Showing Bond/PBond to Cartoon/Ribbons
There has been a prior post on this problem, but I wanted to ask about some asymmetry I see in ChimeraX when displaying residues emanating from ribbons/cartoons. https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-October/002850.html For example, sometimes when I select a residue on a ribbon/cartoon and write "show sel atoms,bonds", I get a floating residue. However, other times I get a nice connection between the beta carbon and the ribbon (the desired behavior). How can users get a consistent behavior where there is a connection from the beta carbon to the ribbon? Good Example - connected to ribbon [cid:6ddcc2ee-f9b2-4060-8e3f-fde8ccc74881] Two floating examples: [cid:46516984-036d-4a39-9713-9056a161548a]
I think this is related to the way the ribbon/cartoon smooths over secondary structures. Beta strands are wavy not flat, for example. There is a similar problem in PyMOL. If we want to show a whole residue then the best way to do that is to turn off the flat strands and the idealisation of helices. PyMOL also has a feature called "side chain helper" where the bonds are connected to the idealised calpha location rather than the actual calpha atom location, which may be a nice feature to have in chimerax too. Best wishes James "Anderson, Jacob via ChimeraX-users" <chimerax-users@cgl.ucsf.edu> escribió:
There has been a prior post on this problem, but I wanted to ask about some asymmetry I see in ChimeraX when displaying residues emanating from ribbons/cartoons.
https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-October/002850.html
For example, sometimes when I select a residue on a ribbon/cartoon and write "show sel atoms,bonds", I get a floating residue. However, other times I get a nice connection between the beta carbon and the ribbon (the desired behavior).
How can users get a consistent behavior where there is a connection from the beta carbon to the ribbon?
Good Example - connected to ribbon [cid:6ddcc2ee-f9b2-4060-8e3f-fde8ccc74881]
Two floating examples: [cid:46516984-036d-4a39-9713-9056a161548a]
Hi Jacob, The topic of that post is slightly different, whether the CA is shown at all. Now, whether the CA falls on the ribbon or not is another issue. It can fall off the ribbon on beta-strands where the the ribbon path is smoothed (by default). Also by default, there will be "tethers" displayed between the CA and the ribbon when the CA is not on the ribbon. This is explained in the cartoon (ribbon) command help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html> See for example Lys 164 in 2mnr, where a tether is shown. If you turn off smoothing the ribbon will always fall exactly on the CA positions: cartoon smooth 0 However, turning off smoothing makes the beta-strands very ripply, like some lasagna noodles, so you may not want to turn off smoothing entirely or on the whole ribbon. Thus your options are to: (A) use weaker smoothing overall, e.g.: cartoon smooth 0.5 (default = 1.0) - and/or - (B) weaken or turn off smoothing only at the particular residue positions where you are seeing the problem, e.g.: cartoon #1/A:164 smooth 0 I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 12, 2022, at 8:32 AM, Anderson, Jacob via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
There has been a prior post on this problem, but I wanted to ask about some asymmetry I see in ChimeraX when displaying residues emanating from ribbons/cartoons.
https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-October/002850.html
For example, sometimes when I select a residue on a ribbon/cartoon and write "show sel atoms,bonds", I get a floating residue. However, other times I get a nice connection between the beta carbon and the ribbon (the desired behavior).
How can users get a consistent behavior where there is a connection from the beta carbon to the ribbon?
Good Example - connected to ribbon <image.png>
Two floating examples: <image.png>
Hi Elaine, The CA tether sounds like a great way to deal with this kind of thing. Perhaps it would be helpful to show CA atoms along with the side chain or include CB tethers too. Best wishes James Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> escribió:
Hi Jacob, The topic of that post is slightly different, whether the CA is shown at all. Now, whether the CA falls on the ribbon or not is another issue. It can fall off the ribbon on beta-strands where the the ribbon path is smoothed (by default). Also by default, there will be "tethers" displayed between the CA and the ribbon when the CA is not on the ribbon. This is explained in the cartoon (ribbon) command help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html>
See for example Lys 164 in 2mnr, where a tether is shown.
