[Chimera-users] Named selection for subset of markers
pett at cgl.ucsf.edu
Mon Dec 8 14:49:55 PST 2008
For the purposes of sessions, molecules/atoms/bonds created by
Chimera's "core" functionality can be treated differently than those
created by Chimera tools (e.g. Volume Tracer), and named selections is
an instance of such a difference. Basically, the core functionality
that restores the named selections can only reference atoms/bonds also
restored by the core functionality and can't reference the atoms/bonds
being created by Volume Tracer during the session restore, so those
atoms/bonds don't make it into the named selection.
This is a design issue and the programmers will talk about it and see
what we can do to remedy it. But for now, you're kind of stuck
unfortunately. I will open a bug report on this issue and include you
on the cc list so that you can follow whatever progress we make on it.
UCSF Computer Graphics Lab
On Dec 8, 2008, at 1:02 PM, Elaine Meng wrote:
> Hi Giovanni,
> I thought markers and atoms would be treated exactly the same, but now
> testing with the marker file I also see this bug.
> I see a problem even without using named selections: when I open the
> marker file, select one marker, save the session, quit, and restart
> the session, the marker is no longer selected.
> We will look into this problem - thanks for reporting it!
> Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Dec 8, 2008, at 11:09 AM, Giovanni Cardone wrote:
>> Hi Elaine,
>> sorry I did not give enough details. My problem is not with atoms in
>> a model, but with bonds and atoms in a marker set.
>> Here is an example: I open tripod.cmm (given below), I select just
>> one bond and one atom, name the selection as oneside, finally save
>> the session as test.py.
>> In the session file, I have the following line:
>> savedSels = [('oneside', )]
>> and if I reopen the session and recall the named selection, nothing
>> is selected.
>> Thank you,
>> <marker_set name="markers in a triangle">
>> <marker id="1" x="42.352" y="29.099" z="50.347" radius="0.5"/>
>> <marker id="2" x="37.892" y="29.805" z="44.673" radius="0.5"/>
>> <marker id="3" x="32.449" y="26.829" z="48.569" radius="0.5"/>
>> <link id1="2" id2="1" r="1" g="1" b="1" radius="0.2"/>
>> <link id1="3" id2="2" r="1" g="1" b="1" radius="0.2"/>
>> <link id1="1" id2="3" r="1" g="1" b="1" radius="0.2"/>
>> On Dec 8, 2008, at 1:50 PM, Elaine Meng wrote:
>>> Hi Giovanni,
>>> I can't tell what you did from what you said.
>>> The proper procedure is to first select those markers or atoms,
>>> then name the selection. Then later you can use that name either
>>> in the Select menu to make those markers or atoms selected again,
>>> or in the command line, which would just perform the command on
>>> those markers but not make them selected again.
>>> In my tests (Dec 7 build) this works fine. I don't have markers
>>> handy, so here is an example with atoms. With markers you could
>>> take a different approach to select them in the first place, but
>>> the remaining steps would be the same.
>>> open 1zik
>>> select @ca
>>> (or use Select menu to select some set of atoms,
>>> or Volume Tracer or interactive picking to select markers)
>>> namesel alphacarbs
>>> (or use Select... Name Selection to give that current selection a
>>> [...now you could clear or change the selection...]
>>> rep sphere alphacarbs
>>> (or use Select... Named Selections... alphacarbs to regenerate
>>> the selection,
>>> then do something to it with the Actions menu)
>>> I hope this helps,
>>> Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
>>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>>> Department of Pharmaceutical Chemistry
>>> University of California, San Francisco
>>> On Dec 8, 2008, at 10:32 AM, Giovanni Cardone wrote:
>>>> Hi all,
>>>> I am trying to save a selection of a subset of markers as a named
>>>> selection. However, the named selection results empty: is it a
>>>> I am using Chimera version 1 build 2552.
>>>> Thanks in advance,
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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