[Chimera-users] Named selection for subset of markers

Giovanni Cardone cardoneg at mail.nih.gov
Mon Dec 8 11:09:55 PST 2008

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  
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.
> 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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