id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3997 Change sym command default to avoid confusing graphical clones Tom Goddard Tom Goddard "As Elaine points out and user Yakhomba experienced the sym command default behavior of making graphical clones instead of distinct copies of molecular subunits can lead to a lot of confusion when subsequently using commands like matchmaker and most others that don't know about clones. Perhaps it would be better to change the sym command default to make copies instead of graphical clones. This would greatly using it for virus capsids. Could have the default smart and make copies for fewer than 9 copies and clones for more. Begin forwarded message: From: Elaine Meng Subject: Fwd: [chimerax-users] Problem with C2 symmetric assemblies Date: November 30, 2020 at 1:13:43 PM PST To: Tom Goddard Cc: meng Elaine Hi Tom, People are constantly being confused by the graphical clones... at least, that's what I'm blaming this problem on. I'm not crazy about ""copies false"" being the default, although I can see the problems with ""copies true"" making ChimeraX slow if there are too many atoms. I tried it with Yaikhomba's symmetry command, which would make half of the dimer in #1 a graphical clone open 1be3 sym #1 assembly 2 newModel false open 3cx5 light simple preset licorice Matchmaker #2 onto #1 looks OK, but matchmaker #1 onto #2 leaves the graphical clone out by itself, e.g. the above commands followed by mm #1/C to #2/C I don't know if that is a bug or just a limitation of using the graphical clone approach. I didn't want to get into that confusing discussion so I just said he needed to use ""copies true"" and deal with the additional model, or fetch bioassembly in the first place. Elaine Begin forwarded message: From: Elaine Meng Subject: Re: [chimerax-users] Problem with C2 symmetric assemblies Date: November 30, 2020 at 1:00:32 PM PST To: ""Y. Mutum"" Cc: ""chimerax-users@cgl.ucsf.edu"" Reply-To: ChimeraX Users Help Hi Yaikhomba, I think you need to use sym #1 assembly 2 copies true 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. 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"". 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."" (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: open 1be3 from pdbe_bio 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. #1.2 from PDBe will have unique chains. For example, the other copy of chain A is chain AA. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco On Nov 30, 2020, at 11:13 AM, Y. Mutum wrote: Hi I have a a C2-symmetric pdb: 1be3 and have created a symmetric assembly using the command. sym #1 assembly 2 newModel false 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. 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? 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. 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. Thanks Yaikhomba _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimerax-users " enhancement closed moderate Higher-Order Structure fixed Elaine Meng all ChimeraX