[Chimera-users] Chimera comparing homodimer with flipped homodimer

Elaine Meng meng at cgl.ucsf.edu
Fri Mar 31 07:39:30 PDT 2017


Hi Kavya,
Your “mm” command matched A to A and B to B, so there was no rotation between the two copies.  It was hard to see if you entered exactly the same “mm” command as in my example (needs to be exactly the same, with colon : dot . and no extra spaces), but it you did, maybe you are using an old version of Chimera that interpreted the command differently.  I only started Chimera and entered those 5 exact commands to get the result I showed. Tested in Chimera version 1.11.2 and recent 1.12 daily build.
Elaine

> On Mar 31, 2017, at 6:55 AM, Kavya Shankar <kavshank at umail.iu.edu> wrote:
> 
> I have attached the screenshots. I have opened the same pdb file.
> 
> Thank you.
> 
> Regards,
> Kavya Shankar
> 
> On Fri, Mar 31, 2017 at 9:37 AM, Kavya Shankar <kavshank at umail.iu.edu> wrote:
> Thank you so much. When I do this I get a rotation angle of 0 degrees. Am I doing something wrong?
> 
> Thank you.
> 
> Regards,
> Kavya Shankar
> 
> On Thu, Mar 30, 2017 at 11:25 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Kavya,
> I didn’t have a good example handy yesterday, but here is a more specific example, in commands:
> 
> open 5hvp
> open 5hvp
> mm #0:.a:.b #1:.b:.a pair ss
> show :241.b
> measure rotation #0 #1
> 
> This opens PDB 5HVP twice, matches it to itself except pairing A in one with B in the other and vice versa, shows only residue 241 in chain B so that you can see pairing is A-B, and measures axis of rotation between the two copies of 5HVP.  The measurement is also reported in the Reply Log (open from Favorites menu):
> 
> Position of 5hvp (#1) relative to 5hvp (#0) coordinates:
>   Matrix rotation and translation
>     -0.32555997   0.82635225  -0.45951350   0.78339640
>      0.82635225   0.01248149  -0.56301524  15.06413576
>     -0.45951350  -0.56301524  -0.68692152  28.23994571
>   Axis   0.58070648   0.71150597  -0.39565040
>   Axis point  -5.75571422  -0.00000000  18.30836454
>   Rotation angle (degrees) 180.00000000
>   Shift along axis   0.00000000
> 
> I also attach an image below.
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> <flip-axis.png>
> 
>> On Mar 29, 2017, at 10:10 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> 
>> Hi Kavya,
>> I think I understood you, but I can only repeat the same answer.  I do not know of any way to get the axis  in Chimera except by first superimposing two copies of the dimer.  Open the AB dimer twice (A1-B1 and A2-B2), superimpose A1 to B2 and B1 to A2.  Then if you still care about where the axis is you can calculate it from the already superimposed structures with “measure rotation.”  
>> Elaine
>> 
>>> On Mar 29, 2017, at 10:05 AM, Kavya Shankar <kavshank at umail.iu.edu> wrote:
>>> 
>>> Hi,
>>> 
>>> To be more specific, I want to find the two-fold symmetry axis in the dimer so that when I rotate the original structure I get another structure that is similar to the first with the chains' positions interchanged.
>>> 
>>> Thank you.
>>> 
>>> Regards,
>>> Kavya Shankar
>>> 
>>> On Wed, Mar 29, 2017 at 12:18 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>> 
>>>> On Mar 29, 2017, at 9:01 AM, Kavya Shankar <kavshank at umail.iu.edu> wrote:
>>>> 
>>>> Hi,
>>>> Is it possible to find the axis of symmetry for a dimer? I am looking to rotate the dimer along this axis by 180 degrees so that I can compare the two structures.
>>>> Thank you.
>>>> Regards,
>>>> Kavya Shankar
>>> 
>>> Hi Kavya,
>>> Why not just match (superimpose) one monomer to the other and compare directly?   At least from the Chimera perspective, the question seems backwards because maybe you could figure out the axis AFTER matching.  However, if the purpose of finding the axis is just to compare the monomers, I would just superimpose them and forget about the axis.  If you had dimer A-B you could either “split” (command) and match A to B, or you could open A-B twice and match A1 to B2 (and/or B1 to A2).  This page discusses the ways to superimpose structures in Chimera; probably Matchmaker (GUI or command) would be the easiest.
>>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
>>> 
>>> After two models are superimposed, you can get the axis and rotation amount with command “measure rotation”
>>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation>
>>> 
>>> I hope this helps,
>>> Elaine
>>> -----
>>> Elaine C. Meng, Ph.D.
>>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>>> Department of Pharmaceutical Chemistry
>>> University of California, San Francisco
>>> 
>>> P.S. seemed like a user question so I put it on the chimera-users list … chimera-dev is more for programming issues
>>> 
>>> 
>>> _______________________________________________
>>> Chimera-dev mailing list
>>> Chimera-dev at cgl.ucsf.edu
>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev
>> 
> 
> 
> 
> <step1.png><step3.png><step4.png><Step2.png>




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