Drawing objects in ChimeraX?
Hi,
I was wondering if it is possible to draw objects in ChimeraX. More specifically, I'd like to show the gridbox used for docking calculations, so it would be nice if I could draw a cube, and even better if it can be drawn as a surface that could have color, transparency, etc.
How to do this in ChimeraX?
Thanks a lot! -- Gustavo Seabra Research Associate Professor Center for Natural Products, Drug Discovery, and Development (CNPD3) Department of Medicinal Chemistry College of Pharmacy University of Florida, Gainesville, FL, USA
Hi Gustavo, There are a few different possibilities:
(1) create a BILD format file describing geometric objects. It is a simple plain-text format described here, typically just created in the text editor of your choice, and you would name the file something.bild and open it in ChimeraX to display the objects. https://rbvi.ucsf.edu/chimerax/docs/user/formats/bild.html
(2) create markers and links, which are essentially fake atoms and bonds. They can be created within ChimeraX using the "Marker Placement" tool or "marker" command, or you can use your own external process to create a marker file and then open it in ChimeraX. https://rbvi.ucsf.edu/chimerax/docs/user/markers.html https://rbvi.ucsf.edu/chimerax/docs/user/tools/markerplacement.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/marker.html
(3) create shapes which are surface models, using the "shape" command: https://rbvi.ucsf.edu/chimerax/docs/user/commands/shape.html
Shape does not have cube option, although you could create a box from repeated use of the "triangle" or "rectangle" option. Still it may make more sense to use one of the other methods to draw a box. If you are using "shape" it may be easier to use triangles to make the box than rectangles, because the triangle option allows specifying the vertex coordinates whereas the rectangle location has to be specified by its center.
(4) create a cube as a surface with only 8 vertices, using Python somehow (sorry somebody else would have to advise on how to do this)
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 23, 2022, at 11:31 AM, de Miranda Seabra, Gustavo via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi,
I was wondering if it is possible to draw objects in ChimeraX. More specifically, I'd like to show the gridbox used for docking calculations, so it would be nice if I could draw a cube, and even better if it can be drawn as a surface that could have color, transparency, etc.
How to do this in ChimeraX?
Thanks a lot!
Gustavo Seabra Research Associate Professor Center for Natural Products, Drug Discovery, and Development (CNPD3) Department of Medicinal Chemistry College of Pharmacy University of Florida, Gainesville, FL, USA _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
You can also use the "slab" option with command "shape rectangle" to get a 3D box, for example,
shape rectangle width 40 height 50 slab 30
But it does not give sharp edges between the xy box sides (see image).
Tom
On Feb 23, 2022, at 12:25 PM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Gustavo, There are a few different possibilities:
(1) create a BILD format file describing geometric objects. It is a simple plain-text format described here, typically just created in the text editor of your choice, and you would name the file something.bild and open it in ChimeraX to display the objects. https://rbvi.ucsf.edu/chimerax/docs/user/formats/bild.html
(2) create markers and links, which are essentially fake atoms and bonds. They can be created within ChimeraX using the "Marker Placement" tool or "marker" command, or you can use your own external process to create a marker file and then open it in ChimeraX. https://rbvi.ucsf.edu/chimerax/docs/user/markers.html https://rbvi.ucsf.edu/chimerax/docs/user/tools/markerplacement.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/marker.html
(3) create shapes which are surface models, using the "shape" command: https://rbvi.ucsf.edu/chimerax/docs/user/commands/shape.html
Shape does not have cube option, although you could create a box from repeated use of the "triangle" or "rectangle" option. Still it may make more sense to use one of the other methods to draw a box. If you are using "shape" it may be easier to use triangles to make the box than rectangles, because the triangle option allows specifying the vertex coordinates whereas the rectangle location has to be specified by its center.
(4) create a cube as a surface with only 8 vertices, using Python somehow (sorry somebody else would have to advise on how to do this)
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 23, 2022, at 11:31 AM, de Miranda Seabra, Gustavo via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi,
I was wondering if it is possible to draw objects in ChimeraX. More specifically, I'd like to show the gridbox used for docking calculations, so it would be nice if I could draw a cube, and even better if it can be drawn as a surface that could have color, transparency, etc.
How to do this in ChimeraX?
Thanks a lot!
Gustavo Seabra Research Associate Professor Center for Natural Products, Drug Discovery, and Development (CNPD3) Department of Medicinal Chemistry College of Pharmacy University of Florida, Gainesville, FL, USA _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
If you use some external process (e.g. not in ChimeraX) to create a file that can be opened in ChimeraX, there are couple more possibilities in this list of "3D object" file formats:
https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#object
Yet another possibility is to make a PDB file that just contains 8 atoms and CONECT records that draw the appropriate bonds to form a cube. ( A bit of ancient history is that I did something like that >25 years ago to display the location of the DOCK scoring grid!)
