[Chimera-users] Different center when display coordinates with bonds or ribbon

[Yang Shi]

Dear Elaine,

Thanks for your help. Your suggestion is very helpful!!

Actually, the CA are in the density map. When I narrowed the ribbon width in ribbon mode and show only CA in atoms/bonds mode, the difference became more clear (attached files). Maybe there are some other algorithms for the ribbon generation, which is not suit for my coordinates and I have not realised. Some helix geometry restrains in ribbon maybe?

Changing the guide atom really helps a lot to in terms of display. But it sounds it can also help those who did not refine their pdb well in some cases. For publication, I think, ideally,  I should not change the guide atom for ribbon. Eventually, I will use atoms/bonds mode, and display side chains with the chain trace for the backbone.

Thank you again!
Best wishes,
Yang


> On 10 Aug 2018, at 21:53, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Yang,
> The standard ribbon for amino acids centers on CA, and as you can see, the CA atoms (alpha-carbons) are towards the lower side of the contour surface in your image.
> 
> You can define a ribbon class that uses C (carbonyl carbon) instead of the CA, which will be shifted upward in the orientation shown in your image.  Use menu: Tools… Depiction… Ribbon Style Editor, and click on the “Residue Class” tab.  The classes should include “amino acid” which is the standard one for amino acids, with CA as the guide atom.  Then you can change guide atom from CA to C and then click Apply to see if it is good enough for you.  I see it makes a helix but narrower than the one using CA, so it might not be good enough.
> 
> In Ribbon Style Editor, if you might want to use that new class later,  you can Save to a new name (since you don’t want to overwrite the regular “amino acid” one).  Then later in the session you can use command “ribclass”  to use that class.
> 
> Ribbon Style Editor:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html>>
> …residue classes:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html#class <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html#class>>
> …ribclass command:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ribclass.html <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ribclass.html>>
> 
> For example, I started with “amino  acid”, changed guide atom to C,  and then saved a new class named “shifted”.  Then later without showing the Ribbon Style Editor again, I can just use the new class with a command like:
> 
> ribclass shifted #1
> 
> … or change it back to default:
> 
> ribclass “amino acid” #1
> 
> In the image attached below, the tan ribbon is the default one, the blue one is the one using C as guide atom.  Using N shifts in the opposite direction 
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> <shifted-ribbon.png>
>> On Aug 10, 2018, at 12:35 PM, 师扬 <sy31802 at 163.com <mailto:sy31802 at 163.com>> wrote:
>> 
>> Dear chimera developers and users,
>> Recently, I met a very strange issue about displaying coordinates in chimera. I found the helices were off-centered with the map, when I open a well refined PDB file and the map it was refined against, and keep an eye on the helices which is automatically displayed by Ribbon. But actually they are will aligned in COOT. And if I hide Ribbon and showed Atoms/Bonds, they were well-aligned. The attached files show the same region with different displaying modes. And I have tried several versions of chimera, the results were the same.
>> Actually, I want to use Ribbon to display these helices. Does anyone know how to fix it?
>> Thanks in advance!
>> Yang
> 

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