Dear ChimeraX developers, Would you please show me how to make this following figure? [cid:01baf593-38aa-4ef0-8392-146a9fb2e78d] I have learned that this is a feature in zone feature and probably solvent accessible surface, but I do not know how to make it. Any hint is much appreciated. Warm regards, B _____________________________________________ Binh A. Nguyen, Ph.D. @ Saelices's Lab Center for Alzheimer’s and Neurodegenerative Diseases Peter O’Donnell Jr. Brain Institute UT Southwestern Medical Center ________________________________ UT Southwestern Medical Center The future of medicine, today.
Dear Binh, It looks more like an electron density map (not solvent-accessible surface). So you would need to open an atomic structure and open its electron density map, and show the structure as sticks and the map as a mesh. For example commands, see the Quick Start Guide, scroll down to the next-to-the last section that shows 1a0m and its density map. This includes a "vol zone" command. <https://rbvi.ucsf.edu/chimerax/docs/quickstart/index.html> Or if you are using the GUI interactively you can adjust the map style (e.g. mesh or not) and level using the Volume Viewer tool, which automatically appears when you open a density map file. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html> If you want a similar thing but only with molecular surface, not density map, then you don't need zone. You can just show the surface for whatever parts you want by specifying in a command or selecting. E.g. open 1gcn hide ribbons show atoms surface :1-8 surface style mesh ...or you could make surface transparent... transparency 50 surface style solid Details of all of the commands are in the help: <https://rbvi.ucsf.edu/chimerax/docs/user/index.html#commands> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 30, 2022, at 1:05 PM, Binh Nguyen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX developers,
Would you please show me how to make this following figure? <image.png>
I have learned that this is a feature in zone feature and probably solvent accessible surface, but I do not know how to make it. Any hint is much appreciated.
Warm regards,
B
_____________________________________________ Binh A. Nguyen, Ph.D. @ Saelices's Lab Center for Alzheimer’s and Neurodegenerative Diseases Peter O’Donnell Jr. Brain Institute UT Southwestern Medical Center
Hi Binh, Looks like an image of one plane of a an amyloid fibril. Here are example commands that make the attached image. open 6y1a hide ~/A,B style stick color byhet open 10669 from emdb vol zone #2 near /A,B range 3 new true volume #3 color gray transp 0.8 level 4 set bgcolor white graphics silhouette true Tom
On Aug 30, 2022, at 1:25 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Binh, It looks more like an electron density map (not solvent-accessible surface). So you would need to open an atomic structure and open its electron density map, and show the structure as sticks and the map as a mesh. For example commands, see the Quick Start Guide, scroll down to the next-to-the last section that shows 1a0m and its density map. This includes a "vol zone" command.
<https://rbvi.ucsf.edu/chimerax/docs/quickstart/index.html>
Or if you are using the GUI interactively you can adjust the map style (e.g. mesh or not) and level using the Volume Viewer tool, which automatically appears when you open a density map file. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html>
If you want a similar thing but only with molecular surface, not density map, then you don't need zone. You can just show the surface for whatever parts you want by specifying in a command or selecting. E.g.
open 1gcn hide ribbons show atoms surface :1-8 surface style mesh
...or you could make surface transparent...
transparency 50 surface style solid
Details of all of the commands are in the help: <https://rbvi.ucsf.edu/chimerax/docs/user/index.html#commands>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 30, 2022, at 1:05 PM, Binh Nguyen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX developers,
Would you please show me how to make this following figure? <image.png>
I have learned that this is a feature in zone feature and probably solvent accessible surface, but I do not know how to make it. Any hint is much appreciated.
