[chimerax-users] keeping multi-chain models locked between chains

[Martti Tolvanen]

Thanks Tom and Eric,

I got the job done as Eric suggested, and I feel that rotating the bonds (using the mouse right button mode) after creating one rigid hexamer was a nice and clean way to change the orientations between subunits. I saved the bond operations in a "hexamer glue" script in case I want to repeat them later. 

-Martti

-----Original Message-----  
From: Tom Goddard [mailto:goddard at sonic.net] 
Sent: 7. helmikuutata 2022 23:37
To: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
Cc: Martti Tolvanen <martti.tolvanen at utu.fi>
Subject: Re: [chimerax-users] keeping multi-chain models locked between chains

Hi Martti,

Another way to go about this is to use the Move Atoms mouse mode in the Right Mouse toolbar.  Select all everything on one side of a linker residue (the helix, and all chains past that point) using the select command.  Then just drag those atoms with the mouse (use simple lighting so it update fast, without having to recompute shadows.)  You may create some bad bond length or bond angles where the selected atoms connect to the unselected ones.  But if you zoom in on that region you can perhaps move it by hand and visually keep that connection reasonable.  There is also a "Minimize" mouse mode that might be able to energy minimize near the distorted linker after the move.

	Tom

> On Feb 4, 2022, at 11:01 AM, Eric Pettersen via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Martti,
> 	It would seem that the simplest way to get the chains to move in tandem is to put some artificial bonds between the disconnected chains before rotating the bond.  For each pair of chains you want to connect, select one atom in each and run the command "bond sel reasonable false".  Then do the rotation you want and again select each pair and use "~bond sel" to break the artificial bond.
> 
> --Eric
> 
>> On Feb 4, 2022, at 7:42 AM, Martti Tolvanen via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>> 
>> Dear ChimeraX gurus and demi-gods,
>> 
>> I have created a hypothetical multimer model for a protein which has a dimeric structure in PDB (with a large protein-protein interface, considered real), but misses the C-terminal part of the full protein sequence. AlphaFold predicts there to be an amphipathic helix in the missing part, as we also did in our theoretical work. The hypothesis is that the protein could form larger multimers by binding either via the face-face interactions, as in the PDB dimer of catalytic domains, or via helix-helix interactions (tail-tail) as in coiled coils, to create multimers of type AB-BA-AB-BA-AB-BA etc., A being the helical domain and B the catalytic domain.  I have created antiparallel coiled-coil-like helix dimers from the helix predicted by AlphaFold with the help of zdock (big thanks for adding the zdock file open functionality in the daily build!) and built a hexamer model using 3fe4 and my best-looking zdock helix pair as templates for orienting the six copies of the monomeric a!
> lphafold model. 
>> 
>> The helix is randomly placed outside of the confident catalytic domain structure in the AlphaFold model, and there is a linker of poor confidence between the domains. With the original orientation of the helix my first-effort hexamer has the catalytic domains partly overlapping, and I'd need to rotate some bonds manually to orient the subunits into realistic positions. I wouldn't care even if I create some serious Ramachandran plot outliers there, when the goal is just to get a visualization for the multimer hypothesis. The problem is that when I rotate any bond in the linker, I either swing one helix out of a coiled-coil pair or one catalytic domain out of the face-to-face dimer interface (depending if I use move small of move large, respectively, in the torsion command). How could I get all six chains into a single chain? I assume that then I would be moving the whole rest of the multimer as a rigid body if I rotate any main-chain bond in the linker regions. ChimeraX ses!
> sion file attached. 
>> 
>> Cheers,
>> -Martti Tolvanen
>> U of Turku, Finland
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