolution" and "level" values. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 4, 2024, at 7:59 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX users!
I am performing visualization of a molecular dynamics trajectory containing a membrane system. I have two questions about surface representation.
1- I've found that the quality of the surface could be mainly controlled using two options gridSpacing and probeRadius so that decreasing the both usually produces better results. Are there other relevant parameters that could improve the quality of the surface ?
2- Setting different degrees of transparency of different selections. In the case when the lipids in the modelled membrane are splitted into two parts (according to the amber force field) I tried to colour the heads and tails differently setting different degree of transparency, using
# first color the entire membrane in blue color ~protein blue surface transparency 40 # color only the headgroups in red setting less transparency color :PC red surface transparency 80
This looks as expected only in the current frame. However, when I start to play a trajectory using coordset, the both selections become equally transparent (setting to 40). Is it possible to control this in a more flexible way ?
Thank you very much in advance
Best regards
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/
Regarding question #2, we have discussed this multiple times on the mailing list with you. Let me summarize those previous discussions. When molecular surfaces are recomputed during an MD trajectory playback the transparency is not copied when different transparency levels are used for different atoms and you will need to use a perframe script to set the transparency each time after the molecular surface is computed (which is tricky to do because automatic molecular surface computation is done after perframe commands, so see the previous mailing list messages for the tricks needed to achieve this, basically you have to close the surface and manually create it at each frame). Tom
On Apr 4, 2024, at 7:59 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX users!
I am performing visualization of a molecular dynamics trajectory containing a membrane system. I have two questions about surface representation.
1- I've found that the quality of the surface could be mainly controlled using two options gridSpacing and probeRadius so that decreasing the both usually produces better results. Are there other relevant parameters that could improve the quality of the surface ?
2- Setting different degrees of transparency of different selections. In the case when the lipids in the modelled membrane are splitted into two parts (according to the amber force field) I tried to colour the heads and tails differently setting different degree of transparency, using
# first color the entire membrane in blue color ~protein blue surface transparency 40 # color only the headgroups in red setting less transparency color :PC red surface transparency 80
This looks as expected only in the current frame. However, when I start to play a trajectory using coordset, the both selections become equally transparent (setting to 40). Is it possible to control this in a more flexible way ?
Thank you very much in advance
Best regards
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/
Thank you very much Tom ! In fact I have tested the perframe method from your previous message but it was much slower compared to the more direct way of the surface recording mentioned in my first message. I just wondered whether it could be fixed (to apply transparency on different layers in future builds of the Chimera-X... Yours with thanks Enrico Il giorno ven 5 apr 2024 alle ore 03:10 Tom Goddard <goddard@sonic.net> ha scritto:
Regarding question #2, we have discussed this multiple times on the mailing list with you. Let me summarize those previous discussions. When molecular surfaces are recomputed during an MD trajectory playback the transparency is not copied when different transparency levels are used for different atoms and you will need to use a perframe script to set the transparency each time after the molecular surface is computed (which is tricky to do because automatic molecular surface computation is done after perframe commands, so see the previous mailing list messages for the tricks needed to achieve this, basically you have to close the surface and manually create it at each frame).
Tom
On Apr 4, 2024, at 7:59 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX users!
I am performing visualization of a molecular dynamics trajectory containing a membrane system. I have two questions about surface representation.
1- I've found that the quality of the surface could be mainly controlled using two options gridSpacing and probeRadius so that decreasing the both usually produces better results. Are there other relevant parameters that could improve the quality of the surface ?
2- Setting different degrees of transparency of different selections. In the case when the lipids in the modelled membrane are splitted into two parts (according to the amber force field) I tried to colour the heads and tails differently setting different degree of transparency, using
# first color the entire membrane in blue color ~protein blue surface transparency 40 # color only the headgroups in red setting less transparency color :PC red surface transparency 80
This looks as expected only in the current frame. However, when I start to play a trajectory using coordset, the both selections become equally transparent (setting to 40). Is it possible to control this in a more flexible way ?
Thank you very much in advance
Best regards
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/
Thank you very much Elaine ! In fact, asI found that the probeRadius is useful for visualisation of the lipids in membrane systems since it could "shapes" their form better (as you have mentioned in your reply). BTW a I noticed decreasing the probeRadius also significantly requires more calculation time. Yours sincerely Enrico Il giorno ven 5 apr 2024 alle ore 00:48 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
I will try to answer #1:
As I understand it, gridSpacing is really the only "quality" setting for surfaces.
Decreasing the probeRadius doesn't change the quality of a solvent-excluded surface, it just changes the shape of surface to include smaller crevices. The figure in the "surface" manual page shows how the probe radius affects the shape of the solvent-excluded surface: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html>
Surface calculation parameters are explained here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#options> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#parameters
As explained in the link above, the "resolution" option does not apply to a solvent-excluded surface, but instead changes the calculation to a Gaussian surface. Gaussian surfaces do not use the atomic VDW radii or probe radius, but instead the specified "resolution" and "level" values.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 4, 2024, at 7:59 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX users!
I am performing visualization of a molecular dynamics trajectory containing a membrane system. I have two questions about surface representation.
