Hi Elaine!

 

Thanks for your response.

I actually didn't have the bases selected as ellipsoids or slabs, so I'm not sure why the methyl groups on the bases weren't showing. So, I just started again with a clean import and the methyl groups are now showing (I added a ball for each). I was fiddling around in the original file a lot, so clearly upset something.

 

 

Thanks for the great advice and best wishes,

 

Maja

 

-----Original Message-----
From: Elaine Meng <meng@cgl.ucsf.edu>
Sent: Thursday, 19 September 2024 11:32 AM
To: Maja Divjak <Maja.Divjak@petermac.org>
Cc: chimerax-users@cgl.ucsf.edu
Subject: Re: [chimerax-users] Displaying methyl groups on DNA?

 

! EXTERNAL EMAIL: Think before you click. If suspicious send to CyberReport@petermac.org

 

hi Maja,

I guess you know the image is not ChimeraX, right?

 

I'm a little confused by the question because when I open that structure (6c1y) all the atoms are shown, including all the methyl carbons.  But maybe you are showing the nucleotide bases as slabs or ellipsoids?  That is the problem, because it will only show the slab or ellipsoid, not the atoms.  You have to show the atoms (optionally with filled rings) to see the methyl groups.  It won't show slab/ellipsoid and the methyl group on the base at the same time, unless you open the structure twice and use atoms for one copy of the residue and slab or ellipsoid for the other copy of the residue.

 

example:

 

open 6c1y

style stick

view /C:6

label /C:6

col byhet

 

You can fill the rings and still see the methylations, e.g.

 

nuc fill

 

However, as soon as you go to slab or ellipsoid representation of that residue, the methyl will not be shown. You can show the methylated base as atoms and show all the other residues as slabs or ellipsoids if you want.

 

I tried opening the structure twice to show ellipsoids in one copy and atoms in the other, and to me it looks like the 5CM ellipsoids are placed strangely (not right on the ring).  I'll ask our nucleotides expert about that.  Just be aware, that ellipsoids or slabs may not work that well with the modified residues.

 

I hope this helps,

Elaine

-----

Elaine C. Meng, Ph.D.

UCSF Chimera(X) team

Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

 

 

> On Sep 18, 2024, at 6:04 PM, Maja Divjak via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

>

> Hi there,

>  Hope you’re well.

>  I’m sure this is a rookie question, but I’m having trouble displaying the methyl groups on a methylated DNA sequence, as shown in PDB 6C1Y.

>  <image001.jpg>  I’ve tried selecting the DNA and then showing the methyl functional group, but this selects all the methyl groups including those in the protein sequence. I also tried selecting the individual bases I know are methylated using eg select #2/C:6, but not sure of the command to show the methyl group following this ie select #2/C:6 show methyl does not work, whereas show methyl as a solo command shows all methyl groups in the whole structure. Couldn’t find anything in the help files, unfortunately.

>  Thanks so much and best wishes,

>  Maja