Elaine
On Feb 23, 2022, at 12:25 PM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Gustavo, There are a few different possibilities:
(1) create a BILD format file describing geometric objects. It is a simple plain-text format described here, typically just created in the text editor of your choice, and you would name the file something.bild and open it in ChimeraX to display the objects. https://rbvi.ucsf.edu/chimerax/docs/user/formats/bild.html
(2) create markers and links, which are essentially fake atoms and bonds. They can be created within ChimeraX using the "Marker Placement" tool or "marker" command, or you can use your own external process to create a marker file and then open it in ChimeraX. https://rbvi.ucsf.edu/chimerax/docs/user/markers.html https://rbvi.ucsf.edu/chimerax/docs/user/tools/markerplacement.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/marker.html
(3) create shapes which are surface models, using the "shape" command: https://rbvi.ucsf.edu/chimerax/docs/user/commands/shape.html
Shape does not have cube option, although you could create a box from repeated use of the "triangle" or "rectangle" option. Still it may make more sense to use one of the other methods to draw a box. If you are using "shape" it may be easier to use triangles to make the box than rectangles, because the triangle option allows specifying the vertex coordinates whereas the rectangle location has to be specified by its center.
(4) create a cube as a surface with only 8 vertices, using Python somehow (sorry somebody else would have to advise on how to do this)
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 23, 2022, at 11:31 AM, de Miranda Seabra, Gustavo via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi,
I was wondering if it is possible to draw objects in ChimeraX. More specifically, I'd like to show the gridbox used for docking calculations, so it would be nice if I could draw a cube, and even better if it can be drawn as a surface that could have color, transparency, etc.
How to do this in ChimeraX?
Thanks a lot!
Gustavo Seabra Research Associate Professor Center for Natural Products, Drug Discovery, and Development (CNPD3) Department of Medicinal Chemistry College of Pharmacy University of Florida, Gainesville, FL, USA _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thanks a lot!
-- Gustavo Seabra Research Associate Professor Center for Natural Products, Drug Discovery, and Development (CNPD3) Department of Medicinal Chemistry College of Pharmacy University of Florida, Gainesville, FL, USA ________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: Wednesday, February 23, 2022 3:36 PM To: de Miranda Seabra, Gustavo seabra@cop.ufl.edu Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Drawing objects in ChimeraX?
[External Email]
If you use some external process (e.g. not in ChimeraX) to create a file that can be opened in ChimeraX, there are couple more possibilities in this list of "3D object" file formats:
<https://urldefense.proofpoint.com/v2/url?u=https-3A__rbvi.ucsf.edu_chimerax_... >
Yet another possibility is to make a PDB file that just contains 8 atoms and CONECT records that draw the appropriate bonds to form a cube. ( A bit of ancient history is that I did something like that >25 years ago to display the location of the DOCK scoring grid!)
Elaine
On Feb 23, 2022, at 12:25 PM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Gustavo, There are a few different possibilities:
(1) create a BILD format file describing geometric objects. It is a simple plain-text format described here, typically just created in the text editor of your choice, and you would name the file something.bild and open it in ChimeraX to display the objects. <https://urldefense.proofpoint.com/v2/url?u=https-3A__rbvi.ucsf.edu_chimerax_... >
(2) create markers and links, which are essentially fake atoms and bonds. They can be created within ChimeraX using the "Marker Placement" tool or "marker" command, or you can use your own external process to create a marker file and then open it in ChimeraX. <https://urldefense.proofpoint.com/v2/url?u=https-3A__rbvi.ucsf.edu_chimerax_... > <https://urldefense.proofpoint.com/v2/url?u=https-3A__rbvi.ucsf.edu_chimerax_... > <https://urldefense.proofpoint.com/v2/url?u=https-3A__rbvi.ucsf.edu_chimerax_... >
(3) create shapes which are surface models, using the "shape" command: <https://urldefense.proofpoint.com/v2/url?u=https-3A__rbvi.ucsf.edu_chimerax_... >
Shape does not have cube option, although you could create a box from repeated use of the "triangle" or "rectangle" option. Still it may make more sense to use one of the other methods to draw a box. If you are using "shape" it may be easier to use triangles to make the box than rectangles, because the triangle option allows specifying the vertex coordinates whereas the rectangle location has to be specified by its center.
(4) create a cube as a surface with only 8 vertices, using Python somehow (sorry somebody else would have to advise on how to do this)
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 23, 2022, at 11:31 AM, de Miranda Seabra, Gustavo via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi,
I was wondering if it is possible to draw objects in ChimeraX. More specifically, I'd like to show the gridbox used for docking calculations, so it would be nice if I could draw a cube, and even better if it can be drawn as a surface that could have color, transparency, etc.
How to do this in ChimeraX?
Thanks a lot!
Gustavo Seabra Research Associate Professor Center for Natural Products, Drug Discovery, and Development (CNPD3) Department of Medicinal Chemistry College of Pharmacy University of Florida, Gainesville, FL, USA _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_mailm...
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_mailm...
participants (3)
-
de Miranda Seabra, Gustavo -
Elaine Meng -
Tom Goddard