[chimerax-users] Superimpose

[Wisoot Chanit]

 Dear Elaine,
Thank you very much again for your kind reply and help. I want make a dimer of GII.3a and GII.3c (same protein) derived from homology modeling by Chimera onto chan A and C of 6ir5. In this step, I need to study more how to make it.
If you have any advice, it would be much appreciated. I will take time to learn more.  Thank you so much. 
Sincerely,
Jay
    On Wednesday, August 4, 2021, 10:27:50 PM GMT+7, Elaine Meng <meng at cgl.ucsf.edu> wrote:  
 
 Hi Jay,When you open 6ir5, it already contains 4 copies of the monomer, chains A-D.  I do not know which dimer you are trying to make, but maybe it's already there?
See info page at RCSB, says global symmetry is cyclic - C2, and global stoichiometry is homo 4-mer<https://www.rcsb.org/structure/6IR5>
>From ChimeraX commands:
open 6ir5color bychain... see attached screenshot ChimeraX window
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 3, 2021, at 10:37 PM, Wisoot Chanit via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:

Dear Elaine,
Thank you very much for your reply. I am sorry to confuse you with less information. I forgot many things on my last paper about making a trimer of rotavirus. I will take this time to study it again. I also forgot command to "sym" to make a dimer for this time.
Sincerely,
Jay 

On Tuesday, August 3, 2021, 09:56:23 PM GMT+7, Elaine Meng <meng at cgl.ucsf.edu> wrote:


Dear Jay,
I do not understand what you are trying to do.  Superimpose what on what? 

If you are talking about the "missing structure" as shown in your screenshot Model panel, that only means that there are some missing residues in one or more loops (see the dashed lines in the structure), but it may not matter for what you are trying to do.  You can still superimpose structures even if they are missing some residues.

The rows shown in your Model panel are not the chains. When I open 6ir5 I can see it has 4 chains, 4 copies of the same protein, although they are all together in a single model #1.  I do not know what you did to get three submodels #2.1-3 for  3fmg, but since it has a trimer assembly defined, I'm guessing maybe you got that by using "sym" to make the trimer. 

If you are talking about that assembly information from the mmCIF file, yes, 3fmg has assembly information that you can click to make a trimer, but 6ir5 does not have assembly information.  I don't know what else to say to help you, however; you would have to provide more information about what exactly you are trying to do.

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


> On Aug 3, 2021, at 2:31 AM, Wisoot Chanit via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear ChimeraX team,
> I am having a quesition. I am going to superimpose 2 monomers of P domain of norovirus GII.3 into a template PDB 6if5, but the template showed that information of its chains are missing. What should I do to make a dimer into 6if5. This is different from PDB 3mfg, which was a templete I used for my previous paper. 
> Thank you.
> Jay
> 
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