Re: [chimerax-users] [Chimera-users] ChimeraX in no-gui mode: visualisation of protein-ligand interactions
See the "color" command for coloring the ligand, and "set" or "graphics" for coloring the background, and "label" (or "2dlabels" but that usually requires you to position them interactively) for labeling. All of these are included in the "making images" page I mentioned near the end of my previous message. Best, Elaine
On Jan 14, 2022, at 3:03 PM, Enrico Martinez jmsstarlight@gmail.com wrote:
Thank you very much, Elaine! I really like ChimeraX and it looks so great for me with all of those presents :-) I will look for the details regarding the options. Just a few addtional questions regarding customizing representation of protein-ligand interactions using ghost preset: In particular: I would like to color ligand (in orange??) To add labels (like Try-193) on the displayed side-chains around the ligands To change background from black to indigo! :-) Many thanks in advance! Cheers Enrico
пт, 14 янв. 2022 г. в 23:48, Elaine Meng meng@cgl.ucsf.edu:
Hello, It isn't my area of expertise, but I don't think you can save images in nogui mode except with Linux OSMesa.
As for your other questions, which commands do certain things...
may you suggest some commands that I may introduce into my batch file to
- delete all models from the multi-model pdb file with the exemption
of the first model. 2) switch from cartoon to surface representation of the protein 3) visualize protein-ligand non-covalent interactions in the current model
(1) close submodels except for first one. Maybe something like command:
close #1.2-end
https://rbvi.ucsf.edu/chimerax/docs/user/commands/close.html
(2) switch from ribbon to molecular surface of protein. Well, you probably want to do some coloring and other stuff besides just hiding ribbon and showing surface, which could be something like commands:
~ribbon surface protein
https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html
Or you could try a surface-showing preset, e.g.
preset ghost
https://rbvi.ucsf.edu/chimerax/docs/user/commands/preset.html
(3) depends what you mean by showing interactions (lines? selection? coloring?). You should take a look at commands "contacts" and/or "hbonds" and choose the options that give what you want. https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/hbonds.html
You will need to spend some time trying the commands since there are an infinite number of possibilities for combinations of coloring and display styles and lighting and graphics effects. See also commands "lighting" and "graphics" and "set"
https://rbvi.ucsf.edu/chimerax/docs/user/commands/lighting.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/set.html
... and the "making images" page with several relevant commands https://rbvi.ucsf.edu/chimerax/docs/user/images.html
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 14, 2022, at 2:17 PM, Enrico Martinez via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Dear Chimera's users! First I wish Happy New Year to everyone! I am just switching from Chimera to ChimeraX that I am going to use in no-gui (batch) mode to prepare screen shots of protein-ligand interactions based on the protein-ligand docking poses. Basically I am loading a pdb file of the complex (consisted of protein and ligand in multi-model format) from the terminal of my macOSX. I have a template for a batch file created in the bash script on the fly, that I used 2 years ago with an early version of ChimeraX.
# a batch file for chimeraX printf "open ${pdb} view; zoom 1.0; turn x 90; turn z -80; wait # options for appearance preset 'overall look' publication # set bg powder blue set silhouettes t; set silhouetteColor indigo; set silhouetteDepthJump 0.02
# make info of the screen 2dlab create title text "${pdb_name}" color red font gothic xpos .04 ypos .92 size 35
# options for light light depthcuestart .4 depthcueend .8; lighting full intensity 1.4 shadows true qualityOfShadows finer
save image ${structure}/${pdb_name}.png format png width 800 height 600 supersample 4 transparentBackground false wait exit" > chimeraX.${pdb_name}.cxc"
then I use it directly in terminal as chimerax-daily chimeraX.${pdb_name}.cxc"
may you suggest some commands that I may introduce into my batch file to
- delete all models from the multi-model pdb file with the exemption
of the first model. 2) switch from cartoon to surface representation of the protein 3) visualize protein-ligand non-covalent interactions in the current model
Yours with thanks Enrico
Thank you Elaine! I played with it today and it looks great! Some additional questions: may I automatically place the 2D label on the top left corner of the screen instead of manually defining its X-Y using xpos ypos? 2dlab create title text "name_of_the_complex" color red font gothic xpos .04 ypos .99 size 40
2) assuming that I open 2 molecules in the same session open A.pdb open B.pdb then I remove all the models with the exemption of the first close #1.2-end How I may superimpose A to B (align the structures) and then hide B.pdb ? Many thanks in advance!! Enrico
сб, 15 янв. 2022 г. в 00:11, Elaine Meng meng@cgl.ucsf.edu:
See the "color" command for coloring the ligand, and "set" or "graphics" for coloring the background, and "label" (or "2dlabels" but that usually requires you to position them interactively) for labeling. All of these are included in the "making images" page I mentioned near the end of my previous message. Best, Elaine
On Jan 14, 2022, at 3:03 PM, Enrico Martinez jmsstarlight@gmail.com wrote:
Thank you very much, Elaine! I really like ChimeraX and it looks so great for me with all of those presents :-) I will look for the details regarding the options. Just a few addtional questions regarding customizing representation of protein-ligand interactions using ghost preset: In particular: I would like to color ligand (in orange??) To add labels (like Try-193) on the displayed side-chains around the ligands To change background from black to indigo! :-) Many thanks in advance! Cheers Enrico
пт, 14 янв. 2022 г. в 23:48, Elaine Meng meng@cgl.ucsf.edu:
Hello, It isn't my area of expertise, but I don't think you can save images in nogui mode except with Linux OSMesa.
