[Chimera-users] New molecule from selection?

Tom Goddard goddard at sonic.net
Fri Apr 3 09:53:28 PDT 2015

Thanks Oliver,

  Of course copying part of a molecule should not be this arcane.  I entered a feature request in our database to make a command that allows easy copying of a selected part of a molecule.

	http://plato.cgl.ucsf.edu/trac/chimera/ticket/13859 <http://plato.cgl.ucsf.edu/trac/chimera/ticket/13859>

This is more likely to go into Chimera 2 than Chimera 1.


> On Apr 2, 2015, at 7:07 PM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 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 <mailto: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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