ChimeraX has no way to color ONE continous surface formed by combining multiple chains with coulombic or hydrophobic. It always color each chain surface separatly . Even though I generated a surface of combined chains by "surface enclose" command, ChimeraX still colors each chian seperately. In Chimera (not ChimearX), I could use surfcat to combine chains, generate one surface for combind chains, and color the surface as one continous. However, that could color large set of molecules. So please make ChimeraX can do the same.
Hi WC, Actually you can do this already: after creating the surface with "surface enclose," then you have to use the "surfaces" keyword of the "mlp" or "coulombic" command to actually use that pre-existing surface instead of calculating new surfaces (which would just be one per chain, as you said). Example: open 1zik surface #1 enclose protein [... then you can look in the model panel and see that the surface is #1.1 ...] mlp surfaces #1.1 ... or ... coulombic surfaces #1.1 <https://rbvi.ucsf.edu/chimerax/docs/user/commands/mlp.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/coulombic.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. we put this message on the chimerax-users list since it's really a how-to question, not a bug
On Aug 13, 2021, at 12:52 PM, W. C. via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
ChimeraX has no way to color ONE continous surface formed by combining multiple chains with coulombic or hydrophobic. It always color each chain surface separatly . Even though I generated a surface of combined chains by "surface enclose" command, ChimeraX still colors each chian seperately. In Chimera (not ChimearX), I could use surfcat to combine chains, generate one surface for combind chains, and color the surface as one continous. However, that could color large set of molecules. So please make ChimeraX can do the same.
Dear Elaine: Thank you so much! I struggled for days trying to achieve it. Yes, you are right and it is the way to do it. The green line in the attached picture is the line between two chains and color is continuously across the interface. Thanks again! WC From: Elaine Meng<mailto:meng@cgl.ucsf.edu> Sent: Friday, August 13, 2021 4:27 PM To: Cao, Wenxiang<mailto:wenxiang.cao@yale.edu> Cc: ChimeraX Users Help<mailto:ChimeraX-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Coulombic color combined surface Hi WC, Actually you can do this already: after creating the surface with "surface enclose," then you have to use the "surfaces" keyword of the "mlp" or "coulombic" command to actually use that pre-existing surface instead of calculating new surfaces (which would just be one per chain, as you said). Example: open 1zik surface #1 enclose protein [... then you can look in the model panel and see that the surface is #1.1 ...] mlp surfaces #1.1 ... or ... coulombic surfaces #1.1 <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fmlp.html&data=04%7C01%7Cwenxiang.cao%40yale.edu%7Cb9eaa60881ba43b79c6f08d95e98a861%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637644832493884419%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=9fGIOGUNxY%2B%2Bd9Q9FPYPBCPThydtr0q%2FK6Vgj2K0Llw%3D&reserved=0> <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fcoulombic.html&data=04%7C01%7Cwenxiang.cao%40yale.edu%7Cb9eaa60881ba43b79c6f08d95e98a861%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637644832493884419%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=VbzzSEy3%2FAg9nR%2Fpk5GJqviM%2Bm7ZHq4zumuxIRnXjPw%3D&reserved=0> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. we put this message on the chimerax-users list since it's really a how-to question, not a bug
On Aug 13, 2021, at 12:52 PM, W. C. via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
ChimeraX has no way to color ONE continous surface formed by combining multiple chains with coulombic or hydrophobic. It always color each chain surface separatly . Even though I generated a surface of combined chains by "surface enclose" command, ChimeraX still colors each chian seperately. In Chimera (not ChimearX), I could use surfcat to combine chains, generate one surface for combind chains, and color the surface as one continous. However, that could color large set of molecules. So please make ChimeraX can do the same.
That's great!! We understand it could be confusing (and annoying if you don't know how to stop it with this "surfaces" option) that the surface you already made would get thrown away and the per-chain surfaces would reappear. You're welcome, Elaine
On Aug 13, 2021, at 1:40 PM, Cao, Wenxiang via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Elaine:
Thank you so much! I struggled for days trying to achieve it. Yes, you are right and it is the way to do it. The green line in the attached picture is the line between two chains and color is continuously across the interface.
Thanks again! WC
From: Elaine Meng Sent: Friday, August 13, 2021 4:27 PM To: Cao, Wenxiang Cc: ChimeraX Users Help Subject: Re: [chimerax-users] Coulombic color combined surface
Hi WC, Actually you can do this already: after creating the surface with "surface enclose," then you have to use the "surfaces" keyword of the "mlp" or "coulombic" command to actually use that pre-existing surface instead of calculating new surfaces (which would just be one per chain, as you said).
Example: open 1zik surface #1 enclose protein
[... then you can look in the model panel and see that the surface is #1.1 ...]
mlp surfaces #1.1 ... or ... coulombic surfaces #1.1
<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fmlp.html&data=04%7C01%7Cwenxiang.cao%40yale.edu%7Cb9eaa60881ba43b79c6f08d95e98a861%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637644832493884419%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=9fGIOGUNxY%2B%2Bd9Q9FPYPBCPThydtr0q%2FK6Vgj2K0Llw%3D&reserved=0> <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fcoulombic.html&data=04%7C01%7Cwenxiang.cao%40yale.edu%7Cb9eaa60881ba43b79c6f08d95e98a861%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C637644832493884419%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=VbzzSEy3%2FAg9nR%2Fpk5GJqviM%2Bm7ZHq4zumuxIRnXjPw%3D&reserved=0>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
P.S. we put this message on the chimerax-users list since it's really a how-to question, not a bug
On Aug 13, 2021, at 12:52 PM, W. C. via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
ChimeraX has no way to color ONE continous surface formed by combining multiple chains with coulombic or hydrophobic. It always color each chain surface separatly . Even though I generated a surface of combined chains by "surface enclose" command, ChimeraX still colors each chian seperately. In Chimera (not ChimearX), I could use surfcat to combine chains, generate one surface for combind chains, and color the surface as one continous. However, that could color large set of molecules. So please make ChimeraX can do the same.
<color one continuous surface.PNG>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
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Cao, Wenxiang -
Elaine Meng -
W. C.