As for your other questions, which commands do certain things...
may you suggest some commands that I may introduce into my batch file to
- delete all models from the multi-model pdb file with the exemption
of the first model. 2) switch from cartoon to surface representation of the protein 3) visualize protein-ligand non-covalent interactions in the current model
(1) close submodels except for first one. Maybe something like command:
close #1.2-end
https://rbvi.ucsf.edu/chimerax/docs/user/commands/close.html
(2) switch from ribbon to molecular surface of protein. Well, you probably want to do some coloring and other stuff besides just hiding ribbon and showing surface, which could be something like commands:
~ribbon surface protein
https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html
Or you could try a surface-showing preset, e.g.
preset ghost
https://rbvi.ucsf.edu/chimerax/docs/user/commands/preset.html
(3) depends what you mean by showing interactions (lines? selection? coloring?). You should take a look at commands "contacts" and/or "hbonds" and choose the options that give what you want. https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/hbonds.html
You will need to spend some time trying the commands since there are an infinite number of possibilities for combinations of coloring and display styles and lighting and graphics effects. See also commands "lighting" and "graphics" and "set"
https://rbvi.ucsf.edu/chimerax/docs/user/commands/lighting.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/set.html
... and the "making images" page with several relevant commands https://rbvi.ucsf.edu/chimerax/docs/user/images.html
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 14, 2022, at 2:17 PM, Enrico Martinez via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Dear Chimera's users! First I wish Happy New Year to everyone! I am just switching from Chimera to ChimeraX that I am going to use in no-gui (batch) mode to prepare screen shots of protein-ligand interactions based on the protein-ligand docking poses. Basically I am loading a pdb file of the complex (consisted of protein and ligand in multi-model format) from the terminal of my macOSX. I have a template for a batch file created in the bash script on the fly, that I used 2 years ago with an early version of ChimeraX.
# a batch file for chimeraX printf "open ${pdb} view; zoom 1.0; turn x 90; turn z -80; wait # options for appearance preset 'overall look' publication # set bg powder blue set silhouettes t; set silhouetteColor indigo; set silhouetteDepthJump 0.02
# make info of the screen 2dlab create title text "${pdb_name}" color red font gothic xpos .04 ypos .92 size 35
# options for light light depthcuestart .4 depthcueend .8; lighting full intensity 1.4 shadows true qualityOfShadows finer
save image ${structure}/${pdb_name}.png format png width 800 height 600 supersample 4 transparentBackground false wait exit" > chimeraX.${pdb_name}.cxc"
then I use it directly in terminal as chimerax-daily chimeraX.${pdb_name}.cxc"
may you suggest some commands that I may introduce into my batch file to
- delete all models from the multi-model pdb file with the exemption
of the first model. 2) switch from cartoon to surface representation of the protein 3) visualize protein-ligand non-covalent interactions in the current model
Yours with thanks Enrico
Thank you Elaine! I played with it today and it looks great! Some additional questions (sorry for it at the first time the thing seems abit tricky): 1)may I automatically place the 2D label on the top left corner of the screen instead of manually defining its X-Y using xpos ypos? 2dlab create title text "name_of_the_complex" color red font gothic xpos .04 ypos .99 size 40
2) assuming that I open 2 molecules in the same session open A.pdb open B.pdb then I remove all the models with the exemption of the first close #1.2-end How could I superimpose A to B (align the structures) and then hide cartoon from B.pdb (keeping only ligand) ?
3) Is there any possibility to put your signature on the screen-shot? like "Observed by Enrico Martinez" ? :-)
Many thanks in advance!! Enrico
сб, 15 янв. 2022 г. в 00:11, Elaine Meng meng@cgl.ucsf.edu:
See the "color" command for coloring the ligand, and "set" or "graphics" for coloring the background, and "label" (or "2dlabels" but that usually requires you to position them interactively) for labeling. All of these are included in the "making images" page I mentioned near the end of my previous message. Best, Elaine
On Jan 14, 2022, at 3:03 PM, Enrico Martinez jmsstarlight@gmail.com wrote:
Thank you very much, Elaine! I really like ChimeraX and it looks so great for me with all of those presents :-) I will look for the details regarding the options. Just a few addtional questions regarding customizing representation of protein-ligand interactions using ghost preset: In particular: I would like to color ligand (in orange??) To add labels (like Try-193) on the displayed side-chains around the ligands To change background from black to indigo! :-) Many thanks in advance! Cheers Enrico
пт, 14 янв. 2022 г. в 23:48, Elaine Meng meng@cgl.ucsf.edu:
Hello, It isn't my area of expertise, but I don't think you can save images in nogui mode except with Linux OSMesa.
