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@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@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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