[Chimera-users] Selector Construction Panel
Eric Pettersen
pett at cgl.ucsf.edu
Tue Oct 30 12:26:14 PDT 2007
Hi Virginia,
The Selector Construction panel could probably stand some interface
improvements for sure. "Existing Selection" has nothing to do with
what's selected in the Chimera window as you construct the selector.
"Existing Selection" grabs whatever is selected in the Chimera window
when the selector is used (either by choosing the selector from
Chimera's Select menu, of invoking it from the Select region of the
construction panel) -- so it can be a different selection every time
it is used. Anyway, you can ignore that because it doesn't really
help you with your problem.
There is no easy way to select all lysines within 8 angstroms of
another lysine in Chimera, so you were on the right track with trying
to construct a selector, but it requires actually putting some custom
Python code in your selector since you need to loop over lysine
residues individually in order to get what you want. So open the
Selector Construction panel, pick "Show workbench selector contents"
in the Panels menu, and paste in:
from chimera import specifier
sel.merge(selection.REPLACE, specifier.evalSpec(":LYS"))
nearRes = []
sel2 = selection.ItemizedSelection()
for r in sel.residues():
sel2.clear()
sel2.add(r)
sel2.merge(selection.REPLACE, specifier.zone(sel2,
specifier.ATOM, None, 8.0, models))
selRes = [sr for sr in sel2.residues() if sr.type == "LYS"]
selRes.remove(r)
nearRes.extend(selRes)
sel.clear()
sel.add(nearRes)
Since the remailer for this list may break long lines, I've also
attached the above as a file. If you are using the X11 version of
Chimera for the Mac, pasting in the text is tricky -- if you're using
that let me know and I can send instructions about how to get the
pasting to work.
--Eric

On Oct 30, 2007, at 10:50 AM, Virginia Pett wrote:
> Eric,
> Yes, my ultimate goal is more complicated than the examples that I
> gave. I would like to find all the Lys residues in the structure
> that are less than 8 Å apart from each other. After several hours
> of frustration with the Selector Construction Panel, I decided to
> try a simpler question in order to test whether I was using the
> Workbench correctly and to test whether any information was being
> saved.
>
> I may not have understood your reply correctly. Here is what I
> tried just now. I selected all atoms NZ (@NZ). THEN I invoked the
> Selector Construction Panel. (In my previous experiments, the
> Construction Panel had been invoked before I made the selection in
> the main window.) Then I proceeded as before, in the Selector
> Construction Panel: Workbench, Load from current. The Status panel
> shows workbench content: Existing Selection. Then Workbench,
> Save, as All NZ atoms, for example. However, as before, when I go
> back to the main window, Select, Clear Selection and then Select
> All NZ atoms, there is nothing selected.
>
> Virginia
>
>
>
>
> On 10/25/07 7:56 PM, "Eric Pettersen" <pett at cgl.ucsf.edu> wrote:
>
>> Hi Virginia,
>> Perhaps you could describe what your ultimate goal here is --
>> there may be an easier way to achieve it than by constructing a
>> custom selector.
>> But in regards to your problem, for the purposes of selector
>> construction the "Existing Selection" isn't what is selected at
>> that instant -- it's what's selected at the time the selector is
>> invoked from Chimera's Select menu. This allows you to build
>> selectors that intersect the peptide backbone with the current
>> selection for example.
>> If you want to make a selector that simply holds what's currently
>> selected, use the Name Selection... entry in Chimera's Select
>> menu. That creates a selector under Named Selections in the
>> Select menu, and will also be remembered in saved sessions.
>>
>> --Eric
>>
>>
>> Eric Pettersen
>>
>>
>> UCSF Computer Graphics Lab
>>
>>
>> pett at cgl.ucsfedu
>>
>>
>> http://www.cgl.ucsf.edu
>>
>>
>>
>> On Oct 25, 2007, at 2:22 PM, Virginia Pett wrote:
>>
>>> Hello,
>>> There is a difficulty with the Selector Construction Panel. I
>>> make a selection in the main window, such as chain A or atom
>>> @NZ. The Inspect Selection panel shows that I have made a
>>> selection. Then in the Selector Construction Panel: Workbench,
>>> Load from current. The Status panel shows workbench content:
>>> Existing Selection. Then Workbench, Save, as chain A, for
>>> example. However, when I go back to the main window, Select,
>>> Clear Selection and then Select, chain A, there is nothing selected.
>>>
>>> I downloaded the latest version of Chimera for Mac OS X a few
>>> days ago (chimera-1.2422-osx_x11.dmg). I’m running it on a
>>> PowerBook G4 with Mac OS X (10.4.10).
>>> Virginia
>>> _____________________________________________________
>>>
>>> Virginia B. Pett
>>> Professor of Chemistry
>>> Department of Chemistry, The College of Wooster
>>> 943 College Mall, Wooster, OH 44691
>>> Telephone: 330-263-2114
>>> Fax: 330-263-2386
>>>
>>>
>>> _______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
>>> http://wwwcgl.ucsf.edu/mailman/listinfo/chimera-users
>>>
>>
>>
>
>
> _____________________________________________________
>
> Virginia B. Pett
> Professor of Chemistry
> Department of Chemistry, The College of Wooster
> 943 College Mall, Wooster, OH 44691
> Telephone: 330-263-2114
> Fax: 330-263-2386
>
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