[Chimera-users] how to move subunits of a pentamer receptor in a controlled way
goddard at sonic.net
Mon Sep 14 16:40:53 PDT 2015
Here are some ideas. I’ll use nictotinic aceytlcholine receptor 2bg9 determined by electron microscopy as an example
turn z 30
move x 1.5 model #0.3
turn z 72
move x 1.5 model #0.4
turn z 72
move x 1.5 model #0.5
turn z 72
move x 1.5 model #0.1
turn z 72
move x 1.5 model #0.2
Here I colored the chains, then split the model #0 into a model for each chain #0.1, #0.2, …, #0.5 so I could easily move each chain, then I moved each chain radially. I started with a z rotation by 30 degrees that put the green chain C along the x axis then to move radially I moved it along the z axis. I moved each chain outward by 1.5 Angstroms. I rotate 72 degrees (360 / 5) before moving the next chain in the sequence along x. I could also have rotated each chain, for example using “turn y 0.7 center #0.3:266.C at CA model #0.3” to rotate by 0.7 degrees using a specific atom in the chain as the pivot.
All this seems simple enough except for a subtle problem. This structure may not have its symmetry axis exactly aligned along the z axis. So to do it right I’d first need to align the symmetry axis along z. It is hard to say where the symmetry axis is because 4 of the 5 chains are different sequences and the structure isn’t really symmetric. To get an idea of how asymmetric it is I open two copies and align one to a rotated copy of the other.
match #1:.E:.A:.B:.C:.D #0:.A:.B:.C:.D:.E
measure rotation #0 #1
The last command will show the rotation axis and in the reply log (Favorites menu) it will give the coordinates of the rotation axis
Axis 0.00785796 -0.00543703 -0.99995434
Axis point 63.57681519 63.30528336 0.00000000
Rotation angle (degrees) 72.08465763
To visually see the difference you can compare spinning the molecule about the z axis for 100 steps of 72 degrees
turn z 72 100 center #2
versus spinning about the axis determined by this alignment (rotation axis is model #2)
turn #2 72 100
If you don’t think the z axis is the correct symmetry axis and instead alignment axis is better you could align that axis perpendicular to the screen (align #2) then save the coordinates (with the "relative to" button in the File / Save PDB… dialog not checked so it uses screen coordinates). Things are even trickier than they look. The above “match” command is wrong. It is aligning the atoms of #1 with those of #0 in the order specified. But the chains don’t have the same number of atoms. So it doesn’t really align chain E to chain A, chain A to chain B, chain B to chain C, etc…. It would be more sensible to use sequence alignment based matches for example with command
mmaker #1:.E:.A:.B:.C:.D #0:.A:.B:.C:.D:.E pair ss
but this gave a worse alignment of the atoms near the center of the channel. In any case it is up to you to figure out the best definition of the symmetry axis given that the structure has only approximate symmetry.
> On Sep 14, 2015, at 11:37 AM, Zhang, Yinghui wrote:
> Dear Sir,
> This is Yinghui Zhang from Massachusetts General Hospital. I am a frequent user of Chimera to understand the structure of a neuronal pentamer receptor which is ion channel. Now we want to do some modification of the receptor by manipulating the coordinates of the atoms of the receptor pdb files. The aim is to move each subunit radially away from the receptor’s central symmetry axis(which should be the central channel axis ) or tilt each subunit outward. The symmetry of the receptor cannot be disrupted and we want to do it in a quantitative manner(move by a specific Å or tilt by a specific degree value). Could you please give us some clues if we can realize these aims in Chimera?
> Many thanks and regards!
> Yinghui Zhang
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