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Thanks!</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Sent:</b> 30 November 2020 21:00<br>
<b>To:</b> Y. Mutum <ym337@cam.ac.uk><br>
<b>Cc:</b> chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] Problem with C2 symmetric assemblies</font>
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<div class="PlainText">Hi Yaikhomba,<br>
I think you need to use <br>
<br>
sym #1 assembly 2 copies true<br>
<br>
Otherwise the symmetry partner will only be a graphical clone, not a true atomic copy. As I understand it, you need full atomic copies to do various analyses and calculations on the coordinates.<br>
<br>
That will give you #1 original 1be3, and #2.1, #2.2 1be3 symmetry partners. If you don't want #1 then use command "close #1".<br>
<br>
Then in commands you can specify the two copies of chain C, for example, as #2.1/C and #2.2/C. If there was just a graphical clone, as from the sym command you used, there is no way to specify the two C chains from two copies of 1be3 separately, since one
of them isn't "real."<br>
<br>
(B) Alternatively, if you must have the dimer as a single model: since ChimeraX does not yet have a "combine" command, you would need to open the assembly as a single model, e.g. from PDBe:<br>
<br>
open 1be3 from pdbe_bio<br>
<br>
<<a href="http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch">http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch</a>><br>
<br>
This will give you both assemblies #1.1 and #1.2, and you know that you only want assembly 2, so you would still need to close #1.1. Then finally you would have assembly 2 as a single model, #1.2. Unfortunately there is no way to get only the assembly you
want if it is not the first one. <br>
<br>
#1.2 from PDBe will have unique chains. For example, the other copy of chain A is chain AA.<br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Nov 30, 2020, at 11:13 AM, Y. Mutum <ym337@cam.ac.uk> wrote:<br>
> <br>
> Hi<br>
> <br>
> I have a a C2-symmetric pdb: 1be3 and have created a symmetric assembly using the command.<br>
> >>> sym #1 assembly 2 newModel false<br>
> <br>
> The idea is to superimpose Chain /C of 1be3 and its symmetry partner with that of 3cx5 (corresponding chains -C and N) to get of deviations b/w the chains.<br>
> However, when I try to 'match #1/C with #2/C, then I am getting only half of the C2 symmetric assembly superimposed. Is there a way to superimpose both of the chains-C of 1be3 to 3cx5?<br>
> <br>
> I could open the model 1be3 twice and then superimpose to the equivalent subunits (chains C and N) of 3cx5, one at a time. But the resulting superimposed assembly 1be3 (from 2 different models) is not going to be the C2 symmetric.<br>
> <br>
> In short, for 1be3: pdb, is it possible to rename the symmetry mate with different chains and get the C2 symmetric assembly as a single model? Say, for this new 1be3 C2-symetric assembly, you rename the second symmetry partners chains - Chain C as C1, Chain
B as B1 for example in that new model. The idea is to have a C2 symmetric model with different chains, so that it can be compared with other models easily.<br>
> <br>
> Thanks<br>
> Yaikhomba<br>
<br>
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