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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.</div>
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Thanks so much!</div>
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jacob</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> JAMES MICHAEL S1JJRUdFUiA= <jmkrieger@cnb.csic.es><br>
<b>Sent:</b> Friday, May 13, 2022 11:12 AM<br>
<b>To:</b> ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><br>
<b>Cc:</b> Anderson, Jacob <jacob_r_anderson@hms.harvard.edu><br>
<b>Subject:</b> Re: [chimerax-users] Showing Bond/PBond to Cartoon/Ribbons</font>
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<div class="PlainText">Perfect. In pymol, this is not the case.<br>
<br>
Best wishes<br>
James<br>
<br>
Elaine Meng <meng@cgl.ucsf.edu> escribió:<br>
<br>
> Hi James,<br>
> The CA atoms are shown when the side chain is shown, or else there <br>
> would be a much bigger gap! The tether is drawn between the CA and <br>
> the ribbon.<br>
> Best,<br>
> Elaine<br>
><br>
>> On May 12, 2022, at 9:49 AM, JAMES MICHAEL S1JJRUdFUiA= <br>
>> <jmkrieger@cnb.csic.es> wrote:<br>
>><br>
>> Hi Elaine,<br>
>><br>
>> The CA tether sounds like a great way to deal with this kind of <br>
>> thing. Perhaps it would be helpful to show CA atoms along with the <br>
>> side chain or include CB tethers too.<br>
>><br>
>> Best wishes<br>
>> James<br>
>><br>
>> Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> escribió:<br>
>><br>
>>> Hi Jacob,<br>
>>> The topic of that post is slightly different, whether the CA is <br>
>>> shown at all. Now, whether the CA falls on the ribbon or not is <br>
>>> another issue. It can fall off the ribbon on beta-strands where <br>
>>> the the ribbon path is smoothed (by default). Also by default, <br>
>>> there will be "tethers" displayed between the CA and the ribbon <br>
>>> when the CA is not on the ribbon. This is explained in the <br>
>>> cartoon (ribbon) command help:<br>
>>> <<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html">https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html</a>><br>
>>><br>
>>> See for example Lys 164 in 2mnr, where a tether is shown.<br>
>>><br>
>>> If you turn off smoothing the ribbon will always fall exactly on <br>
>>> the CA positions:<br>
>>><br>
>>> cartoon smooth 0<br>
>>><br>
>>> However, turning off smoothing makes the beta-strands very <br>
>>> ripply, like some lasagna noodles, so you may not want to turn off <br>
>>> smoothing entirely or on the whole ribbon. Thus your options are <br>
>>> to:<br>
>>><br>
>>> (A) use weaker smoothing overall, e.g.:<br>
>>><br>
>>> cartoon smooth 0.5<br>
>>> (default = 1.0)<br>
>>><br>
>>> - and/or -<br>
>>><br>
>>> (B) weaken or turn off smoothing only at the particular residue <br>
>>> positions where you are seeing the problem, e.g.:<br>
>>><br>
>>> cartoon #1/A:164 smooth 0<br>
>>><br>
>>> I hope this helps,<br>
>>> Elaine<br>
>>> -----<br>
>>> Elaine C. Meng, Ph.D.<br>
>>> UCSF Chimera(X) team<br>
>>> Department of Pharmaceutical Chemistry<br>
>>> University of California, San Francisco<br>
>>><br>
>>>> On May 12, 2022, at 8:32 AM, Anderson, Jacob via ChimeraX-users <br>
>>>> <chimerax-users@cgl.ucsf.edu> wrote:<br>
>>>><br>
>>>> There has been a prior post on this problem, but I wanted to ask <br>
>>>> about some asymmetry I see in ChimeraX when displaying residues <br>
>>>> emanating from ribbons/cartoons.<br>
>>>><br>
>>>> <a href="https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-October/002850.html">
https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-October/002850.html</a><br>
>>>><br>
>>>> For example, sometimes when I select a residue on a <br>
>>>> ribbon/cartoon and write "show sel atoms,bonds", I get a floating <br>
>>>> residue. However, other times I get a nice connection between the <br>
>>>> beta carbon and the ribbon (the desired behavior).<br>
>>>><br>
>>>> How can users get a consistent behavior where there is a <br>
>>>> connection from the beta carbon to the ribbon?<br>
>>>><br>
>>>> Good Example - connected to ribbon<br>
>>>> <image.png><br>
>>>><br>
>>>> Two floating examples:<br>
>>>> <image.png><br>
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