[Chimera-users] Named selection for subset of markers

[Eric Pettersen]

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.

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu


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
> -----
> 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
>                      http://www.cgl.ucsf.edu/home/meng/index.html
>
> 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,
>> Giovanni
>>
>>
>>
>> tripod.cmm
>> <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"/>
>> </marker_set>
>>
>>
>> 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.
>>>
>>> Example:
>>> 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
>>> name)
>>>
>>> [...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
>>> -----
>>> 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
>>>                   http://www.cgl.ucsf.edu/home/meng/index.html
>>>
>>>
>>>
>>> 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
>>>> normal
>>>> behavior?
>>>> I am using Chimera version 1 build 2552.
>>>> Thanks in advance,
>>>> Giovanni
>>
>
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