Re: [chimerax-users] [ChimeraX] #3464: partial surface mesh
Hi Rory, There is no "hydrophobic surface" ... maybe you mean the molecular surface shown as solid (not dot or mesh)? Chimera's presets include "hydrophobicity surface" which is perhaps misleading, simply means the molecular surface colored by hydrophobicity. What exactly are you trying to do? Show protein as mesh surface and ligand as solid surface? You can definitely do it (or any combination of mesh surface on some atoms, solid on some other atoms) by opening multiple copies of the structure, as we said in previous messages. Then in the solid-surface copy, only show the parts of the surface you want as solid. In the mesh-surface copy, show the parts you want as mesh. For example, here is an example that shows H-ras as mesh surface with its ligand GCP as solid surface (image attached below), commands: open 121p open 121p surf #1 & protein surf #2:gcp surf style #1 mesh transp #1 50 surfaces color #2 gold surfaces hide solvent This can all be done with the menu as well, but it would take a lot more typing to enter that whole procedure. I Cc'd chimerax-users@cgl.ucsf.edu which is the recommended address for asking ChimeraX questions (for future reference). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 6, 2020, at 10:30 AM, Gordon, Rory <rory.gordon.19@ucl.ac.uk> wrote:
Hi Guys,
Further to previous email, just tried fiddling with the transparency settings.
I can get the protein structure to change through the transparency gradient for hydrophobic surface.
However, for the substrate/ligands there seems to be binary system where you can either have full transparency or none at all.
The hydrophobic surface can be coloured both for the protein and substrate/ligand.
Cheers,
Rory From: Gordon, Rory <rory.gordon.19@ucl.ac.uk> Sent: 06 July 2020 18:26 To: Tom Goddard <goddard@sonic.net>; Elaine Meng <meng@cgl.ucsf.edu> Cc: Eric Pettersen <pett@cgl.ucsf.edu> Subject: Re: [ChimeraX] #3464: partial surface mesh
Hi Tom, Elaine and Eric
I tried to establish the mesh surface with the whole protein structure selected through the GUI. I can only get the hydrophobic surface which I can colour with B-factor.
The options of Mesh, Dot or Solid don't seem to change anything.
Not sure how to get round this, so any help would be appreciated.
Cheers,
Rory
From: Tom Goddard <goddard@sonic.net> Sent: 02 July 2020 18:24 To: Elaine Meng <meng@cgl.ucsf.edu> Cc: Gordon, Rory <rory.gordon.19@ucl.ac.uk>; Eric Pettersen <pett@cgl.ucsf.edu> Subject: Re: [ChimeraX] #3464: partial surface mesh
Another trick that makes these meshes look nicer is to make them about 50-80% transparent (command "transp #2 70"). It gives the mesh an airy look.
Tom
On Jul 2, 2020, at 10:17 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Rory, Here is an example image where I opened the same structure twice. I showed one copy with mesh surface and the second one with solid surface, and then simply hid parts of the solid surface. This is the way that Tom mentioned. Elaine
<example.png>
On Jul 2, 2020, at 3:29 AM, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:
#3464: partial surface mesh ---------------------------------------+---------------------------- Reporter: rory.gordon.19@… | Owner: Eric Pettersen Type: defect | Status: closed Priority: normal | Milestone: Component: Surface | Version: Resolution: fixed | Keywords: Blocked By: | Blocking: Notify when closed: | Platform: all Project: ChimeraX | ---------------------------------------+----------------------------
Comment (by rory.gordon.19@…):
{{{ Hi Eric,
Thanks for your email.
I had actually seen a graphic in a publication which gave me that idea.
Thanks anyway for the pointers.