Warm regards,
B
_____________________________________________ Binh A. Nguyen, Ph.D. @ Saelices's Lab Center for Alzheimer’s and Neurodegenerative Diseases Peter O’Donnell Jr. Brain Institute UT Southwestern Medical Center
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Dear Tom, Thank you so much. It looks perfect. and Yes, a layer from our Amyloid. Best, B _____________________________________________ Binh A. Nguyen, Ph.D. @ Saelices's Lab Center for Alzheimer’s and Neurodegenerative Diseases Peter O’Donnell Jr. Brain Institute UT Southwestern Medical Center ________________________________ From: Tom Goddard <goddard@sonic.net> Sent: Tuesday, August 30, 2022 3:49 PM To: Binh Nguyen <AnBinh.Nguyen@UTSouthwestern.edu> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Help with Zone features EXTERNAL MAIL Hi Binh, Looks like an image of one plane of a an amyloid fibril. Here are example commands that make the attached image. open 6y1a hide ~/A,B style stick color byhet open 10669 from emdb vol zone #2 near /A,B range 3 new true volume #3 color gray transp 0.8 level 4 set bgcolor white graphics silhouette true Tom [cid:87179850-7B9F-4EE5-8FD8-9BE5409E5318] On Aug 30, 2022, at 1:25 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Dear Binh, It looks more like an electron density map (not solvent-accessible surface). So you would need to open an atomic structure and open its electron density map, and show the structure as sticks and the map as a mesh. For example commands, see the Quick Start Guide, scroll down to the next-to-the last section that shows 1a0m and its density map. This includes a "vol zone" command. <https://rbvi.ucsf.edu/chimerax/docs/quickstart/index.html> Or if you are using the GUI interactively you can adjust the map style (e.g. mesh or not) and level using the Volume Viewer tool, which automatically appears when you open a density map file. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html> If you want a similar thing but only with molecular surface, not density map, then you don't need zone. You can just show the surface for whatever parts you want by specifying in a command or selecting. E.g. open 1gcn hide ribbons show atoms surface :1-8 surface style mesh ...or you could make surface transparent... transparency 50 surface style solid Details of all of the commands are in the help: <https://rbvi.ucsf.edu/chimerax/docs/user/index.html#commands> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco On Aug 30, 2022, at 1:05 PM, Binh Nguyen via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Dear ChimeraX developers, Would you please show me how to make this following figure? <image.png> I have learned that this is a feature in zone feature and probably solvent accessible surface, but I do not know how to make it. Any hint is much appreciated. Warm regards, B _____________________________________________ Binh A. Nguyen, Ph.D. @ Saelices's Lab Center for Alzheimer’s and Neurodegenerative Diseases Peter O’Donnell Jr. Brain Institute UT Southwestern Medical Center _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying. ________________________________ UT Southwestern Medical Center The future of medicine, today.
It looks like the example image Binh provided also used either `lighting flat` or `lighting soft`. At least I get something a bit closer to the example image when I rerun Tom’s example and add either of these lighting commands. Cheers, Guillaume
On 30 Aug 2022, at 22:49, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Binh,
Looks like an image of one plane of a an amyloid fibril. Here are example commands that make the attached image.
open 6y1a hide ~/A,B style stick color byhet open 10669 from emdb vol zone #2 near /A,B range 3 new true volume #3 color gray transp 0.8 level 4 set bgcolor white graphics silhouette true
Tom
<6y1a.png>
On Aug 30, 2022, at 1:25 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Dear Binh, It looks more like an electron density map (not solvent-accessible surface). So you would need to open an atomic structure and open its electron density map, and show the structure as sticks and the map as a mesh. For example commands, see the Quick Start Guide, scroll down to the next-to-the last section that shows 1a0m and its density map. This includes a "vol zone" command.
<https://rbvi.ucsf.edu/chimerax/docs/quickstart/index.html <https://rbvi.ucsf.edu/chimerax/docs/quickstart/index.html>>
Or if you are using the GUI interactively you can adjust the map style (e.g. mesh or not) and level using the Volume Viewer tool, which automatically appears when you open a density map file. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html <https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html>>
If you want a similar thing but only with molecular surface, not density map, then you don't need zone. You can just show the surface for whatever parts you want by specifying in a command or selecting. E.g.
open 1gcn hide ribbons show atoms surface :1-8 surface style mesh
...or you could make surface transparent...
transparency 50 surface style solid
Details of all of the commands are in the help: <https://rbvi.ucsf.edu/chimerax/docs/user/index.html#commands <https://rbvi.ucsf.edu/chimerax/docs/user/index.html#commands>>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 30, 2022, at 1:05 PM, Binh Nguyen via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Dear ChimeraX developers,
Would you please show me how to make this following figure? <image.png>
I have learned that this is a feature in zone feature and probably solvent accessible surface, but I do not know how to make it. Any hint is much appreciated.
