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

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

Tom


On Apr 2, 2015, at 7:07 PM, Oliver Clarke <olibclarke@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@cgl.ucsf.edu> wrote:

On Dec 11, 2014, at 7:34 AM, Oliver Clarke <olibclarke@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



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