[Chimera-users] Connect and align duplicated models
goddard at sonic.net
Wed Oct 12 15:13:41 PDT 2011
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.
3ghg contains two copies of the coiled coil so delete one copy
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,
> 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
> 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
> 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
>> 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.
>>> 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.
>>> 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:
>>>> 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
>>>> I want to duplicate the model, and connect them in a chain
>>>> 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?
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
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