Surface representation for small compounds
Dear ChimeraX users I am also experimenting on the representation of the surfaces of small compounds surface ligand gridSpacing 0.5 probeRadius 1.2 color ligand white target s transparency 90 This creates a relatively large transparent surface around the small compound. How would it be possible to reduce the volume of the surface ? Also I did not understand how to change the style of the surface among dot/mesh etc since adding style dot did not work. I would appreciate any further creative examples of how to change the representation of a small compound in the case when I need to make it more "coarse-graining" , hiding some precise details of the structure ? Many thanks in advance ! Enrico
Hello, This works fine for me: open 1gcn surf surf style dot However, the dot style can be very hard to see since the linewidth (dot size) is small and you cannot increase it, and/or the surface vertices are spaced rather far apart. Here are two ideas for making a low-resolution surface for atoms: (A) instead of a standard molecular surface, make a gaussian surface by using "surface" with the "resolution" option <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html> - OR - (B) try making a density map from the ligand with "molmap" ... then you can adjust the isosurface level, etc. like for other density maps <https://rbvi.ucsf.edu/chimerax/docs/user/commands/molmap.html> See the help links above for additional options such as to control vertex spacing of these surfaces. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 7, 2024, at 2:06 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX users
I am also experimenting on the representation of the surfaces of small compounds
surface ligand gridSpacing 0.5 probeRadius 1.2 color ligand white target s transparency 90
This creates a relatively large transparent surface around the small compound. How would it be possible to reduce the volume of the surface ?
Also I did not understand how to change the style of the surface among dot/mesh etc since adding style dot did not work.
I would appreciate any further creative examples of how to change the representation of a small compound in the case when I need to make it more "coarse-graining" , hiding some precise details of the structure ?
Many thanks in advance !
Enrico
MAny thanks Elaine ! Actually the molmap is a great option, and it does what I need. I noticed that it always displays a "frozen" map selected for a particular frame in the case of multi-frame pdb. Would it be possible to update the generated map for each frame of my multi model pdb visualized as the md trajectory (open ./trajectory.pdb coordset true) ? Yours with thanks Enrico Il giorno gio 8 feb 2024 alle ore 23:28 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
Hello, This works fine for me:
open 1gcn surf surf style dot
However, the dot style can be very hard to see since the linewidth (dot size) is small and you cannot increase it, and/or the surface vertices are spaced rather far apart.
Here are two ideas for making a low-resolution surface for atoms:
(A) instead of a standard molecular surface, make a gaussian surface by using "surface" with the "resolution" option <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html>
- OR -
(B) try making a density map from the ligand with "molmap" ... then you can adjust the isosurface level, etc. like for other density maps <https://rbvi.ucsf.edu/chimerax/docs/user/commands/molmap.html>
See the help links above for additional options such as to control vertex spacing of these surfaces.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 7, 2024, at 2:06 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX users
I am also experimenting on the representation of the surfaces of small compounds
surface ligand gridSpacing 0.5 probeRadius 1.2 color ligand white target s transparency 90
This creates a relatively large transparent surface around the small compound. How would it be possible to reduce the volume of the surface ?
Also I did not understand how to change the style of the surface among dot/mesh etc since adding style dot did not work.
I would appreciate any further creative examples of how to change the representation of a small compound in the case when I need to make it more "coarse-graining" , hiding some precise details of the structure ?
Many thanks in advance !
Enrico
P.S. and for the surface style actually it works for the whole surface like demonstrated in your example, but unfortunately it does not work for the selection e.g. surf :lig style dot Il giorno ven 9 feb 2024 alle ore 10:04 Enrico Martinez <jmsstarlight@gmail.com> ha scritto:
MAny thanks Elaine !
Actually the molmap is a great option, and it does what I need.
I noticed that it always displays a "frozen" map selected for a particular frame in the case of multi-frame pdb. Would it be possible to update the generated map for each frame of my multi model pdb visualized as the md trajectory (open ./trajectory.pdb coordset true) ?
Yours with thanks
Enrico
Il giorno gio 8 feb 2024 alle ore 23:28 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
Hello, This works fine for me:
open 1gcn surf surf style dot
However, the dot style can be very hard to see since the linewidth (dot size) is small and you cannot increase it, and/or the surface vertices are spaced rather far apart.
Here are two ideas for making a low-resolution surface for atoms:
(A) instead of a standard molecular surface, make a gaussian surface by using "surface" with the "resolution" option <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html>
- OR -
(B) try making a density map from the ligand with "molmap" ... then you can adjust the isosurface level, etc. like for other density maps <https://rbvi.ucsf.edu/chimerax/docs/user/commands/molmap.html>
See the help links above for additional options such as to control vertex spacing of these surfaces.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 7, 2024, at 2:06 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX users
I am also experimenting on the representation of the surfaces of small compounds
surface ligand gridSpacing 0.5 probeRadius 1.2 color ligand white target s transparency 90
This creates a relatively large transparent surface around the small compound. How would it be possible to reduce the volume of the surface ?
Also I did not understand how to change the style of the surface among dot/mesh etc since adding style dot did not work.
I would appreciate any further creative examples of how to change the representation of a small compound in the case when I need to make it more "coarse-graining" , hiding some precise details of the structure ?
Many thanks in advance !
Enrico
The "surface style" command always applies to the whole surface model (different parts of the same model can't have different styles). Also as shown in the usage on the help page, if you specify a surface model, the specification needs to be after the whole command "surface style": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#style> Example: open 2gbp surface :bgc surf style #1.2 dot I hope this helps, Elaine
On Feb 9, 2024, at 1:18 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
P.S. and for the surface style actually it works for the whole surface like demonstrated in your example, but unfortunately it does not work for the selection e.g.
surf :lig style dot
Il giorno ven 9 feb 2024 alle ore 10:04 Enrico Martinez <jmsstarlight@gmail.com> ha scritto:
MAny thanks Elaine !
