[chimerax-users] Assembling 2 proteins

Tue Jul 26 20:18:55 PDT 2022

Good day Meng,

I'm trying to find the tutorial for the measuring the pore diameter. Can you please help me which protocol goes well with it.

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

________________________________
From: SANTOSH RAMA BHADRA RAO TATA <19807877 at students.latrobe.edu.au>
Sent: Monday, 18 July 2022 2:32 PM
To: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] Assembling 2 proteins

Dear Meng,

It worked thank you very much for your suggestions. I was able to create the pentamer.

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

________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Wednesday, 1 June 2022 1:50 AM
To: SANTOSH RAMA BHADRA RAO TATA <19807877 at students.latrobe.edu.au>
Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] Assembling 2 proteins

Hi Tata Santosh Rama Bhadra Rao,
I already gave my suggestions in the previous message, so there is not really anything else I can do to teach you.

Since you didn't give the details of all the steps that you tried and which step(s) gave results you didn't like, I can't tell you how to do it differently.

My only idea is to go back to what I already suggested: you could use Matchmaker if you already had a pentamer, which you show in the bottom figures. So, following the instructions in my first reply, maybe you can take the chains shown in the top figures and match them onto the chains in the bottom figures to make the pentamer. However, that will only work if the proteins are very similar. If you did it already and it gave the bad result, maybe these proteins are not similar enough to use that approach.

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

> On May 30, 2022, at 9:22 PM, SANTOSH RAMA BHADRA RAO TATA <19807877 at students.latrobe.edu.au> wrote:
>
> Hi Elaine,
>
> I tried doing and it came out like this. Final 2 figures are homomeric pentamers. First 2 are heteromers with 3A subunits (A, B, D chains) and 2D (C, E chains) subunits. Could you please help me or teach me assembling them properly.
>
> 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
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Sent: Wednesday, 25 May 2022 2:08 AM
> To: SANTOSH RAMA BHADRA RAO TATA <19807877 at students.latrobe.edu.au>
> Cc: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
> Subject: Re: [chimerax-users] Assembling 2 proteins
>
> 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<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<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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