[Chimera-users] Help with symmetry of fusion protein

[Elaine Meng]

Hi Hasan,
I already answered this in every possible way.  To review:

(1) make sure the sym copies are as atoms, not surfaces (do not use "surfaces true" option of "sym")
(2) make sure you choose ALL the models in the save pdb dialog
(3) there are two choices for saving multiple models: single file or multiple files, both work, but I prefer single for convenience
(4) after saving, check the saved file in Chimera, not some other program!!  We can't be experts on the other programs too.

For example:
open 1fav
sym #0
... then in Model Panel I have trimer as models #0, #1.1, and #1.2...

Using File... Save PDB, I choose ALL 3 models to save (actually in my case, all three are already chosen/highlighted in the dialog, so I don't have to change anything).  I save to single file.  Then I quit, restart, and open that single file, and all three are shown.

We are not Pymol users so there is no reason to expect we can solve all your issues in that program... however, if you saved a single file, it's possible that Pymol is only showing the first one in that file instead of all the copies.  Here is a link about what you have to do in Pymol to get them all to show (split states or something like that):
<https://pymolwiki.org/index.php/States>

I hope this helps,
Elaine

> On Apr 15, 2020, at 3:33 AM, Hasan Khan <hmk7865 at gmail.com> wrote:
> 
> Hi Elaine 
> Thank you for your prompt response, I’m sorry I should’ve clarified a few things I’m very new to this. 
> I’ve tried every combination of saving the structure as a PDB but each time I open it in a software like Pymol only a single monomer of the original PDB file is shown instead of the symmetry structure I’ve produced. This is what I meant by unable to save it, it just seems that the entire icosahedral structure is not being saved in a way I could open it in pymol. Now I don’t know if the process is affected due to me aligning 10 single monomers onto a di-pentamer of the original PDB file first, but it was the only way to produce a symmetry structure of the new fusion I made. 
> Thanks again.
> Kind regards,
> Hk.
> 
> 
>> On 14 Apr 2020, at 16:33, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> 
>> Also, when you use "sym" you would need to generate atomic copies, not using "surfaces true" which would only make surfaces instead.
>> 
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html#options>
>> 
>> Elaine
>> 
>> 
>>> On Apr 14, 2020, at 8:29 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>> 
>>> Hi HK,
>>> It is unclear what exactly you had in your modeling session, or what you mean by "unable to" (error message? empty file?  saved but in wrong position??)  I don't see any reason why you couldn't save the structures if they were open and shown in your session.  Since sym may have generated multiple models, all I can say is to make sure you chose all of them in the Save PDB dialog (or specify all of them in the saving command) and save transformed coordinates, or coordinates relative to a consistent reference.
>>> 
>>> It should be possible to save a Chimera session file as well.
>>> 
>>> 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 14, 2020, at 5:29 AM, Hasan khan <hmk7865 at gmail.com> wrote:
>>>> 
>>>> Hi there I was hoping I could get some help with a modelling challenge that I am having as I am very new to protein modelling as a whole and Chimera.
>>>> 
>>>> So I developed a fusion protein of a single monomer of an encapsulin structure (PDB:3DKT), I wanted to build the final icosahedral structure with the added fusion protein. So I tried to align 10 of the fusion monomers to the di-pentamer of the original PDB file and ran the sym command generating the native structure with the added fusion protein. 
>>>> I am unable to save this symmetry structure and I'm not sure if its due to the alignment of the 10 monomers onto the di-pentamer that I did first and then ran the sym command using coordinates of the original PDB or if Chimera is not able to produce coordinates for the structure in a new PDB. When I export it as a PDB the coordinates are not saved. So I was wondering if there is a way I could save this newly generated structure as other methods are not currently working. 
>>>> 
>>>> Thank you 
>>>> Kind regards 
>>>> HK