[Chimera-users] Helix Display Artefact

[Elaine Meng]

Hi Sebastian,
Yes, it is different in ChimeraX.  Excerpt below from the ChimeraX "cartoon" command docs:

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html>
=-=-=
The transverse orientation of a residue's ribbon segment is set according to the type of secondary structure and/or polymer:
	• nucleic acid – at C5' by the C5'→C1' vector
	• peptide helix – at CA by a vector perpendicular to both the CAi-1→CA and CA→CAi+1 vectors 
	• peptide strand – at CA by a vector parallel to both the preceding and following peptide planes (like their line of intersection)

=-=-=
Best,
Elaine

> On Dec 28, 2021, at 9:53 AM, Sebastian Guettler via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi Elaine,
> 
> Thank you! You are right, the carbonyl is somewhat tipped outward. Regularisation of the region in Coot resolves the helix display problem. It looks like I will need to revisit my last refinement step. Out of curiosity: does ChimeraX use a different ribbon calculation method, as the display issue is unique to Chimera?
> 
> Thank you,
> Sebastian
> 
> 
> On 28/12/2021, 17:21, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:
> 
>    CAUTION: This email originated from outside of the ICR. Do not click links or open attachments unless you recognize the sender's email address and know the content is safe.
> 
> 
>    Hi Sebastian,
>    This may not be easy to circumvent, i.e. may simply be a pathological case for how the ribbon orientation is calculated.   As you said, the problem is not of secondary structure assignment, since it's defined as helix, just drawn strangely.
> 
>    Without actually seeing the atomic coordinates, my guess is that the carbonyl is tipped outward.  You could move the carbonyl O to a more "canonical" location and see if that helps.  Or (equivalently) replace that stretch of residues with another for which the ribbon is drawn nicely.
> 
>    In the Ribbon Style Editor (in menu under Tools... Depiction) in the Residue Class tab you can see that the orientation atom for amino acids is O.  I don't think there are any other good choices for standard amino acids... editing the Class settings is more for when you have different polymers e.g. beta-amino acids.  The documentation says a bit more about how the atoms are used in drawing the ribbon:
>    <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html#class>
> 
>    I hope this helps,
>    -----
>    Elaine C. Meng, Ph.D.
>    UCSF Chimera(X) team
>    Department of Pharmaceutical Chemistry
>    University of California, San Francisco
> 
> 
>> On Dec 28, 2021, at 8:44 AM, Sebastian Guettler via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>> 
>> Dear Chimera users,
>> 
>> I have a problem with what I think is some sort of a helix display artefact is UCSF Chimera (including the latest release, 1.16). I attach an image. In cartoon display, the helix appears turned inside out for the last turn. It is displayed normally in ChimeraX and PyMol, and the display problem is independent of the secondary structure assignment algorithm (dssp, ksdssp, Stride). Any suggestions on how to solve this issue are welcome.
>> 
>> Thank you,
>> Sebastian
>> 
>> ---------------------------------------------
>> Sebastian Guettler, PhD
>> Team Leader
>> The Institute of Cancer Research (ICR)
>> Divisions of Structural Biology and Cancer Biology
>> London, UK
>> ---------------------------------------------
>> <image001.jpg>
>> 
>> The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.
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> 
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