[Chimera-users] Connect and align duplicated models

Tom Goddard goddard at sonic.net
Wed Oct 12 15:13:41 PDT 2011

Hi Joe,

   I suspect the sym command made the molecule copy in the wrong place 
because the two original copies of 3ghg (#0 and #1) do not have the same 
atom coordinates.  This causes the measure rotation command to give the 
wrong rotation parameters.  This would happen if your two original 
copies came from the Unit Cell dialog.  That dialog creates copies of 
the molecule with different atom coordinates.  Instead you want to start 
with two copies of 3ghg with identical atom coordinates -- for example 
just open it twice.

     open 3ghg
     open 3ghg

3ghg contains two copies of the coiled coil so delete one copy

     del :.G-L,.Q-T

Now move model #1 relative to model #0 as you like.  Then use measure 
rotation and the sym command.  I did this and it worked fine as shown in 
the attached image.  The reason this is different from using two copies 
of the molecule made by unit cell is rather technical.  The unit cell 
dialog makes copies of the molecules where the atoms have different 
x,y,z coordinates in the two copies.  The procedure I just described 
uses two molecule copies with the same atom coordinates but the models 
have different coordinate systems.  Moving one molecule relative to the 
other just changes the coordinate system of the moved molecule, not the 
actual atom x,y,z coordinate values.

   The second problem you observed is that the molecule made by the sym 
command appears wrong -- as if it has all kinds of long bonds.  This 
could be a bug in the code that makes the molecule copy or a bug in your 
graphics driver.  I don't see that with Mac Chimera.  If you can make it 
happen again, then save a session and use menu Help / Report a Bug..., 
say the molecule drawing is wrong, and attach the session file.


> Thanks, Elaine and Tom,
> Tom,
>     I tried what you suggested but only generating one extra copy of
> model #1. But sym command created a weird-looking model at the same
> place where the original #1 is
> (http://dl.dropbox.com/u/3757507/chinema3.png).
> Below is the output of my "measure rotation #0 #1":
> Position of single_3ghg_monomer.pdb #2 (#1) relative to
> single_3ghg_monomer.pdb (#0) coordinates:
>    Matrix rotation and translation
>       0.79947388   0.29593455  -0.52274683  66.20071818
>      -0.40522870  -0.37669835  -0.83299943 -113.45813726
>      -0.44343118   0.87779331  -0.18123932 -31.01344468
>    Axis   0.92445135  -0.04285935  -0.37888360
>    Axis point   0.00000000 -54.63874726 -41.89926982
>    Rotation angle (degrees) 112.28611242
>    Shift along axis  77.81257053
> And the sym command I used is:
> sym #1 group h,77.81,112.286,2 axis 0.92445,-0.04286,-0.37888 center
> 0,-54.6387,-41.89927 coord #0
> Thanks,
> Joe
> On Tue, Oct 11, 2011 at 6:42 PM, Tom Goddard<goddard at sonic.net>  wrote:
>> Hi Joe,
>>   Elaine's suggestion is the way to go.  If you have two copies of your
>> molecule #0 and #1 and you want to add additional subunits use the "measure
>> rotation" and the sym commands to do it.  Here's an example.  Notice I take
>> the axis, axis point, rotation angle, and shift along axis from the measure
>> rotation and use those in the "sym" command to create 4 additional copies
>> using helical symmetry.  A single rotation and translation always specifies
>> a helical symmetry (rotation about an axis and shift along that axis).  In
>> the case where the shift along the axis is 0 you get cyclic symmetry.
>>   You'll probably find the "sym" command documentation useful
>>     http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html
>>   Tom
>> measure rotation #0 #1
>> Reply log:
>> Position of 1E6J (#1) relative to 1E6J (#0) coordinates:
>>   Matrix rotation and translation
>>      0.96949029  -0.23745478  -0.06085881  98.69560733
>>      0.03663564   0.38584119  -0.92183752   7.88875940
>>      0.24237657   0.89148292   0.38276860   7.78837497
>>   Axis   0.97552284  -0.16313335   0.14745407
>>   Axis point   0.00000000  17.01960113  14.23231084
>>   Rotation angle (degrees)  68.34295730
>>   Shift along axis  96.14132684
>> sym #1 group h,96.14,68.34,5 axis 0.9755,-0.1631,0.14745 center
>> 0,17.02,14.23 coord #0
>>> Hi Joe,
>>> Hmm, well, you could measure the transformation between your first and
>>> second copies with "measure rotation."  Then, if that corresponds to some
>>> symmetry group or product of groups, you could generate multiple additional
>>> copies with a single "sym" command using the "group" option.
>>> <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation>
>>> <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html>
>>> However, I'm not sure how easy or difficult it would be to figure out the
>>> necessary sym command from the information given in the Reply Log from the
>>> measure command, i.e. whether it is a simple helical relationship or
>>> something more complicated.  Maybe a python script to repeatedly apply the
>>> transformation to additional copies would be more effective (beyond my skill
>>> set, sorry).
>>> I'm not the most knowledgable here on this particular topic; perhaps the
>>> others will have clearer ideas of how to attack the problem, or a script.
>>>   Best,
>>> Elaine
>>> ----------
>>> Elaine C. Meng, Ph.D.
>>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>>> Department of Pharmaceutical Chemistry
>>> University of California, San Francisco
>>> On Oct 11, 2011, at 1:04 PM, Joe Ping-Lin Hsiao wrote:
>>>> Hi,
>>>> I are trying to use Chimera to produce duplicates of one fibrinogen,
>>>> rotate and move them, and concatenate together in a certain way.
>>>> The fibrinogen looks like this
>>>> (http://dl.dropbox.com/u/3757507/chimera1.png).
>>>> I want to duplicate the model, and connect them in a chain
>>>> (http://dl.dropbox.com/u/3757507/chimera2.png).
>>>> The second image shows only two instances, but there will be more.
>>>> Currently I do it by hand, including rotating and aligning them in
>>>> correct z positions.
>>>> But it take a lot of time to do it because the duplicates generated by
>>>> using Tools/Higher-order structure/Unit Cell are not in the same
>>>> plane. I have to look back and forth in different directions to make
>>>> sure them are aligned.
>>>> So I are wondering is there any way to automate this process, such as
>>>> apply the previous transformation to a new duplicate?
>>>> Thanks,
>>>> Joe
>>> _______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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