If you turn off smoothing the ribbon will always fall exactly on the CA positions:
cartoon smooth 0
However, turning off smoothing makes the beta-strands very ripply, like some lasagna noodles, so you may not want to turn off smoothing entirely or on the whole ribbon. Thus your options are to:
(A) use weaker smoothing overall, e.g.:
cartoon smooth 0.5 (default = 1.0)
- and/or -
(B) weaken or turn off smoothing only at the particular residue positions where you are seeing the problem, e.g.:
cartoon #1/A:164 smooth 0
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 12, 2022, at 8:32 AM, Anderson, Jacob via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
There has been a prior post on this problem, but I wanted to ask about some asymmetry I see in ChimeraX when displaying residues emanating from ribbons/cartoons.
https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-October/002850.html
For example, sometimes when I select a residue on a ribbon/cartoon and write "show sel atoms,bonds", I get a floating residue. However, other times I get a nice connection between the beta carbon and the ribbon (the desired behavior).
How can users get a consistent behavior where there is a connection from the beta carbon to the ribbon?
Good Example - connected to ribbon <image.png>
Two floating examples: <image.png>
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Hi James, The CA atoms are shown when the side chain is shown, or else there would be a much bigger gap! The tether is drawn between the CA and the ribbon. Best, Elaine
On May 12, 2022, at 9:49 AM, JAMES MICHAEL S1JJRUdFUiA= <jmkrieger@cnb.csic.es> wrote:
Hi Elaine,
The CA tether sounds like a great way to deal with this kind of thing. Perhaps it would be helpful to show CA atoms along with the side chain or include CB tethers too.
Best wishes James
Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> escribió:
Hi Jacob, The topic of that post is slightly different, whether the CA is shown at all. Now, whether the CA falls on the ribbon or not is another issue. It can fall off the ribbon on beta-strands where the the ribbon path is smoothed (by default). Also by default, there will be "tethers" displayed between the CA and the ribbon when the CA is not on the ribbon. This is explained in the cartoon (ribbon) command help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html>
See for example Lys 164 in 2mnr, where a tether is shown.
If you turn off smoothing the ribbon will always fall exactly on the CA positions:
cartoon smooth 0
However, turning off smoothing makes the beta-strands very ripply, like some lasagna noodles, so you may not want to turn off smoothing entirely or on the whole ribbon. Thus your options are to:
(A) use weaker smoothing overall, e.g.:
cartoon smooth 0.5 (default = 1.0)
- and/or -
(B) weaken or turn off smoothing only at the particular residue positions where you are seeing the problem, e.g.:
cartoon #1/A:164 smooth 0
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 12, 2022, at 8:32 AM, Anderson, Jacob via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
There has been a prior post on this problem, but I wanted to ask about some asymmetry I see in ChimeraX when displaying residues emanating from ribbons/cartoons.
https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-October/002850.html
For example, sometimes when I select a residue on a ribbon/cartoon and write "show sel atoms,bonds", I get a floating residue. However, other times I get a nice connection between the beta carbon and the ribbon (the desired behavior).
How can users get a consistent behavior where there is a connection from the beta carbon to the ribbon?
Good Example - connected to ribbon <image.png>
Two floating examples: <image.png>
Perfect. In pymol, this is not the case. Best wishes James Elaine Meng <meng@cgl.ucsf.edu> escribió:
Hi James, The CA atoms are shown when the side chain is shown, or else there would be a much bigger gap! The tether is drawn between the CA and the ribbon. Best, Elaine
On May 12, 2022, at 9:49 AM, JAMES MICHAEL S1JJRUdFUiA= <jmkrieger@cnb.csic.es> wrote:
Hi Elaine,
The CA tether sounds like a great way to deal with this kind of thing. Perhaps it would be helpful to show CA atoms along with the side chain or include CB tethers too.
Best wishes James
Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> escribió:
Hi Jacob, The topic of that post is slightly different, whether the CA is shown at all. Now, whether the CA falls on the ribbon or not is another issue. It can fall off the ribbon on beta-strands where the the ribbon path is smoothed (by default). Also by default, there will be "tethers" displayed between the CA and the ribbon when the CA is not on the ribbon. This is explained in the cartoon (ribbon) command help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html>
See for example Lys 164 in 2mnr, where a tether is shown.
