Thanks so much. That worked. Another question. When colored by elements, the color of carbons in side chains is different from the cartoons. Any chance I can change the color of carbons to the same color as the cartoons.

From: Elaine Meng <meng@cgl.ucsf.edu>
Date: Friday, August 18, 2023 at 9:19 AM
To: Zhang, Miao <zhang@chapman.edu>
Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu>
Subject: Re: [chimerax-users] Show side chain, main chain, and cartoon at the same time

External Message


[External Message]

Dear Miao Zhang,
It is easy to show cartoons and sidechain atoms for any residues that you want (e.g. with "cartoon" and "show" commands or by clicking the toolbar icons that display cartoons and atoms, respectively).  However, the tricky part is that if you want to also show mainchain, you have to use the option "suppress false" with "cartoon" command because normally cartoon will prevent showing mainchain.

Here is an example to show sidechain + mainchain + cartoon in potassium channel structure 1bl8.  Commands below with "..." to mean explanations that are not commands:

open 1bl8

... by default it already shows the atoms near the ions but you can hide all atoms first to start from a clean state

hide

... select residues near ions (4.0 angstroms in this example) and then show their atoms ... at first only sidechain will be shown

select ions :<4.0
show sel

... now use the cartoon option to also show mainchain at same time, and then clear the selection

cartoon suppress false
~sel

... you could also just give chain ID and residue numbers instead of using a selection zone, for example residues 30-38 of chain D.  The cartoon is already in the suppress-false state so you don't have to give that command again:

show /D:30-38

... Even though suppress false is turned on, you don't *have* to show mainchain. This setting just allows you to hide/show those atoms as you wish.  So you can still hide the main chain atoms where you don't want to see them, for example:

hide /D:30-38@n,c,o

... (you still need to keep the CA atoms shown or else the side chains will not be attached)

See help pages for all the commands above in the User Guide for more details.
<https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Findex.html&data=05%7C01%7Czhang%40chapman.edu%7Caa41e63062f1441d9d1408dba006e0d1%7C809929af2d2545bf9837089eb9cfbd01%7C1%7C0%7C638279723631640988%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=dncoLgGU85m0WOevP4hUTcLTwQcdixHaWXQFeCvgVdI%3D&reserved=0>

You may also want to try some tutorials to become more familiar with ChimeraX:
<https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2Ftutorials.html&data=05%7C01%7Czhang%40chapman.edu%7Caa41e63062f1441d9d1408dba006e0d1%7C809929af2d2545bf9837089eb9cfbd01%7C1%7C0%7C638279723631640988%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=dfczrkkWmRYhDTIUwXYzNH%2BcAacctTrElnyLyRfm4as%3D&reserved=0>

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

> On Aug 17, 2023, at 9:50 PM, Zhang, Miao via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Dear colleagues
> I am new to ChimeraX. I am trying to figure out how to show side chain, main chain, and cartoon at the same time in a protein structure. Like the one below made in other software. Could you please help?
> <image001.png>
> Best,
> - - - - - - - - - - - - - - - - -
> Miao Zhang   Ph.D.
> Associate Professor
> Chapman University School of Pharmacy
> 9401 Jeronimo Rd, Suite 297W
> Irvine, CA 92618
> Phone: 714-516-5478
> http://www.chapman.edu/our-faculty/miao-zhang
>
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