Warm regards,
B
_____________________________________________ Binh A. Nguyen, Ph.D. @ Saelices's Lab Center for Alzheimer’s and Neurodegenerative Diseases Peter O’Donnell Jr. Brain Institute UT Southwestern Medical Center
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto: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
Dear Elaine, Thanks for the instructions. This is what I got, but the map density edge is not as sharp compared to the reference figure (my first email). Is there anything else that I can improve? [cid:c5fc944f-33ff-425a-9454-3c0510e9e67d] Thank you so much, B _____________________________________________ Binh A. Nguyen, Ph.D. @ Saelices's Lab Center for Alzheimer’s and Neurodegenerative Diseases Peter O’Donnell Jr. Brain Institute UT Southwestern Medical Center ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, August 30, 2022 3:25 PM To: Binh Nguyen <AnBinh.Nguyen@UTSouthwestern.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Help with Zone features EXTERNAL MAIL Dear Binh, It looks more like an electron density map (not solvent-accessible surface). So you would need to open an atomic structure and open its electron density map, and show the structure as sticks and the map as a mesh. For example commands, see the Quick Start Guide, scroll down to the next-to-the last section that shows 1a0m and its density map. This includes a "vol zone" command. <https://rbvi.ucsf.edu/chimerax/docs/quickstart/index.html> Or if you are using the GUI interactively you can adjust the map style (e.g. mesh or not) and level using the Volume Viewer tool, which automatically appears when you open a density map file. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html> If you want a similar thing but only with molecular surface, not density map, then you don't need zone. You can just show the surface for whatever parts you want by specifying in a command or selecting. E.g. open 1gcn hide ribbons show atoms surface :1-8 surface style mesh ...or you could make surface transparent... transparency 50 surface style solid Details of all of the commands are in the help: <https://rbvi.ucsf.edu/chimerax/docs/user/index.html#commands> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 30, 2022, at 1:05 PM, Binh Nguyen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX developers,
Would you please show me how to make this following figure? <image.png>
I have learned that this is a feature in zone feature and probably solvent accessible surface, but I do not know how to make it. Any hint is much appreciated.
Warm regards,
B
_____________________________________________ Binh A. Nguyen, Ph.D. @ Saelices's Lab Center for Alzheimer’s and Neurodegenerative Diseases Peter O’Donnell Jr. Brain Institute UT Southwestern Medical Center
CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying. ________________________________ UT Southwestern Medical Center The future of medicine, today.
Hi Binh, That is simply showing silhouette edges (black outlines), e.g. click the Graphics tab on the toolbar across the top and then click the icon that looks like a seahorse. Same as using command graphics silhouettes true <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.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 Aug 30, 2022, at 1:51 PM, Binh Nguyen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Elaine,
Thanks for the instructions. This is what I got, but the map density edge is not as sharp compared to the reference figure (my first email). Is there anything else that I can improve?
<image.png>
Thank you so much,
B
Awesome thanks Elaine. B _____________________________________________ Binh A. Nguyen, Ph.D. @ Saelices's Lab Center for Alzheimer’s and Neurodegenerative Diseases Peter O’Donnell Jr. Brain Institute UT Southwestern Medical Center ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Tuesday, August 30, 2022 3:55 PM To: Binh Nguyen <AnBinh.Nguyen@UTSouthwestern.edu> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Help with Zone features EXTERNAL MAIL Hi Binh, That is simply showing silhouette edges (black outlines), e.g. click the Graphics tab on the toolbar across the top and then click the icon that looks like a seahorse. Same as using command graphics silhouettes true <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.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 Aug 30, 2022, at 1:51 PM, Binh Nguyen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Elaine,
Thanks for the instructions. This is what I got, but the map density edge is not as sharp compared to the reference figure (my first email). Is there anything else that I can improve?
<image.png>
Thank you so much,
B
CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying. ________________________________ UT Southwestern Medical Center The future of medicine, today.
participants (4)
-
Binh Nguyen -
Elaine Meng -
Guillaume Gaullier -
Tom Goddard