[chimerax-users] [Chimera-users] color by zone in chimeraX

[Elaine Meng]

Hi Pranav,
You have to use color zone after doing the clipping, as mentioned in this recent post:

<https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-November/001642.html>

If there wasn't any clipping when you used color zone, the clipping surfaces did not yet exist and did not get colored.

Best,
Elaine

> On Nov 20, 2020, at 10:59 AM, Pranav Shah <p.shah.lab at gmail.com> wrote:
> 
> Amazing! Thank you!
> 
> May I also know how I can color clipping planes with the same colors?
> 
> Best,
> Pranav
> --
> Pranav Shah
> Postdoctoral Research Fellow.
> 
> Division of Structural Biology,
> Wellcome Trust Centre for Human Genetics,
> University of Oxford,
> Roosevelt Drive, Oxford OX3 7BN,
> UK
> On Fri, Nov 20, 2020 at 6:45 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> 
>> Hi Pranav,
>> I believe you need to use "copies true" in the sym command to make the full assembly using "real" atomic copies rather than graphical clones.  Color zone and other commands only recognize the real atomic copies.
>> 
>> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#copies>
>> 
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>> 
>>> On Nov 20, 2020, at 10:21 AM, Pranav Shah <p.shah.lab at gmail.com> wrote:
>>> 
>>> Hi Elaine,
>>> 
>>> Further to this query, I have a virus.pdb and virus.mrc. I symmetry
>>> expanded the virus.pdb using
>>> sym #1 assembly 1
>>> and then ran color by zone
>>> color  zone  #2 near  #3  distance 5
>>> 
>>> Where
>>> #1 = virus asym unit
>>> #2 = virus.mrc
>>> #3 =  symmetrised #1
>>> 
>>> however this results in only the surface in the asymmetric unit
>>> inheriting the model colors. How do I propagate the colors of all the
>>> chains to the entire surface of the capsid?
>>> 
>>> Best,
>>> Pranav
>> 
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