[Chimera-users] Defining glycosidic bond of nucleotide objects

Eric Pettersen pett at cgl.ucsf.edu
Tue Apr 4 16:48:08 PDT 2017

Hi Charles-Alexandre,
	It turns out you don’t really have to do anything to get 481D to be displayed as nucleotides correctly, just bring up the Nucleotides tool and turn on the slab or rungs depictions.  Also, if I open 2BJ6, an HNA-RNA hybrid, Chimera show slabs for both strands that look fine as far as I can tell.  Can you determine what the differences are between your HNA residues and the PDB-standard ones found in 2BJ6 (6HA, 6HC, 6HG, 6HT)?  It may be easier to change the names of your atoms with the “setattr” command than to try to use Ribbon Style Editor here.


	Eric Pettersen
	UCSF Computer Graphics Lab

For reference, to change atom name Z to Y:

setattr a name Y @Z

to swap Z with Y (by using an intermediate name of X)

setattr a name X @Y  (temporarily rename Y atoms to X)
setattr a name Y @Z  (rename Z atoms to Y)
setattr a name Z @X  (rename X atoms to Z)

> On Apr 4, 2017, at 4:18 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Charles-Alexandre,
> Unfortunately our “nucleotides” expert is away this week, so we may need to wait for a definitive answer. Your guess is probably right, but there is no user-interface way to set the slab-controlling atom names.  The GUI just assumes they are pyrimidine or purine base types attached to C1’. 
> I tried swapping C1’ and C2’ atom names (just using a text-editor) in the first 3 residues of PDB 481D (HNA duplex) and then could show them as slabs or ladder rungs seemingly attached to the ribbon.  Some of the HNA atoms then had to behidden manually. However, I haven’t done the stuff you did with your own ribbon style, and it’s possible the name-swapping could cause some other problems.  It may work, but admittedly it is inconvenient and inelegant!
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>> On Apr 4, 2017, at 2:54 AM, Charles-Alexandre Mattelaer <charlesalexandre.mattelaer at kuleuven.be> wrote:
>> Dear Chimera-users
>> I'm currently doing modeling on hexitol nucleic acids and using Chimera to visualize the trajectories. Since the atoms in the hexitol-ring are numbered differently than in the standard ribose, Chimera has some difficulties displaying the correct ribbon (backbone) and slab (bases). I've been able to define my own ribbon style using the Ribbon Style Editor and creating a new ribbon style based on the standard 'nuleic acid' trace and replacing the existing backbone atoms with the corresponding atom names for the non-standard hexitol residues. 
>> The main problem is setting a slab object to replace the base atoms. The 'nucleotide objects' settings are based on a glycosidic bond on the C1' of ribose. In HNA the glycosidic bonds are found on C2' of hexitol. I believe this is causing the problem. Additionally, I can add that using the 'ladder'-like objects, a gap between the 'steps' and the backbone occurs. (I've tried setting the base as anchor but to no avail.) I was wondering if there would be a way to redefine the anchor atom of the nucleotide objects? (I searched in the manual but haven't found any ways to redefine the anchor itself.) This would greatly improve visibility of larger oligonucleotides and would help me a lot. 
>> Kind regards and thank you in advance
>> Charles-Alexandre Mattelaer
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