If you turn off smoothing the ribbon will always fall exactly on the CA positions:
cartoon smooth 0
However, turning off smoothing makes the beta-strands very ripply, like some lasagna noodles, so you may not want to turn off smoothing entirely or on the whole ribbon. Thus your options are to:
(A) use weaker smoothing overall, e.g.:
cartoon smooth 0.5 (default = 1.0)
- and/or -
(B) weaken or turn off smoothing only at the particular residue positions where you are seeing the problem, e.g.:
cartoon #1/A:164 smooth 0
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 12, 2022, at 8:32 AM, Anderson, Jacob via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
There has been a prior post on this problem, but I wanted to ask about some asymmetry I see in ChimeraX when displaying residues emanating from ribbons/cartoons.
https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-October/002850.html
For example, sometimes when I select a residue on a ribbon/cartoon and write "show sel atoms,bonds", I get a floating residue. However, other times I get a nice connection between the beta carbon and the ribbon (the desired behavior).
How can users get a consistent behavior where there is a connection from the beta carbon to the ribbon?
Good Example - connected to ribbon <image.png>
Two floating examples: <image.png>
Thanks for everyone's input! With this feedback, Ill go back to the session files and see if I can smooth/desmooth to make the residues less floaty. Thanks so much! jacob ________________________________ From: JAMES MICHAEL S1JJRUdFUiA= <jmkrieger@cnb.csic.es> Sent: Friday, May 13, 2022 11:12 AM To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Cc: Anderson, Jacob <jacob_r_anderson@hms.harvard.edu> Subject: Re: [chimerax-users] Showing Bond/PBond to Cartoon/Ribbons Perfect. In pymol, this is not the case. Best wishes James Elaine Meng <meng@cgl.ucsf.edu> escribió:
Hi James, The CA atoms are shown when the side chain is shown, or else there would be a much bigger gap! The tether is drawn between the CA and the ribbon. Best, Elaine
On May 12, 2022, at 9:49 AM, JAMES MICHAEL S1JJRUdFUiA= <jmkrieger@cnb.csic.es> wrote:
Hi Elaine,
The CA tether sounds like a great way to deal with this kind of thing. Perhaps it would be helpful to show CA atoms along with the side chain or include CB tethers too.
Best wishes James
Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> escribió:
Hi Jacob, The topic of that post is slightly different, whether the CA is shown at all. Now, whether the CA falls on the ribbon or not is another issue. It can fall off the ribbon on beta-strands where the the ribbon path is smoothed (by default). Also by default, there will be "tethers" displayed between the CA and the ribbon when the CA is not on the ribbon. This is explained in the cartoon (ribbon) command help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html>
See for example Lys 164 in 2mnr, where a tether is shown.
If you turn off smoothing the ribbon will always fall exactly on the CA positions:
cartoon smooth 0
However, turning off smoothing makes the beta-strands very ripply, like some lasagna noodles, so you may not want to turn off smoothing entirely or on the whole ribbon. Thus your options are to:
(A) use weaker smoothing overall, e.g.:
cartoon smooth 0.5 (default = 1.0)
- and/or -
(B) weaken or turn off smoothing only at the particular residue positions where you are seeing the problem, e.g.:
cartoon #1/A:164 smooth 0
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 12, 2022, at 8:32 AM, Anderson, Jacob via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
There has been a prior post on this problem, but I wanted to ask about some asymmetry I see in ChimeraX when displaying residues emanating from ribbons/cartoons.
https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-October/002850.html
For example, sometimes when I select a residue on a ribbon/cartoon and write "show sel atoms,bonds", I get a floating residue. However, other times I get a nice connection between the beta carbon and the ribbon (the desired behavior).
How can users get a consistent behavior where there is a connection from the beta carbon to the ribbon?
Good Example - connected to ribbon <image.png>
Two floating examples: <image.png>
participants (3)
-
Anderson, Jacob -
Elaine Meng -
JAMES MICHAEL S1JJRUdFUiA=