Discrete coloring and secondary structure assignment.
Hi, I'm trying to generate a ribbons diagram where the secondary structures are defined by user and colored by user. I'm running into a problem where half of the amino acid is assigned the secondary structure and the entire residue is assigned the color. This makes for a strange image. Attached is an image. Notice how the coloring starts before the secondary structure. Any help is appreciated.? Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031
HI Reza, You cannot change that - the secondary structure ribbon shape is defined to change in the middle of a single residue, and the coloring is per residue. Some other programs also work this way (including Pymol, I believe). If you want the coloring to end abruptly with the secondary structure ribbon shape change, use Chimera instead. In your image, the ribbons look sort of smudgy/sooty, suggesting you are using "soft" lighting. In general, ambient-occlusion lighting may not work well for sparse representations like ribbons and sticks; they are best for space-filling representations like spheres and surfaces. You could see if "lighting gentle" is any better than soft, but if it still looks smudgy, other lighting may be better (e.g. "light simple" or "light simple shadows true"). If that seems too shiny to you, could also try "material dull". <http://rbvi.ucsf.edu/chimerax/docs/user/commands/lighting.html> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/material.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 13, 2020, at 3:52 PM, Reza Khayat <rkhayat@ccny.cuny.edu> wrote:
Hi,
I'm trying to generate a ribbons diagram where the secondary structures are defined by user and colored by user. I'm running into a problem where half of the amino acid is assigned the secondary structure and the entire residue is assigned the color. This makes for a strange image. Attached is an image. Notice how the coloring starts before the secondary structure. Any help is appreciated.
Best wishes, Reza
Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031 <example.png>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Elaine, Thanks. You are correct, I am using ambient occlusion. While occlusion was meant for space-filling images, I think the effect it has on ribbon diagrams is very cool. It looks rustic. It's unfortunate that the residue coloring and secondary structure assignments can't start at the same place. Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031 ________________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, August 13, 2020 7:20 PM To: Reza Khayat Cc: ChimeraX Users Help Subject: [EXTERNAL] Re: [chimerax-users] Discrete coloring and secondary structure assignment. HI Reza, You cannot change that - the secondary structure ribbon shape is defined to change in the middle of a single residue, and the coloring is per residue. Some other programs also work this way (including Pymol, I believe). If you want the coloring to end abruptly with the secondary structure ribbon shape change, use Chimera instead. In your image, the ribbons look sort of smudgy/sooty, suggesting you are using "soft" lighting. In general, ambient-occlusion lighting may not work well for sparse representations like ribbons and sticks; they are best for space-filling representations like spheres and surfaces. You could see if "lighting gentle" is any better than soft, but if it still looks smudgy, other lighting may be better (e.g. "light simple" or "light simple shadows true"). If that seems too shiny to you, could also try "material dull". <https://urldefense.proofpoint.com/v2/url?u=http-3A__rbvi.ucsf.edu_chimerax_d... > <https://urldefense.proofpoint.com/v2/url?u=http-3A__rbvi.ucsf.edu_chimerax_d... > 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 13, 2020, at 3:52 PM, Reza Khayat <rkhayat@ccny.cuny.edu> wrote:
Hi,
I'm trying to generate a ribbons diagram where the secondary structures are defined by user and colored by user. I'm running into a problem where half of the amino acid is assigned the secondary structure and the entire residue is assigned the color. This makes for a strange image. Attached is an image. Notice how the coloring starts before the secondary structure. Any help is appreciated.
Best wishes, Reza
Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031 <example.png>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://urldefense.proofpoint.com/v2/url?u=https-3A__plato.cgl.ucsf.edu_mail...
Hi Reza, Actually, there is an undocumented option that will change the C-terminal end of a secondary structure representation to the middle of the peptide bond where the coloring changes (if the two residues are different colors): cartoon style ssEnds long I.e. it will move the strand arrow point to where the color changes. However, there is no corresponding option for the N-terminal end. I thought that the "ssEnds" option had been removed years ago, but experiments show that it still works! With ssEnds long the representation starts at CA and ends in the middle of a peptide bond. With ssEnds short (default) the representation starts at CA and ends at CA. 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 13, 2020, at 4:31 PM, Reza Khayat <rkhayat@ccny.cuny.edu> wrote:
Hi Elaine,
Thanks. You are correct, I am using ambient occlusion. While occlusion was meant for space-filling images, I think the effect it has on ribbon diagrams is very cool. It looks rustic. It's unfortunate that the residue coloring and secondary structure assignments can't start at the same place.
Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031
________________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, August 13, 2020 7:20 PM To: Reza Khayat Cc: ChimeraX Users Help Subject: [EXTERNAL] Re: [chimerax-users] Discrete coloring and secondary structure assignment.