Actually the molmap is a great option, and it does what I need.
I noticed that it always displays a "frozen" map selected for a particular frame in the case of multi-frame pdb. Would it be possible to update the generated map for each frame of my multi model pdb visualized as the md trajectory (open ./trajectory.pdb coordset true) ?
Yours with thanks
Enrico
Il giorno gio 8 feb 2024 alle ore 23:28 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
Hello, This works fine for me:
open 1gcn surf surf style dot
However, the dot style can be very hard to see since the linewidth (dot size) is small and you cannot increase it, and/or the surface vertices are spaced rather far apart.
Here are two ideas for making a low-resolution surface for atoms:
(A) instead of a standard molecular surface, make a gaussian surface by using "surface" with the "resolution" option <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html>
- OR -
(B) try making a density map from the ligand with "molmap" ... then you can adjust the isosurface level, etc. like for other density maps <https://rbvi.ucsf.edu/chimerax/docs/user/commands/molmap.html>
See the help links above for additional options such as to control vertex spacing of these surfaces.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 7, 2024, at 2:06 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX users
I am also experimenting on the representation of the surfaces of small compounds
surface ligand gridSpacing 0.5 probeRadius 1.2 color ligand white target s transparency 90
This creates a relatively large transparent surface around the small compound. How would it be possible to reduce the volume of the surface ?
Also I did not understand how to change the style of the surface among dot/mesh etc since adding style dot did not work.
I would appreciate any further creative examples of how to change the representation of a small compound in the case when I need to make it more "coarse-graining" , hiding some precise details of the structure ?
Many thanks 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/
Okay thank you very much Elaine ! So I have 2 questions: 1) about mol map: As I mentioned this always displays a "frozen" map selected for a particular frame in the case of multi-frame pdb (loaded trajectory) Would it be possible to update the generated map for each frame ? 2) about ball and stick representing : is it possible to reduce the resolution of the balls for a small compound selection in order that it’s 3D structure appears to be like a mystery? 😃 Thanks in advance! Le ven. 9 févr. 2024 à 17:40, Elaine Meng <meng@cgl.ucsf.edu> a écrit :
The "surface style" command always applies to the whole surface model (different parts of the same model can't have different styles). Also as shown in the usage on the help page, if you specify a surface model, the specification needs to be after the whole command "surface style": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#style>
Example: open 2gbp surface :bgc surf style #1.2 dot
I hope this helps, Elaine
On Feb 9, 2024, at 1:18 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
P.S. and for the surface style actually it works for the whole surface like demonstrated in your example, but unfortunately it does not work for the selection e.g.
surf :lig style dot
Il giorno ven 9 feb 2024 alle ore 10:04 Enrico Martinez <jmsstarlight@gmail.com> ha scritto:
MAny thanks Elaine !
Actually the molmap is a great option, and it does what I need.
I noticed that it always displays a "frozen" map selected for a particular frame in the case of multi-frame pdb. Would it be possible to update the generated map for each frame of my multi model pdb visualized as the md trajectory (open ./trajectory.pdb coordset true) ?
Yours with thanks
Enrico
Il giorno gio 8 feb 2024 alle ore 23:28 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
Hello, This works fine for me:
open 1gcn surf surf style dot
However, the dot style can be very hard to see since the linewidth
(dot size) is small and you cannot increase it, and/or the surface vertices are spaced rather far apart.
Here are two ideas for making a low-resolution surface for atoms:
(A) instead of a standard molecular surface, make a gaussian surface
by using "surface" with the "resolution" option
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html>
- OR -
(B) try making a density map from the ligand with "molmap" ... then you can adjust the isosurface level, etc. like for other density maps <https://rbvi.ucsf.edu/chimerax/docs/user/commands/molmap.html>
See the help links above for additional options such as to control vertex spacing of these surfaces.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 7, 2024, at 2:06 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX users
I am also experimenting on the representation of the surfaces of small compounds
surface ligand gridSpacing 0.5 probeRadius 1.2 color ligand white target s transparency 90
This creates a relatively large transparent surface around the small compound. How would it be possible to reduce the volume of the surface ?
Also I did not understand how to change the style of the surface among dot/mesh etc since adding style dot did not work.
I would appreciate any further creative examples of how to change the representation of a small compound in the case when I need to make it more "coarse-graining" , hiding some precise details of the structure ?
Many thanks 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/
(1) in your script, you would have to use "perframe" to define a set of commands to run at each frame at the same time the "coordset" coordset is playing the trajectory. The perframe commands would include "close" to close the previous molmap, "molmap" to make a new molmap, and maybe others. See "perframe" help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html> (2) I have no idea what you mean by decrease resolution of balls. You can change their size (e.g. see "size" command) but you can't make them blurry or fuzzy, if that's what you mean. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/size.html> If you need fancy special effects you may need to use some general movie editing software instead of trying to do it all in ChimeraX. I don't do that, so I don't have any specific recommendations. 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 Feb 9, 2024, at 10:39 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Okay thank you very much Elaine !
So I have 2 questions:
1) about mol map: As I mentioned this always displays a "frozen" map selected for a particular frame in the case of multi-frame pdb (loaded trajectory) Would it be possible to update the generated map for each frame ?
2) about ball and stick representing : is it possible to reduce the resolution of the balls for a small compound selection in order that it’s 3D structure appears to be like a mystery? 😃
Thanks in advance!
participants (2)
-
Elaine Meng -
Enrico Martinez