[chimerax-users] xchimera multiscale model

[Ana Sofia Ramos]

Hi Elaine,
I manage to make the representation of the nanoparticle, but now I would
like to link a molecule (from a different pdb) to each chain (C- or N-term)
of the nanoparticle, and between both I need to add a link of 10 a.a.. I
tried to use the build model but I cannot find the option join models in
chimeraX. I hope that you can also help me with that. Please, can you let me
know how to make it?
Kind regards,
Ana

-----Mensagem original-----
De: Elaine Meng <meng at cgl.ucsf.edu> 
Enviada: 17 de março de 2021 18:36
Para: Ana Sofia Ramos <ramos.anasofiaferreira at gmail.com>
Cc: chimerax-users at cgl.ucsf.edu
Assunto: Re: [chimerax-users] xchimera multiscale model

Hi Ana,
ChimeraX does not have a Multiscale Models tool like the one in Chimera.
However, you can use the ChimeraX "sym" command, e.g. something like
commands:

open 1hqk
hide solvent
style stick
sym #1 assembly 1 surfaceOnly true resolution 10

... but you should look at the "sym" command help because there are lots of
options, and you might decide to use different options or different values
of the options.  Use command "help sym" to see the help page included in
your download, or see the copy at our website:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.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 Mar 17, 2021, at 9:53 AM, Ana Sofia Ramos
<ramos.anasofiaferreira at gmail.com> wrote:
> 
> Hi, 
> I am having some difficulties in using xchimera, and I would like to ask
you if you could help me. 
> I want to make a representation of a virus-like nanoparticle using the pdb
1HQK. I have searched in the tutorial of xchimera but I could not find the
general instructions, but I found them in the tutorial of chimera
(multiscale model), however, the options are not present in my installation
xchimera (and also in my installation of chimera). Then, I thought that
maybe you could tell me how to make it in xchimera. 
>  
> Thank you very much for your attention. 
> Kind regards,
> Ana