Sure, if you tell me that works. I wasn't sure if #2 had all 60 or just the other 59 and it would have been another several minutes experimenting. Elaine
On Jun 21, 2024, at 1:53 PM, Tom Goddard <goddard@sonic.net> wrote:
How about execute the second sym command with copies true on model #2 which has the first 60 copies?
Tom
On Jun 21, 2024, at 1:50 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Sigh, I was trying to enlist help in answering the question directly considering I've already spent hours messing around with it... especially if you think it is simple to explain. I don't think it is obvious to expect different numbers of copies just because you wanted them to be atomic instead of graphical.
If she wants 3600 full atomic copies how would she do that??
Elaine
On Jun 21, 2024, at 1:35 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Elaine,
If you don't use copies true, then the first sym command changes model #1 rendering to include 60 graphical clones, and then the second sym command also on model #1 makes 60 graphical clones of the previous 60 graphical clones, so you now have 3600 graphical clones in model #1. You can see this with "info #1" which says "3600 instances".
If you use the "copies true" option then the sym command makes a new model #2 with 60 copies. The second sym command on #1 with copies true makes 60 more copies as model #3. Of course that is a very different result then the sequence without copies true because the copies true version makes new models instead of modifying the original model.
This all makes sense to me.
Tom
On Jun 21, 2024, at 1:25 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Tom, maybe you can figure it out??
OK I give up, I did extensive tests and can't figure it out either. I regenerated the original starting molecule (I think), attached as temp.pdb
Then the overall result visible with the following, which is what she apparently wants (except with real atomic copies) although I worry it may have double copies in places, is a very packed-looking sphere:
sym #1 i,2n5 center 20,20,20 sym #1 i,2n3 center 20,20,20
However if you start over with temp.pdb and then do the following, you get something much more patchy/holey
sym #1 i,2n5 center 20,20,20 copies true sym #1 i,2n3 center 20,20,20 copies true
I thought it might have something to do with copies replacing other copies but I tried with newModel true and still had seemingly the same issues.
Maybe the more-packed appearance is actually a bug if sym w/o copies true makes more graphical copies of ones that are already graphical copies.
Elaine
<temp.pdb>
Begin forwarded message:
From: "Noriega, Heather via ChimeraX-users" <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Re: Help_saving Date: June 21, 2024 at 12:14:50 PM PDT To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Reply-To: "Noriega, Heather" <heather.noriega@bison.howard.edu>
Hello,
It is quite baffling to me why it does this. I am going to add different sessions to show you what I see. I have included each session to try and separate to explain myself and not confuse. Three of the sessions do not include the copies true command: (sym_2n3, sym_2n5, sym_both). The one with both (sym_2n3 and sym_2n5) gives me the niosome I am quite interested in with an aqueous and lipophilic compartment. I want to do a simple measure of the volume inside the large compartment, but would like to minimize the niosome as a whole first, hence needing a pdb file. However, I have done the same with the next three sessions, but adding copies true command and it is not coming up with the same result for sym_both_copiestrue.
I hope this helps to try and understand what I am looking for, and maybe you have an answer as to why there are different results for Sym_both and Sym_both_copiestrue.
Thank you,
Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega@bison.howard.edu 520-203-1883
On Fri, Jun 21, 2024 at 2:33 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Heather,
I don't really understand why you needed two sym commands instead of one (must be something specific about your structure(s)), but whenever you want to actually save the PDB of any parts that "sym" adds you would need to include "copies true" when you add them.
You could just do the experiment with and without it yourself and see what you get. Or save two separate PDB files, one from each command, to make sure you aren't getting duplicates of the same atoms exactly on top of each other from using sym twice.
Elaine
On Jun 21, 2024, at 9:45 AM, Noriega, Heather via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I do not want to save the shape of a sphere. I was using that for something else while creating the nano.
Ok, that is what I did wrong. I did not include the copies true command. I have a question. I used the commands:
Sym #1 i,2n3 center 20,20,20 and Sym #1 2n5 center 20,20,20 to create the sphere. Would I have to add copies true to both commands?
sym#1 i,2n3 center 20,20,20 copies true sym#1 i,2n5 center 20,20,20 copies true
And then continue with the saving process for PDB
Thank you,
Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega@bison.howard.edu 520-203-1883
On Fri, Jun 21, 2024 at 12:37 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Heather, I can't tell what you are trying to save exactly but here are two issues:
(1) when you used "sym" the Log said it was making graphical clones. (The log contents are included in the session file.) If you want full atomic copies instead of graphical clones you have to use "copies true" as explained in the help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#copies>
(2) The big sphere seems to be a surface model, and you can't save a surface model as PDB format. Maybe you used the "shape" command, which creates surface models. But I can't tell from your message whether you are trying to save that in the file or not.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
> On Jun 21, 2024, at 9:16 AM, Noriega, Heather via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: > > Hello, > > I have a question. I created this sphere nanoparticle and have been trying to save it as a PDB (the whole sphere). But when I save "selected atoms, " I try to re-open the PDB file. It only shows the original single Span-60 that was used. Is there a way to save the copies and nanoparticles as a whole so I can minimize them altogether? > > I attached the session below for your reference. > > Thanks, Happy Friday! > > Thank you, > > Heather Noriega > PhD-Pharmaceutical Science student > Howard University > heather.noriega@bison.howard.edu > 520-203-1883 > <nano_span_60.cxs>
<sym_2n5_copiestrue.cxs> <sym_2n3_copiestrue.cxs> <sym_2n5.cxs> <sym_2n3.cxs> <sym_both.cxs> <sym_both_copiestrue.cxs>
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Elaine Meng