Cheers,
Rory ________________________________ From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> Sent: 01 July 2020 18:23 Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; meng@cgl.ucsf.edu <meng@cgl.ucsf.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Gordon, Rory <rory.gordon.19@ucl.ac.uk> Subject: Re: [ChimeraX] #3464: partial surface mesh (was: ChimeraX bug report submission)
#3464: partial surface mesh ---------------------------------------+---------------------------- Reporter: rory.gordon.19@… | Owner: Eric Pettersen Type: defect | Status: accepted Priority: normal | Milestone: Component: Unassigned | Version: Resolution: | Keywords: Blocked By: | Blocking: Notify when closed: | Platform: all Project: ChimeraX | ---------------------------------------+---------------------------- Changes (by Eric Pettersen):
* status: new => accepted * cc: Tom Goddard, Elaine Meng (added) * project: => ChimeraX * platform: => all * owner: (none) => Eric Pettersen
Comment:
Hi Rory, I don't believe you can change just part of a surface into mesh, it's all or nothing. You can make that part of the surface partially transparent instead with Actions→Surface→Transparency.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
----- Tom, should the command "surface style (#!4 & sel) mesh" actually do nothing (with part of the surface selected)? That seems surprising. Seems like it should change the whole surface into mesh. Is that a bug or am I misunderstanding something?
--Eric
-- Ticket URL: <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F3464%23comment%3A1&data=02%7C01%7C%7Cb50922f7c1a5440c438908d81de37918%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637292210119419879&sdata=GSVMvSlVzE7eo%2FbcWesHMjUigJgWIvMFzU1efXANpRI%3D&reserved=0> ChimeraX <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2F&data=02%7C01%7C%7Cb50922f7c1a5440c438908d81de37918%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637292210119429876&sdata=WAAsovWYcC03Q8hQTVRlAK2lbNXj2ULqvEo00cNukV0%3D&reserved=0> ChimeraX Issue Tracker }}}
-- Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3464#comment:7> ChimeraX <http://www.rbvi.ucsf.edu/chimerax/> ChimeraX Issue Tracker
Hi Elaine, Thanks for your email and pointers on how to create figures which contain both solid and meshed surface. This was very helpful. I managed to create the figures through using the method that you described. Thanks again, Rory ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 06 July 2020 20:00 To: Gordon, Rory <rory.gordon.19@ucl.ac.uk> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [ChimeraX] #3464: partial surface mesh Hi Rory, There is no "hydrophobic surface" ... maybe you mean the molecular surface shown as solid (not dot or mesh)? Chimera's presets include "hydrophobicity surface" which is perhaps misleading, simply means the molecular surface colored by hydrophobicity. What exactly are you trying to do? Show protein as mesh surface and ligand as solid surface? You can definitely do it (or any combination of mesh surface on some atoms, solid on some other atoms) by opening multiple copies of the structure, as we said in previous messages. Then in the solid-surface copy, only show the parts of the surface you want as solid. In the mesh-surface copy, show the parts you want as mesh. For example, here is an example that shows H-ras as mesh surface with its ligand GCP as solid surface (image attached below), commands: open 121p open 121p surf #1 & protein surf #2:gcp surf style #1 mesh transp #1 50 surfaces color #2 gold surfaces hide solvent This can all be done with the menu as well, but it would take a lot more typing to enter that whole procedure. I Cc'd chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> which is the recommended address for asking ChimeraX questions (for future reference). