[chimerax-users] xchimera multiscale model

[Elaine Meng]

Hi Ana,
Sorry, ChimeraX does not yet have the join models feature.  You may need to use Chimera for the building, but (unfortunately) I can imagine it might be too slow with something this large. 

Other than trying to use Chimera for the whole thing, one other idea is to use Chimera just to put the linker onto each different molecule, then in ChimeraX, open the nanoparticle and each of the linker-other-molecules and move by hand the linker-other-molecules into the orientations and positions that you want them relative to the nanoparticle (without making any bonds since there is no join models).  However, that would also be a pain to do each one and get it in the right place, even though you can use the mouse mode to rotate/translate only the selected model, it would be time-consuming.  Then if you really need something that looks like a bond, you could add a pseudobond between each linker-other-molecule and the nanoparticle subunit:
<https://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html>

Mouse modes are described e.g. for the Right Mouse toolbar, although you can assign them to any button: see "rotate/translate selected models" for moving some models while others stay in place:
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html>

I don't know if either of these approaches (Chimera only, or combining the programs) is possible to do with reasonable effort.  You may need to find a different way to do it, sorry.

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


> On Mar 18, 2021, at 5:41 AM, Ana Sofia Ramos <ramos.anasofiaferreira at gmail.com> wrote:
> 
> 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
> 
> 
> 
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