[chimerax-users] xchimera multiscale model

[Ana Sofia Ramos]

Hi Elaine,
I am writing to you to thank you for your kind explanation! I have made as you suggested. I have added some atoms to the structure and saved as pdb. After, I did copy and past of the lines with the symmetry information. Then I have just typed in the command line: sym #1 biomt surfaceOnly true ,
and I got the assembled particle, however, one of the segments of atoms that I added did not assemble as I would like.
Thank you very much for your help! It was really useful!
Kind regards,
Ana

-----Mensagem original-----
De: Elaine Meng <meng at cgl.ucsf.edu> 
Enviada: 24 de março de 2021 18:37
Para: Ana Sofia Ramos <ramos.anasofiaferreira at gmail.com>
Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
Assunto: Re: [chimerax-users] xchimera multiscale model

To clarify: ChimeraX "sym" mostly uses the assembly info from mmCIF format input files only.  Both ChimeraX and Chimera "sym" can also use BIOMT lines from PDB files if you use the "biomt" command option, but lots of PDB files do not contain BIOMT lines.

This is explained in the "sym" page, which you can see with ChimeraX command "help sym" or view the copy on our website here:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#top>

Elaine

> On Mar 24, 2021, at 7:45 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Ana,
> I don't think I understand your question, or whether you are asking about Chimera or ChimeraX.  In either program, however, "sym" can add more copies of a structure if the PDB header of its input file includes the symmetry information.  So if you added some atoms to the structure and saved as PDB, you may need to use a text-editor to copy the lines with that symmetry information from the original PDB file and paste them into your new modified PDB file, if it does not already contain those lines.  However, what you get from sym after that will just be many copies of the same thing, not with different proteins attached by linkers.
> I hope this helps,
> Elaine
> 
>> On Mar 24, 2021, at 5:40 AM, Ana Sofia Ramos <ramos.anasofiaferreira at gmail.com> wrote:
>> 
>> Hi Elaine,
>> Thank you very much for your help. I liked your ideas. 
>> The sessions from chimera and chimerax are not compatible, but I could generate the pdb of the linked molecules, and to make the rest I have to switch to chimerax. I would like to know if it still possible to assemble the new pdb using the sym command. 
>> All the best,
>> Ana
>> 
>> -----Mensagem original-----
>> De: Elaine Meng <meng at cgl.ucsf.edu>
>> Enviada: 18 de março de 2021 17:07
>> Para: Ana Sofia Ramos <ramos.anasofiaferreira at gmail.com>
>> Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
>> Assunto: Re: [chimerax-users] xchimera multiscale model
>> 
>> 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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