Hi If you can align your two models using matchmaker, you should be able to save the coordinates of your model (relative to the model with bioMT data). A simple copy and paste of the bioMT matrices in a text editor should then suffice. Best D Sent from my iPhone

On 18 Apr 2018, at 18:23, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi Joe, Besides the “group biomt” option of “sym,” there is also “group #N” where N is the model number of another model. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html#options>

However, I believe you would need to match your structure onto model N pretty well before using that. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Apr 18, 2018, at 9:43 AM, Healey, Joe <J.R.J.Healey@warwick.ac.uk> wrote:

Hi Chimera Team,

I'm familiar with the sym command within chimera, specifying particular degrees of rotational symmetry for instance.

As the biological unit feature tends to work quite nicely for this for a number of the proteins that I'm working on, I was wondering if there is a simple way to apply the BIOMT matrix for one protein to another?

The proteins I want to apply them to are homology models of the equivalent proteins, so their biological unit information should be meaningful.

If its possible to do this in chimera that would be great, but if you have any alternative suggestions (perhaps its possible to copy the BIOMT lines from one PDB text file to another?

Joe Healey

_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

You may need to save PDB of the fitted copy relative to the structure with biomt, and then read that new file in and apply the matrix from the reference structure (or do it the way David Bhella suggested). You can specify axis, center, and all that stuff in the “sym” command but I’m guessing figuring out what to specify would be exceedingly difficult compared to using the biomt of your reference structure. Elaine

On Apr 18, 2018, at 11:08 AM, Healey, Joe <J.R.J.Healey@warwick.ac.uk> wrote:

Hi Elaine, Thanks for getting back to me, I didn't realise it was as simple as that, though it turns out I may have been barking up the wrong tree somewhat.

I assumed more of the structures I was using had symmetry information than it appears they do, as they are EM resolved generally (and are C6 symmetrical).

I would expect I could achieve what I want with C6 symmetry, but as you can see in the images I've attached, the C6 symmetry is 'inside out', relative to the reference structure I'm trying to replicate. It looks like I need to specify a different axis of symmetry, but to also tell it to 'flip' how the molecules are being placed.

Here is my model in blue fitted well to a subunit of this structure (PDBID 1Y12) <before_sym.png> I'm trying to replicate this donut shape, but it seems the model has no symmetry information I can use (sym #1 group #0 won't work , if #0 is the reference structure).

This is what I get from sym #1 group C6, hopefully you can understand what I'm getting at.

<after_sym.png> I've attached the model I'm trying to position if you have any thoughts about how to achieve this.

Hopefully there's a programmatic solution as I'll be intending to do this a number of times. Many thanks - I hope I've explained myself clear enough! Joe

From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 18 April 2018 18:15:36 To: Healey, Joe Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] BIOMT symmetry matrices

Hi Joe, Besides the “group biomt” option of “sym,” there is also “group #N” where N is the model number of another model. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html#options>

However, I believe you would need to match your structure onto model N pretty well before using that. I hope this helps, Elaine

...

On Apr 18, 2018, at 9:43 AM, Healey, Joe <J.R.J.Healey@warwick.ac.uk> wrote:

Hi Chimera Team,

I'm familiar with the sym command within chimera, specifying particular degrees of rotational symmetry for instance.

As the biological unit feature tends to work quite nicely for this for a number of the proteins that I'm working on, I was wondering if there is a simple way to apply the BIOMT matrix for one protein to another?

The proteins I want to apply them to are homology models of the equivalent proteins, so their biological unit information should be meaningful.

If its possible to do this in chimera that would be great, but if you have any alternative suggestions (perhaps its possible to copy the BIOMT lines from one PDB text file to another?

Joe Healey

Hi Joe, As per my original suggestion, you’d use “sym” with “group #N” where N is the model with the BIOMT information included. The models you use “sym” on, however, may need to already be in the coordinate system of that model (i.e. already matched and written out relative to it, then read back in). Maybe I’m misunderstanding the quetion... Elaine

On Apr 19, 2018, at 6:24 AM, Healey, Joe <J.R.J.Healey@warwick.ac.uk> wrote:

Hi Elaine/David,

Yeah that was my thinking with the axis etc. I have no idea how I'd begin to calculate the distances and centre of rotation (plus I'm on a bit of a deadline so can't fiddle with this indefinitely).

