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. Best, Oliver.
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
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 <mailto: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 <http://www.cgl.ucsf.edu/>
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. 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 <mailto:pett@cgl.ucsf.edu>> wrote:
On Dec 11, 2014, at 7:34 AM, Oliver Clarke <olibclarke@gmail.com <mailto: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 <http://www.cgl.ucsf.edu/>
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Eric Pettersen -
Oliver Clarke -
Tom Goddard