1- I've found that the quality of the surface could be mainly controlled using two options gridSpacing and probeRadius so that decreasing the both usually produces better results. Are there other relevant parameters that could improve the quality of the surface ?
2- Setting different degrees of transparency of different selections. In the case when the lipids in the modelled membrane are splitted into two parts (according to the amber force field) I tried to colour the heads and tails differently setting different degree of transparency, using
# first color the entire membrane in blue color ~protein blue surface transparency 40 # color only the headgroups in red setting less transparency color :PC red surface transparency 80
This looks as expected only in the current frame. However, when I start to play a trajectory using coordset, the both selections become equally transparent (setting to 40). Is it possible to control this in a more flexible way ?
Thank you very much in advance
Best regards
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/
The time to play an MD movie with molecular surfaces is going to be dominated by the surface calculation time, and it will make no difference how transparency is applied. Propagating per-atom transparency as the surface is recomputed will probably never be implemented due to lack of resources. Tom
On Apr 5, 2024, at 2:39 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Thank you very much Tom !
In fact I have tested the perframe method from your previous message but it was much slower compared to the more direct way of the surface recording mentioned in my first message. I just wondered whether it could be fixed (to apply transparency on different layers in future builds of the Chimera-X...
Yours with thanks
Enrico
Il giorno ven 5 apr 2024 alle ore 03:10 Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> ha scritto:
Regarding question #2, we have discussed this multiple times on the mailing list with you. Let me summarize those previous discussions. When molecular surfaces are recomputed during an MD trajectory playback the transparency is not copied when different transparency levels are used for different atoms and you will need to use a perframe script to set the transparency each time after the molecular surface is computed (which is tricky to do because automatic molecular surface computation is done after perframe commands, so see the previous mailing list messages for the tricks needed to achieve this, basically you have to close the surface and manually create it at each frame).
Tom
On Apr 4, 2024, at 7:59 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Dear ChimeraX users!
I am performing visualization of a molecular dynamics trajectory containing a membrane system. I have two questions about surface representation.
1- I've found that the quality of the surface could be mainly controlled using two options gridSpacing and probeRadius so that decreasing the both usually produces better results. Are there other relevant parameters that could improve the quality of the surface ?
2- Setting different degrees of transparency of different selections. In the case when the lipids in the modelled membrane are splitted into two parts (according to the amber force field) I tried to colour the heads and tails differently setting different degree of transparency, using
# first color the entire membrane in blue color ~protein blue surface transparency 40 # color only the headgroups in red setting less transparency color :PC red surface transparency 80
This looks as expected only in the current frame. However, when I start to play a trajectory using coordset, the both selections become equally transparent (setting to 40). Is it possible to control this in a more flexible way ?
Thank you very much in advance
Best regards
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/
Very helpful, thank you very much Tom ! All the best Enrico Il giorno ven 5 apr 2024 alle ore 21:24 Tom Goddard <goddard@sonic.net> ha scritto:
The time to play an MD movie with molecular surfaces is going to be dominated by the surface calculation time, and it will make no difference how transparency is applied. Propagating per-atom transparency as the surface is recomputed will probably never be implemented due to lack of resources.
Tom
On Apr 5, 2024, at 2:39 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Thank you very much Tom !
In fact I have tested the perframe method from your previous message but it was much slower compared to the more direct way of the surface recording mentioned in my first message. I just wondered whether it could be fixed (to apply transparency on different layers in future builds of the Chimera-X...
Yours with thanks
Enrico
Il giorno ven 5 apr 2024 alle ore 03:10 Tom Goddard <goddard@sonic.net> ha scritto:
Regarding question #2, we have discussed this multiple times on the mailing list with you. Let me summarize those previous discussions. When molecular surfaces are recomputed during an MD trajectory playback the transparency is not copied when different transparency levels are used for different atoms and you will need to use a perframe script to set the transparency each time after the molecular surface is computed (which is tricky to do because automatic molecular surface computation is done after perframe commands, so see the previous mailing list messages for the tricks needed to achieve this, basically you have to close the surface and manually create it at each frame).
Tom
On Apr 4, 2024, at 7:59 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX users!
I am performing visualization of a molecular dynamics trajectory containing a membrane system. I have two questions about surface representation.
1- I've found that the quality of the surface could be mainly controlled using two options gridSpacing and probeRadius so that decreasing the both usually produces better results. Are there other relevant parameters that could improve the quality of the surface ?
2- Setting different degrees of transparency of different selections. In the case when the lipids in the modelled membrane are splitted into two parts (according to the amber force field) I tried to colour the heads and tails differently setting different degree of transparency, using
# first color the entire membrane in blue color ~protein blue surface transparency 40 # color only the headgroups in red setting less transparency color :PC red surface transparency 80
This looks as expected only in the current frame. However, when I start to play a trajectory using coordset, the both selections become equally transparent (setting to 40). Is it possible to control this in a more flexible way ?
Thank you very much in advance
Best regards
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/
participants (3)
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Elaine Meng -
Enrico Martinez -
Tom Goddard