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
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
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
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
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@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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participants (3)
-
Elaine Meng -
Eric Pettersen -
Giovanni Cardone