[Chimera-users] Multiple fitting of structures in to EM densities

Tom Goddard goddard at sonic.net
Wed May 10 14:04:04 PDT 2017


Hi Joe,

  These maps have both C6 and helical symmetry, and as I said before you should fit one copy of each of the two proteins and then apply symmetry with the sym command, for example,

	sym #1 group c6 coord #0

where #1 is an atomic model and #0 is the map would apply C6 symmetry and the sym documentation shows how to also handle the helical part.

	https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html>

  The method of randomly placing and optimizing fits and detecting collisions is simply not going to work for too many reasons to mention, and is the wrong approach anyways since  you don’t want to create an assembly that does not follow the exact symmetry.

	Tom

> On May 10, 2017, at 1:46 AM, Healey, Joe <J.R.J.Healey at warwick.ac.uk> wrote:
> 
> Hi Tom,
> 
> Apologies, I must have switched the numbers as I typed. The EM density is EMD-6271 and EMD-6270. If you fetch 6270 with fitted PDB's, it should be fairly obvious what I mean when it comes to fitting 2 different rings of proteins, however I wish to do this with my own structures in to their map, rather than the structures they have.
> 
> The structures I have a simulations/homology models, so they don't contain any BIOMT/symmetry information, thus I think I'm left with the only option being fitting each protein individually. Since I plan to do this quite a lot, I'd rather not have to resort to doing it by hand (and if it can be scripted - all the better).
> 
> I envisage the problem like this (correct me if you think this approach won't work though):
> 1. Open the first protein. Fit the first protein for each ring (1 monomer)
> 2. Continue to open models consecutively (or copy the existing one)
> 3. With each new model that is opened, fit it, but somehow determine if the same space is occupied with another model, if so, try elsewhere
> 
> I believe the fit-in-map function can be given a random starting position, such that fitting in to different densities could be achieved without manual initial placement. I think the conceptual step I'm stuck on would just be knowing whether chimera has any means of knowing whether 2 PDBs are occupying the same space (and/or EM density) - and then effectively using this as a conditional to re-attempt placement?
> 
> Thanks for the help thus far,
> 
> Joe
> 
> Joe Healey
> 
>                                        
> M.Sc. B.Sc. (Hons) MSRB
> PhD Student
> MOAC CDT, Senate House
> University of Warwick
> Coventry
> CV47AL
> Mob: +44 (0) 7536 042620  |  Email: J.R.J.Healey at warwick.ac.uk <mailto:J.R.J.Healey at warwick.ac.uk>
> 
> Jointly working in:
> Waterfield Lab <http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/> (WMS Microbiology and Infection Unit)
> and the Gibson Lab <http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry)
> 
> Twitter: @JRJHealey <https://twitter.com/JRJHealey>  |  Website: MOAC Page <http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738 <http://orcid.org/0000-0002-9569-6738>
> From: Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>>
> Sent: 10 May 2017 02:00:57
> To: Healey, Joe
> Cc: chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Multiple fitting of structures in to EM densities
>  
> Hi Joe,
> 
>   It doesn’t look like EMDB 6720, mammalian respiratory supercomplex is made up of hexamer rings.  Is that the structure you mean?
> 
>   In you have 3 or 4 stacked hexamer rings for each of 2 proteins and they are exactly symmetric, or at least the map was reconstructed by imposing symmetry, then I would only fit one copy of an atomic model, and then create all the other copies using the Chimera “sym” command so they are exactly placed according to the symmetry.  If there really is no exact symmetry then you do have to fit each copy individually.  The Chimera "Fit in Map” tool or equivalent fitmap command does a local optimization based on an initial placement of the atomic model in the map — it uses gradient ascent to maximize correlation — so it will just find a local best fit.  So in this case I would hand place each copy of the atomic model, trying to get the position right to better than half the protein diameter (say 10 or 20 Angstroms) and the orientation angle not too far off (say no further than 60 degrees), then use the Chimera fitmap command or dialog on each.  If the map is high resloution like EMDB 6720 at 3.6 Angstroms you can probably fit copies without them moving to an adjacent position.  At much lower resolution like 15 Angstroms, the copies will tend to move all to the highest density.  Then you need to use the fitmap sequence or symmetry options to take into account clashes between the copies.
> 
> Tom
> 
>> On May 9, 2017, at 8:07 AM, Healey, Joe  wrote:
>> 
>> Dear chimera team,
>> 
>> I have a large EM density I would like to fully populate with a number of copies of a protein. To be more specific, the EM density is of 2 concentric protein rings (EMDB-6720), and each concentric ring is stacked 3 or 4 times. Each ring is a hexamer, so I would like to populate every single ring with 6 copies of each protein (but the inner and outer rings are 2 different proteins).
>> 
>> What would be the best mechanism to iteratively import a protein, populate an EM density space, then move on to the next one? Currently, I think if I was to simply open several copies of the protein, they would probably all try to fit within the same EM density position, leaving the rest of the structure empty?
>> 
>> My apologies if this isn't totally clear, I've tried to explain it as best as I think I can. I'm happy to accept solutions in 'chimera language', python (or I also have Jaime's Pychimera installed).
>> 
>> Many thanks
>> 
>> Joe Healey
>> 
>>                                        
>> M.Sc. B.Sc. (Hons) MSRB
>> PhD Student
>> MOAC CDT, Senate House
>> University of Warwick
>> Coventry
>> CV47AL
>> 
>> 
>> Jointly working in:
>> Waterfield Lab <http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/> (WMS Microbiology and Infection Unit)
>> and the Gibson Lab <http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry)
>> 
>> Twitter: @JRJHealey <https://twitter.com/JRJHealey>  |  Website: MOAC Page <http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738 <http://orcid.org/0000-0002-9569-6738>_______________________________________________
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