[Chimera-users] Connect and align duplicated models

[Joe Ping-Lin Hsiao]

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
>>
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>
>
>