[Chimera-users] Named selection for subset of markers

[Elaine Meng]

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
>