Your alternative suggestion seems to have worked (and I realised part of the error I was making). I was downloading the biounits by default. I assumed they would have the BIOMT data of their subunits, whereas what I should have been doing was downloading the asymmetric unit and applying that rotation matrix.

One last question in that case, since I think this might be the 'elegant' way to program this:

Lets say I have a file with a some 'master' biounit data that I've copied out of one of the correct models. Could I apply this 'externally' through chimera, without it having to be part of the loaded model?

I imagine this would require some python scripting, but I'm envisaging something like:

• Open some model of interest • Fit the model to a reference if necessary. • Apply the rotation matrix supplied from an external 'master' text file (possibly by 'injecting' it in to an open model in chimera?)

Any thoughts?

Joe Healey

M.Sc. B.Sc. (Hons) MRSB PhD Student MOAC CDT, Senate House University of Warwick Coventry CV47AL Mob: +44 (0) 7536 042620 | Email: J.R.J.Healey@warwick.ac.uk

Jointly working in: Waterfield Lab (WMS Microbiology and Infection Unit) and the Gibson Lab (Warwick Chemistry)

Twitter: @JRJHealey | Website: MOAC Page | ORCID: orcid.org/0000-0002-9569-6738 From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 18 April 2018 19:22:01 To: Healey, Joe Cc: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] BIOMT symmetry matrices

You may need to save PDB of the fitted copy relative to the structure with biomt, and then read that new file in and apply the matrix from the reference structure (or do it the way David Bhella suggested).

You can specify axis, center, and all that stuff in the “sym” command but I’m guessing figuring out what to specify would be exceedingly difficult compared to using the biomt of your reference structure.

Elaine

...

On Apr 18, 2018, at 11:08 AM, Healey, Joe <J.R.J.Healey@warwick.ac.uk> wrote:

Hi Elaine, Thanks for getting back to me, I didn't realise it was as simple as that, though it turns out I may have been barking up the wrong tree somewhat.

I assumed more of the structures I was using had symmetry information than it appears they do, as they are EM resolved generally (and are C6 symmetrical).

I would expect I could achieve what I want with C6 symmetry, but as you can see in the images I've attached, the C6 symmetry is 'inside out', relative to the reference structure I'm trying to replicate. It looks like I need to specify a different axis of symmetry, but to also tell it to 'flip' how the molecules are being placed.

Here is my model in blue fitted well to a subunit of this structure (PDBID 1Y12) <before_sym.png> I'm trying to replicate this donut shape, but it seems the model has no symmetry information I can use (sym #1 group #0 won't work , if #0 is the reference structure).

This is what I get from sym #1 group C6, hopefully you can understand what I'm getting at.

<after_sym.png> I've attached the model I'm trying to position if you have any thoughts about how to achieve this.

Hopefully there's a programmatic solution as I'll be intending to do this a number of times. Many thanks - I hope I've explained myself clear enough! Joe

From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 18 April 2018 18:15:36 To: Healey, Joe Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] BIOMT symmetry matrices

Hi Joe, Besides the “group biomt” option of “sym,” there is also “group #N” where N is the model number of another model. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html#options>

However, I believe you would need to match your structure onto model N pretty well before using that. I hope this helps, Elaine

...

On Apr 18, 2018, at 9:43 AM, Healey, Joe <J.R.J.Healey@warwick.ac.uk> wrote:

Hi Chimera Team,

I'm familiar with the sym command within chimera, specifying particular degrees of rotational symmetry for instance.

As the biological unit feature tends to work quite nicely for this for a number of the proteins that I'm working on, I was wondering if there is a simple way to apply the BIOMT matrix for one protein to another?

The proteins I want to apply them to are homology models of the equivalent proteins, so their biological unit information should be meaningful.

If its possible to do this in chimera that would be great, but if you have any alternative suggestions (perhaps its possible to copy the BIOMT lines from one PDB text file to another?

Joe Healey

_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users