[chimerax-users] [chimeraX-users] to display cylinder and helical ribbon of one chain

[Elaine Meng]

Hi Yingyi,
Presets always apply to everything.  Only the Actions menu is limited to selection, not Presets.  
<http://rbvi.ucsf.edu/chimerax/docs/user/menu.html#presets>
<http://rbvi.ucsf.edu/chimerax/docs/user/menu.html#actions>

If you already have multiple copies of the structure open and you want to change only one,  you can't use a preset.  Instead you would have to use another method:

(1) typing in commands (cartoon, cartoon style) with specification of which model (#1,#2) and sometimes which residues (:2-56) to act on
 - or -
(2) selection of a model or its parts and then using the Actions menu

One easy way with Presets, however, is to open the structure once, then use the "cylinders/stubs" preset, and then open the structure the second time.  After that you would still need to hide parts of both models and then make their cartoons the same color if you want it to look like there's only one cartoon.

To hide exactly the right parts of each model, you would still need to type in commands to hide/show cartoons for specific residues, for example as in the previous thread:
<http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-April/001068.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 9, 2020, at 8:35 PM, Yingyi Zhang <yingyizhangg at gmail.com> wrote:
> 
> Dear Elaine,
> 
> Great thanks for your confirmation. I thought it might work as you told me to have another copy and display in separate styles.
> However, I tried to select one of the models (pdb) I have, and then [Present] > Cylinder/Stubs, the display changed for all my opened models.
> Did I do something wrong? Or is it due to my version used -  version 0.91 (2019-12-10)? 
> Many thanks for your help.
> 
> Best,
> Yingyi
> 
> On Thu, Jul 9, 2020 at 12:25 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Dear Yingyi,
> The "cartoon style" settings like tube helices (cylinders) apply only to the whole model. 
> 
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style>
> 
> However, you can do what you want by  opening your structure twice. In one copy, use the tube helix style, and show only cartoon for the parts you want as cylinders (hide the cartoon of the rest of the chain).  In the other copy, use the ribbon helix style, and hide the cartoon for the part that is shown in the first copy.
> 
> To make the ribbons of the two copies connect smoothly, it seems that you need to extend at least 2 residues beyond the ends of a helix in the model shown as tubes, as detailed in in this previous thread:
> <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-April/001068.html>
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> > On Jul 8, 2020, at 2:22 AM, Yingyi Zhang <yingyizhangg at gmail.com> wrote:
> > 
> > Dear ChimeraX Team,
> > 
> > I have one model (pdb format), which contains multiple chains. Each chain (chain A for instance) consists of several helices.
> > 
> > Is it possible to display ChainA in this manner - first two helices as cylinders but the others as ribbons?
> > 
> > I tried to specify the residues, but it always changed the entire presence of the model, including the un-selected ones. Could you help me with this? I am still not very familiar with chimeraX.
> > 
> > Thank you very much.
> > Best regards,
> > 
> > Yingyi