HI Reza, You cannot change that - the secondary structure ribbon shape is defined to change in the middle of a single residue, and the coloring is per residue. Some other programs also work this way (including Pymol, I believe).
If you want the coloring to end abruptly with the secondary structure ribbon shape change, use Chimera instead.
In your image, the ribbons look sort of smudgy/sooty, suggesting you are using "soft" lighting. In general, ambient-occlusion lighting may not work well for sparse representations like ribbons and sticks; they are best for space-filling representations like spheres and surfaces. You could see if "lighting gentle" is any better than soft, but if it still looks smudgy, other lighting may be better (e.g. "light simple" or "light simple shadows true"). If that seems too shiny to you, could also try "material dull".
<https://urldefense.proofpoint.com/v2/url?u=http-3A__rbvi.ucsf.edu_chimerax_d... > <https://urldefense.proofpoint.com/v2/url?u=http-3A__rbvi.ucsf.edu_chimerax_d... >
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 13, 2020, at 3:52 PM, Reza Khayat <rkhayat@ccny.cuny.edu> wrote:
Hi,
I'm trying to generate a ribbons diagram where the secondary structures are defined by user and colored by user. I'm running into a problem where half of the amino acid is assigned the secondary structure and the entire residue is assigned the color. This makes for a strange image. Attached is an image. Notice how the coloring starts before the secondary structure. Any help is appreciated.
Best wishes, Reza
Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031 <example.png>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://urldefense.proofpoint.com/v2/url?u=https-3A__plato.cgl.ucsf.edu_mail...
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thank you, will give it a try! Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031 ________________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, August 13, 2020 7:45 PM To: Reza Khayat Cc: ChimeraX Users Help Subject: Re: [chimerax-users] [EXTERNAL] Re: Discrete coloring and secondary structure assignment. Hi Reza, Actually, there is an undocumented option that will change the C-terminal end of a secondary structure representation to the middle of the peptide bond where the coloring changes (if the two residues are different colors): cartoon style ssEnds long I.e. it will move the strand arrow point to where the color changes. However, there is no corresponding option for the N-terminal end. I thought that the "ssEnds" option had been removed years ago, but experiments show that it still works! With ssEnds long the representation starts at CA and ends in the middle of a peptide bond. With ssEnds short (default) the representation starts at CA and ends at CA. 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 13, 2020, at 4:31 PM, Reza Khayat <rkhayat@ccny.cuny.edu> wrote:
Hi Elaine,
Thanks. You are correct, I am using ambient occlusion. While occlusion was meant for space-filling images, I think the effect it has on ribbon diagrams is very cool. It looks rustic. It's unfortunate that the residue coloring and secondary structure assignments can't start at the same place.
Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031
________________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, August 13, 2020 7:20 PM To: Reza Khayat Cc: ChimeraX Users Help Subject: [EXTERNAL] Re: [chimerax-users] Discrete coloring and secondary structure assignment.
HI Reza, You cannot change that - the secondary structure ribbon shape is defined to change in the middle of a single residue, and the coloring is per residue. Some other programs also work this way (including Pymol, I believe).
If you want the coloring to end abruptly with the secondary structure ribbon shape change, use Chimera instead.
In your image, the ribbons look sort of smudgy/sooty, suggesting you are using "soft" lighting. In general, ambient-occlusion lighting may not work well for sparse representations like ribbons and sticks; they are best for space-filling representations like spheres and surfaces. You could see if "lighting gentle" is any better than soft, but if it still looks smudgy, other lighting may be better (e.g. "light simple" or "light simple shadows true"). If that seems too shiny to you, could also try "material dull".
<https://urldefense.proofpoint.com/v2/url?u=http-3A__rbvi.ucsf.edu_chimerax_d... > <https://urldefense.proofpoint.com/v2/url?u=http-3A__rbvi.ucsf.edu_chimerax_d... >
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 13, 2020, at 3:52 PM, Reza Khayat <rkhayat@ccny.cuny.edu> wrote:
Hi,
I'm trying to generate a ribbons diagram where the secondary structures are defined by user and colored by user. I'm running into a problem where half of the amino acid is assigned the secondary structure and the entire residue is assigned the color. This makes for a strange image. Attached is an image. Notice how the coloring starts before the secondary structure. Any help is appreciated.
Best wishes, Reza
Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031 <example.png>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://urldefense.proofpoint.com/v2/url?u=https-3A__plato.cgl.ucsf.edu_mail...
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://urldefense.proofpoint.com/v2/url?u=https-3A__plato.cgl.ucsf.edu_mail...
participants (2)
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Elaine Meng -
Reza Khayat