As for your other questions, which commands do certain things...
may you suggest some commands that I may introduce into my batch file to
- delete all models from the multi-model pdb file with the exemption
of the first model. 2) switch from cartoon to surface representation of the protein 3) visualize protein-ligand non-covalent interactions in the current model
(1) close submodels except for first one. Maybe something like command:
close #1.2-end
https://rbvi.ucsf.edu/chimerax/docs/user/commands/close.html
(2) switch from ribbon to molecular surface of protein. Well, you probably want to do some coloring and other stuff besides just hiding ribbon and showing surface, which could be something like commands:
~ribbon surface protein
https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html
Or you could try a surface-showing preset, e.g.
preset ghost
https://rbvi.ucsf.edu/chimerax/docs/user/commands/preset.html
(3) depends what you mean by showing interactions (lines? selection? coloring?). You should take a look at commands "contacts" and/or "hbonds" and choose the options that give what you want. https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/hbonds.html
You will need to spend some time trying the commands since there are an infinite number of possibilities for combinations of coloring and display styles and lighting and graphics effects. See also commands "lighting" and "graphics" and "set"
https://rbvi.ucsf.edu/chimerax/docs/user/commands/lighting.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html https://rbvi.ucsf.edu/chimerax/docs/user/commands/set.html
... and the "making images" page with several relevant commands https://rbvi.ucsf.edu/chimerax/docs/user/images.html
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 14, 2022, at 2:17 PM, Enrico Martinez via Chimera-users chimera-users@cgl.ucsf.edu wrote:
Dear Chimera's users! First I wish Happy New Year to everyone! I am just switching from Chimera to ChimeraX that I am going to use in no-gui (batch) mode to prepare screen shots of protein-ligand interactions based on the protein-ligand docking poses. Basically I am loading a pdb file of the complex (consisted of protein and ligand in multi-model format) from the terminal of my macOSX. I have a template for a batch file created in the bash script on the fly, that I used 2 years ago with an early version of ChimeraX.
# a batch file for chimeraX printf "open ${pdb} view; zoom 1.0; turn x 90; turn z -80; wait # options for appearance preset 'overall look' publication # set bg powder blue set silhouettes t; set silhouetteColor indigo; set silhouetteDepthJump 0.02
# make info of the screen 2dlab create title text "${pdb_name}" color red font gothic xpos .04 ypos .92 size 35
# options for light light depthcuestart .4 depthcueend .8; lighting full intensity 1.4 shadows true qualityOfShadows finer
save image ${structure}/${pdb_name}.png format png width 800 height 600 supersample 4 transparentBackground false wait exit" > chimeraX.${pdb_name}.cxc"
then I use it directly in terminal as chimerax-daily chimeraX.${pdb_name}.cxc"
may you suggest some commands that I may introduce into my batch file to
- delete all models from the multi-model pdb file with the exemption
of the first model. 2) switch from cartoon to surface representation of the protein 3) visualize protein-ligand non-covalent interactions in the current model
Yours with thanks Enrico
Hello, If you are asking about ChimeraX, please just e-mail chimerax-users@cgl.ucsf.edu (not chimera-users@cgl.ucsf.edu so we can avoid confusing people between the two programs).
Trying to answer your ChimeraX questions interleaved below.
On Jan 15, 2022, at 9:43 AM, Enrico Martinez jmsstarlight@gmail.com wrote:
Thank you Elaine! I played with it today and it looks great! Some additional questions (sorry for it at the first time the thing seems abit tricky): 1)may I automatically place the 2D label on the top left corner of the screen instead of manually defining its X-Y using xpos ypos? 2dlab create title text "name_of_the_complex" color red font gothic xpos .04 ypos .99 size 40
You have to put the position in the command. The only other way is moving it by hand, which is probably not what you want to do.
- assuming that I open 2 molecules in the same session
open A.pdb open B.pdb then I remove all the models with the exemption of the first close #1.2-end How could I superimpose A to B (align the structures) and then hide cartoon from B.pdb (keeping only ligand) ?
See "matchmaker" command for aligning structures and "show" "hide" "cartoon" "surtace" commands for hiding and showing different types of display. There are many ways to specify certain atoms or models in a command (hide, show, cartoon, color, etc.): you can do it by model number, residue number, residue name, chemical element, etc. How to specify atoms in command line is explained in this page:
https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html
For example, ChimeraX commands:
matchmaker #1 to #2 view ~cartoon #2 hide #2 & protein hide solvent
- Is there any possibility to put your signature on the screen-shot?
like "Observed by Enrico Martinez" ? :-)
Sure you can put whatever text you want on the image (titles, credits, arrows, ...) with the 2dlabels command.
Many thanks in advance!! Enrico
participants (2)
-
Elaine Meng -
Enrico Martinez