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco [cid:EF604256-3D95-4380-9C2B-8916BEFAE15D@gateway.sonic.net] On Jul 6, 2020, at 10:30 AM, Gordon, Rory <rory.gordon.19@ucl.ac.uk<mailto:rory.gordon.19@ucl.ac.uk>> wrote: Hi Guys, Further to previous email, just tried fiddling with the transparency settings. I can get the protein structure to change through the transparency gradient for hydrophobic surface. However, for the substrate/ligands there seems to be binary system where you can either have full transparency or none at all. The hydrophobic surface can be coloured both for the protein and substrate/ligand. Cheers, Rory From: Gordon, Rory <rory.gordon.19@ucl.ac.uk<mailto:rory.gordon.19@ucl.ac.uk>> Sent: 06 July 2020 18:26 To: Tom Goddard <goddard@sonic.net<mailto:goddard@sonic.net>>; Elaine Meng <meng@cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> Cc: Eric Pettersen <pett@cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>> Subject: Re: [ChimeraX] #3464: partial surface mesh Hi Tom, Elaine and Eric I tried to establish the mesh surface with the whole protein structure selected through the GUI. I can only get the hydrophobic surface which I can colour with B-factor. The options of Mesh, Dot or Solid don't seem to change anything. Not sure how to get round this, so any help would be appreciated. Cheers, Rory From: Tom Goddard <goddard@sonic.net<mailto:goddard@sonic.net>> Sent: 02 July 2020 18:24 To: Elaine Meng <meng@cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> Cc: Gordon, Rory <rory.gordon.19@ucl.ac.uk<mailto:rory.gordon.19@ucl.ac.uk>>; Eric Pettersen <pett@cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>> Subject: Re: [ChimeraX] #3464: partial surface mesh Another trick that makes these meshes look nicer is to make them about 50-80% transparent (command "transp #2 70"). It gives the mesh an airy look. Tom On Jul 2, 2020, at 10:17 AM, Elaine Meng <meng@cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> wrote: Hi Rory, Here is an example image where I opened the same structure twice. I showed one copy with mesh surface and the second one with solid surface, and then simply hid parts of the solid surface. This is the way that Tom mentioned. Elaine <example.png> On Jul 2, 2020, at 3:29 AM, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote: #3464: partial surface mesh ---------------------------------------+---------------------------- Reporter: rory.gordon.19@… | Owner: Eric Pettersen Type: defect | Status: closed Priority: normal | Milestone: Component: Surface | Version: Resolution: fixed | Keywords: Blocked By: | Blocking: Notify when closed: | Platform: all Project: ChimeraX | ---------------------------------------+---------------------------- Comment (by rory.gordon.19@…): {{{ Hi Eric, Thanks for your email. I had actually seen a graphic in a publication which gave me that idea. Thanks anyway for the pointers. Cheers, Rory ________________________________ From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> Sent: 01 July 2020 18:23 Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; meng@cgl.ucsf.edu <meng@cgl.ucsf.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Gordon, Rory <rory.gordon.19@ucl.ac.uk> Subject: Re: [ChimeraX] #3464: partial surface mesh (was: ChimeraX bug report submission) #3464: partial surface mesh ---------------------------------------+---------------------------- Reporter: rory.gordon.19@… | Owner: Eric Pettersen Type: defect | Status: accepted Priority: normal | Milestone: Component: Unassigned | Version: Resolution: | Keywords: Blocked By: | Blocking: Notify when closed: | Platform: all Project: ChimeraX | ---------------------------------------+---------------------------- Changes (by Eric Pettersen): * status: new => accepted * cc: Tom Goddard, Elaine Meng (added) * project: => ChimeraX * platform: => all * owner: (none) => Eric Pettersen Comment: Hi Rory, I don't believe you can change just part of a surface into mesh, it's all or nothing. You can make that part of the surface partially transparent instead with Actions→Surface→Transparency. --Eric Eric Pettersen UCSF Computer Graphics Lab ----- Tom, should the command "surface style (#!4 & sel) mesh" actually do nothing (with part of the surface selected)? That seems surprising. Seems like it should change the whole surface into mesh. Is that a bug or am I misunderstanding something? --Eric -- Ticket URL: <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F3464%23comment%3A1&data=02%7C01%7C%7Cb50922f7c1a5440c438908d81de37918%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637292210119419879&sdata=GSVMvSlVzE7eo%2FbcWesHMjUigJgWIvMFzU1efXANpRI%3D&reserved=0> ChimeraX <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2F&data=02%7C01%7C%7Cb50922f7c1a5440c438908d81de37918%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637292210119429876&sdata=WAAsovWYcC03Q8hQTVRlAK2lbNXj2ULqvEo00cNukV0%3D&reserved=0> ChimeraX Issue Tracker }}} -- Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3464#comment:7> ChimeraX <http://www.rbvi.ucsf.edu/chimerax/> ChimeraX Issue Tracker
participants (2)
-
Elaine Meng -
Gordon, Rory