[chimerax-users] Showing Bond/PBond to Cartoon/Ribbons

[Anderson, Jacob]

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 at cnb.csic.es>
Sent: Friday, May 13, 2022 11:12 AM
To: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
Cc: Anderson, Jacob <jacob_r_anderson at 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 at 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 at 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 at 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 at 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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