[Chimera-users] Measuring dimer rotation

Tom Goddard goddard at cgl.ucsf.edu
Wed Jun 2 11:40:18 PDT 2010 

The bug where mmaker did not match chains C with C and D with D has been 
fixed today and the order specified in the command should be respected 
in tomorrow's daily builds.

     Tom

> Hi Bobby,
>
>   The place to send Chimera questions is the Chimera mailing list 
> chimera-users at cgl.ucsf.edu.
>
>   Here are some ideas about how to measure the rotation of one dimer 
> of your homotetramer on ligand binding.  Say the tetramer has chains 
> A,B,C,D and we want to see how dimer CD has moved relative to dimer AB 
> from unbound to bound PDB models.  The idea is to use the Chimera 
> "match" command with the showMatrix option.
>
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html
>
> First step is that I want to create PDB files for bound and unbound 
> states where the AB dimers are aligned.  Suppose model #0 is unbound 
> and model #1 is bound.  This command will move the bound model AB to 
> overlap the unbound model AB
>
>     match #1:.A,.B #0:.A,.B
>
> Now align bound CD with unbound CD and report the rotation/translation 
> with the showMatrix option:
>
>     match showMatrix true #1:.C,.D #0:.C,.D
>
> The output in the Reply Log (Favorites menu) looks like the 
> following.  I used a dimer example instead of a tetramer to produce 
> this output.
>
> Executing match ['#0:.B at CA', '#1:.A at CA'], no iteration
> Motion from original file coordinates
>   Matrix rotation and translation
>     -0.31727374  -0.31084290   0.89594311  19.18030808
>     -0.30378517   0.92828353   0.21448604   7.82438547
>     -0.89836070  -0.20412345  -0.38894945  20.67993251
>   Axis  -0.22719634   0.97384144   0.00383052
>   Axis point  17.54082727   0.00000000   3.53442960
>   Rotation angle (degrees) 112.89041450
>   Shift along axis   3.34122976
> Motion from last position
>   Matrix rotation and translation
>     -0.31727374  -0.31084290   0.89594311  19.18030808
>     -0.30378517   0.92828353   0.21448604   7.82438547
>     -0.89836070  -0.20412345  -0.38894945  20.67993251
>   Axis  -0.22719634   0.97384144   0.00383052
>   Axis point  17.54082727   0.00000000   3.53442960
>   Rotation angle (degrees) 112.89041450
>   Shift along axis   3.34122976
> RMSD between 16 atom pairs is 0.482 angstroms
>
> You would look at motion from last position, specifically the rotation 
> angle.
>
> For your case (tetramers built from 1pfk and 2pfk) there is a problem 
> that the exact same atoms are not in the two tetramers.  The match 
> command requires that you specify an exact pairing of atoms.  You can 
> use the Match Maker dialog or mmaker command which will figure out the 
> atom pairing for you.  But match maker doesn't report the motion so 
> you would use the "measure rotation" command to do that.
>
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html
>
> mmaker #1:.A,.B #0:.A,.B pair ss
> write relative #0 #1 /tmp/bound-ab-aligned.pdb
> close #1
> open #1 /tmp/bound-ab-aligned.pdb
> mmaker #1:.C,.D #0:.C,.D pair ss
> measure rotation #1 #0 showSlabs true
>
> Here I aligned the AB dimer then saved the bound version to a file, 
> closed the bound model, and opened the saved file.  Did that 
> close/open business because the measure rotation command is going to 
> report values relative to the original file orientations.  It doesn't 
> report the motion from the last position because it doesn't remember 
> what the last position was.
>
> The match and mmaker commands rotate the coordinate axes for one model 
> and the "measure rotation" command reports the rotation between the 
> coordinate axes of two models.  Each model has its own coordinate axes 
> which are initially aligned when the data is opened.
>
> I tried this with tetramers built from 1pfk and 2pfk dimers using the 
> Chimera unit cell tool (2x2x2 cells) and the "combine" command and 
> displayed the results with ellipsoids using the "measure intertia" 
> command with the perChain true option.  I've attached an image that 
> shows the AB dimer in yellow, the CD dimer in blue and pink, 1pfk in 
> solid and 2pfk in mesh, with separate rotation axes for the C and D 
> rotations which appear quite different and are 2 to 3 degrees.
>
> I encountered an unpleasant bug that you saw before with the Chimera 
> morph conformations tools that mmaker did not match chains C with C 
> and D with D, instead matching C with D and D with C.  It seems there 
> is currently no way to control this other than modifying the PDB files 
> (renumbering atoms?).  Changing the order of the C and D in ":.C,.D" 
> did not help.  I've filed (another) bug report for this.
>
>     http://plato.cgl.ucsf.edu/trac/chimera/ticket/8501
>
>   Tom
>
>
>
>
>
> -------- Original Message --------
> From: Bobby Laird
> To: Thomas Goddard
> Date: 6/2/10 8:38 AM
>> Hi Tom,
>>
>> I was not sure if you would remember me so I attached the previous 
>> e-mails that you were kins enough to CC to me a few months ago.   I 
>> was wondering if you could give me any advice.   I am still 
>> attempting to compare the quaternary structure of a homotetramer (320 
>> aa's for each monomer).   More specifically it appears that when 
>> certain ligands are bound there is a rotation about one of the 
>> dimer-dimer interfaces.   I used the axis function in chimera to 
>> approximate angles in order to get a degree of rotation and was 
>> wondering if you could give me a basic explanation of how the program 
>> calculates these angles?   Also, I wanted to create a very simplified 
>> cartoon figure of each of the pdb's so that I can superimpose and 
>> emphasize the rotation that occurs.   Do you have any idea how I 
>> could accomplish this?   I have tried rendering space filled models 
>> and removing the lighting so that the figure appears 2-D but when I 
>> overlay the pdb's the textures become very obvious.   Sorry for 
>> dumping all this on you but I wasn't quite sure where to go with 
>> these questions.  Thank you very much for for your time.
>>
>> Bobby Laird
>
>
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>    

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