[chimerax-users] Assembling 2 proteins

[Elaine Meng]

Hello Tata Santosh Rama Bhadra Rao,
It all depends on what information you have already.  If you don't know how the pentamer is supposed to look (how the proteins fit together), then there may not be enough information: ChimeraX is not going to predict the pentamer structure for you.

You said "5 different proteins" which I interpret to mean they are not 5 copies of the same thing, that it is a heteropentamer and not a homopentamer.  If they were 5 copies of the same thing (homopentamer), then you might be able to use the "sym" command to build it from one copy,  if the input file contains symmetry matrices in the header, or you know the symmetry and can specify it separately:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html>

Otherwise:
You would only use Matchmaker if you also have an already-known structure of a similar pentamer.  Then you would open the structure of that pentamer, open the structures of your five proteins (if the same one is multiple copies in the pentamer, you would open it multiple times), and then match each one of them to the similar subunit of the known pentamer.  In other words, you would open 6 different PDB files and then use Matchmaker 5 times, once to match each of your proteins to the corresponding subunit of the pentamer.  

Just start Matchmaker (menu: Tools... Structure Comparison... Matchmaker) and in that dialog's Chain Pairing, choose "Specific chain(s) in reference structure with specific chain(s) in match structure".  Choose one of your protein chains as the match structure and choose the corresponding chain in the known pentamer as the reference. Apply. Repeat with your second protein chain, etc.

Here is the Matchmaker help with detailed explanations of all the options:
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html#top>

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




> On May 23, 2022, at 9:49 PM, SANTOSH RAMA BHADRA RAO TATA via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi,
> 
> I would like to create a pentamer, how can I assemble 5 different proteins subunits into a pentamer. I was trying to use matchmaker but I couldn't. can you please help me with some video how to get in use it  or if there is any other way to use the software and create pentamer please let me know. 
> 
> Thanking you,
> 
> With best wishes,
> Tata Santosh Rama Bhadra Rao,
> PhD Scholar,
> C/O Prof Helen Irving,
> La Trobe university,
> Bendigo, Vic-3550,
> Australia.
> Email: 19807877 at students.latrobe.edu.au; 
>             S.Tata at latrobe.edu.au
> Phone: 0499263974
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