[Chimera-users] New molecule from selection?

Oliver Clarke olibclarke at gmail.com
Thu Apr 2 19:07:36 PDT 2015


This is an old thread, but I finally worked out an alias that does the trick (copying an arbitrary selection as a new molecule without disturbing open models), so I figured I’d post it here in case it is of use to any one else. It is a little ugly and quite slow for large models, but it seems to work reliably.

alias ^copysel save ~/tmp1.py ; del ~sel ; combine sel close true modelid 1000; write relative 1000 #1000 ~/sel.pdb  ; close all ; open ~/tmp1.py ; open ~/sel.pdb

Cheers,
Oliver.
> On Dec 12, 2014, at 2:38 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> 
> On Dec 11, 2014, at 7:34 AM, Oliver Clarke <olibclarke at gmail.com <mailto:olibclarke at gmail.com>> wrote:
> 
>> Hi,
>> 
>> This may already be implemented, but I couldn’t find it - the nearest equivalent feature I know of is copy/combine, but that only works on whole models, not taking into account selections.
>> 
>> I was wondering if it would be possible to implement a feature creating a new model comprised of all atoms in the current selection? This would be particularly helpful when combining many parts of multiple models, or when creating a separate model consisting of a subselection of the current model.
>> 
>> This can be done at present using a combination of copy/combine and selecting and deleting those parts of the copied molecules that are not in the selection, but this gets messy for complicated selections.
> 
> Hi Olivier,
> 	This is a reasonable request/idea, and I'll open a feature-request ticket for it.  However, with our current focus on implementing Chimera 2, it may be some time before this feature gets implemented (in Chimera 1 or Chimera 2!).
> 	Perhaps there's an easier workflow?  Select all the parts you want put into the new model, invert the selection, delete the unwanted parts, and then combine into a new model.  You may want to save a session before the delete step, depending on what you want to do with the new model relative to the old models.
> 	 I hope this helps.
> 
> --Eric
> 
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu <http://www.cgl.ucsf.edu/>
> 

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