[Chimera-users] Measuring hexamer asymmetry

[Tom Goddard]

Hi Elena,

  Ok.  The “measure rotation” command shows the rotation axis defined by the rigid motion of one subunit onto another — it has nothing to do with the hexamer axis.  I think you are asking for is that if you take subunit 1, rotate it 60 degrees about the hexamer axis, then compare the orientation and translation of subunit 2 to that moved copy of subunit 1.  Then do the same for subunits 3,4,5,6.  To do this take subunit 1 and make 5 rotated copies by 60,120,180,240,300 degrees and save that as a new hexamer PDB file. Now open the asymmetric hexamer and this symmetric hexamer.  If the subunits are chain ids A,B,C,D,E,F then use “measure rotation #0:.B #1:.B”, “measure rotation #0:.C #1:.C", ….  This will still show a rotation axis that is not the hexamer axis which indicates the rotation needed to make the exact symmetry copy of subunit 1 rotate onto the asymmetric subunit 2, and it will give the translation, rotation axis and angle in the reply log.  Maybe you are not interested in how the symmetric copies of subunit 1 rotate when being aligned to asymmetric subunits 2,3,4….  Then you can just ignore this rotation information and get the translation from the reply log.

	Tom

> On Jan 5, 2017, at 7:38 AM, Elena Zehr  wrote:
> 
> Hi Tom,
> 
> Thank you very much for you response. Yes within the asymmetric hexamer subunits have different conformations. To test your advice on RMSD, I first generated hexamer by using six copies of the same subunit to align to the original hexametric structure, then I closed  the original hexametric structure. The asymmetric hexamer now  consisted of subunits with identical  conformation, please note the hexamer is still asymmetric. Then I opened a monomer with the same conformation as the subunits within the newly-generated hexamer, and calculated rotation and translation matrices between the first protomer within the hexamer and the rest of the subunits (#2-6). The central axis for each of the calculations deviated from each other.
> 
> My issue is the following: to make the calculations reliable I wish to have the same central axis running through the center of the hexamer and not the axes between #1 and #2 or #1 and #4, etc. which deviate from each other due to the asymmetry of the hexametric structure. Is it possible? For example I wish to calculate the central axis of the whole hexamer and then use it as a reference to calculate rotation and translation for each subunit (#2-5) around the ring with respect to the subunit #1 and the central axis of the whole hexamer. Is it possible to define parameters for the central axis in the command line together with “measure rotation #1 #2 or #1 and #4” ?
> 
> 
> Many thanks,
> Elena
> 
> 
> On Jan 4, 2017, at 4:47 PM, Tom Goddard wrote:
> 
>> Hi Elena,
>> 
>>   Elaine asked me to look at your problem measuring orientation of subunits of a hexamer.  Does your hexamer have cyclic symmetry?  If so I think the reason the displayed axes don’t appear to align with the hexamer symmetry axis is because your alignment of one subunit to another is not good.  You can get the root mean square deviation of C-alpha positions for the alignment by looking in the Reply Log (menu Favorites) after running the match maker command, for example,
>> 
>>    RMSD between 308 pruned atom pairs is 0.361 angstroms; (across all 308 pairs: 0.361)
>> 
>> From your picture with blue and tan complexes it does not appear they are aligned at all.  If the sequences of the subunits are very different then match maker may not be able to align them.
>> 
>> 	Tom
>> 
>> 
>> 
>> Begin forwarded message:
>> 
>>> From: Elena Zehr 
>>> Subject: Re: user-defined rotation axis
>>> Date: January 4, 2017 at 1:09:10 PM PST
>>> To: Elaine Meng 
>>> 
>>> Dea Elaine,
>>> 
>>> Thank you for getting back to me so soon. Sorry for sending you my question again. 
>>> 
>>> I am getting the following (see attached image) Where the central axis between protomer A and B is different than the one between protomer A and F. I wish to have the same central axis that would be the central axis of the hexamer, otherwise I assume my measurements are not accurate. I get the same if I use the hexamers or separate monomers 
>>> 
>>> 
>> <axis.tiff>
>>> On Jan 4, 2017, at 1:15 PM, Elaine Meng  wrote:
>>> 
>>> Begin forwarded message:
>>> 
>>>> From: Elena Zehr 
>>>> Subject: Re: user-defined rotation axis
>>>> Date: January 4, 2017 at 1:09:10 PM PST
>>>> To: Elaine Meng 
>>>> 
>>>> Dea Elaine,
>>>> 
>>>> Thank you for getting back to me so soon. Sorry for sending you my question again. 
>>>> 
>>>> I am getting the following (see attached image) Where the central axis between protomer A and B is different than the one between protomer A and F. I wish to have the same central axis that would be the central axis of the hexamer, otherwise I assume my measurements are not accurate. I get the same if I use the hexamers or separate monomers 
>>>> 
>>>> 
>>> <axis.tif>
>> 
> 

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