[chimera-dev] adding an atom at the centroid of a blob
Jean Didier Pie Marechal
JeanDidier.Marechal at uab.cat
Wed Jan 13 08:01:32 PST 2010
Hi everyone,
I have obtained cavities for a given atom selection using surfnet and I want to put an atom at the centroid of the main blob. I know how to do this for a selected set of atom but I am struggling with the surfaces.
At this point, I splitted it (accelator Sc) and then I can select the blob I am interested in. But how could I create a particular object for this blob? From there, how could I add an atom (i.e. helium) and the centroid of the blob?
Thanks for any help,
JD
Dr. Jean-Didier Maréchal
Lecturer
Computational Biotechnological Chemistry @ Transmet
Unitat de Química Física
Departament de Química
Universitat Autònoma de Barcelona
Edifici C.n.
08193 Cerdanyola (Barcelona)
Tel: +34.935814936
e-mail: JeanDidier.Marechal at uab.es
----- Missatge original -----
De: chimera-dev-request at cgl.ucsf.edu
Data: Dimarts, Desembre 15, 2009 9:00 pm
Assumpte: Chimera-dev Digest, Vol 71, Issue 4
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> Today's Topics:
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> 1. Re: [Chimera-users] Programmer's Guide feedback....
> (Eric Pettersen)
> 2. Re: [Chimera-users] Programmer's Guide feedback.... (Tom
> Goddard) 3. Re: [Chimera-users] Programmer's Guide feedback....
> (Eric Pettersen)
>
>
> --------------------------------------------------------------------
> --
>
> Message: 1
> Date: Tue, 15 Dec 2009 10:55:42 -0800
> From: Eric Pettersen <pett at cgl.ucsf.edu>
> To: chimera-dev at cgl.ucsf.edu
> Subject: Re: [chimera-dev] [Chimera-users] Programmer's Guide
> feedback....
> Message-ID: <61EC3E93-8EE5-48E0-AB71-4705D5162EE4 at cgl.ucsf.edu>
> Content-Type: text/plain; charset="us-ascii"; Format="flowed";
> DelSp="yes"
>
> On Dec 15, 2009, at 9:36 AM, Tom Goddard wrote:
>
> > 4. The ToolbarButton.py doesn't work unless the "import re" and
>
> > "import chimera" are in the function body. This is because
> Chimera
> > deletes all globals after loading a file. This has often been a
> > headache for me and Chimera should not delete globals.
>
> This is a behavior of Python. We load scripts into their own
> temporary module to avoid pollution of the Chimera main namespace
> (e.g. if the script defined globals named "id" or "sum" or "type"
> they
> would override built-in functions of the same name for all future
> script executions!). When Chimera unloads the temporary module,
> Python nulls out it's global namespace (to give garbage collection
> a
> shot at working).
>
> Now perhaps Chimera shouldn't unload the module. I think this
> would
> be a reasonable change. Perhaps it could be discussed at our next
> internal Chimera developers' meeting to ensure that I'm not
> forgetting
> any other ramifications that the change might have.
>
> --Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
> http://www.cgl.ucsf.edu
>
>
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> ------------------------------
>
> Message: 2
> Date: Tue, 15 Dec 2009 11:10:30 -0800
> From: Tom Goddard <goddard at cgl.ucsf.edu>
> To: Eric Pettersen <pett at cgl.ucsf.edu>
> Cc: chimera-dev at cgl.ucsf.edu
> Subject: Re: [chimera-dev] [Chimera-users] Programmer's Guide
> feedback....
> Message-ID: <4B27DF26.1080904 at cgl.ucsf.edu>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
> Hi Eric,
>
> The case I have been burned by many times is where all globals of
> ChimeraExtension.py are deleted. In both the ChimeraExtension.py
> case
> and opening a *.py file with File / Open the trouble is that if the
> Python code registers a callback and the callback function tries to
> use
> a name in the global name space like calling another function
> defined in
> the same file or a global import then it fails. This is extremely
> confusing when it happens.
>
> Tom
>
>
> -------- Original Message --------
> Subject: Re: [chimera-dev] [Chimera-users] Programmer's Guide
> feedback....From: Eric Pettersen
> To: chimera-dev
> Date: 12/15/09 10:55 AM
> > On Dec 15, 2009, at 9:36 AM, Tom Goddard wrote:
> >
> >> 4. The ToolbarButton.py doesn't work unless the "import re"
> and
> >> "import chimera" are in the function body. This is because
> Chimera
> >> deletes all globals after loading a file. This has often been a
> >> headache for me and Chimera should not delete globals.
> >
> > This is a behavior of Python. We load scripts into their own
> > temporary module to avoid pollution of the Chimera main namespace
> > (/e.g./ if the script defined globals named "id" or "sum" or
> "type"
> > they would override built-in functions of the same name for all
> future
> > script executions!). When Chimera unloads the temporary module,
> > Python nulls out it's global namespace (to give garbage
> collection a
> > shot at working).
> >
> > Now perhaps Chimera shouldn't unload the module. I think this
> would
> > be a reasonable change. Perhaps it could be discussed at our
> next
> > internal Chimera developers' meeting to ensure that I'm not
> forgetting
> > any other ramifications that the change might have.
> >
> > --Eric
> >
> > Eric Pettersen
> > UCSF Computer Graphics Lab
> > http://www.cgl.ucsf.edu
> >
> >
> > ------------------------------------------------------------------
> ------
> >
> > _______________________________________________
> > Chimera-dev mailing list
> > Chimera-dev at cgl.ucsf.edu
> > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev
> >
>
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> ------------------------------
>
> Message: 3
> Date: Tue, 15 Dec 2009 11:24:28 -0800
> From: Eric Pettersen <pett at cgl.ucsf.edu>
> To: Tom Goddard <goddard at cgl.ucsf.edu>
> Cc: chimera-dev at cgl.ucsf.edu
> Subject: Re: [chimera-dev] [Chimera-users] Programmer's Guide
> feedback....
> Message-ID: <EDCA8098-C839-42BF-B540-92E9776B8241 at cgl.ucsf.edu>
> Content-Type: text/plain; charset="us-ascii"; Format="flowed";
> DelSp="yes"
>
> Hi Tom,
> This is actually a separate instance of basically the same
> behavior.
> At Chimera startup the extension manager loads (and unloads) all
> the
> ChimeraExtension.py files. I guess we could also discuss if this
> behavior is critical to the extension manager and whether it's
> desirable to change it.
>
> --Eric
>
> On Dec 15, 2009, at 11:10 AM, Tom Goddard wrote:
>
> > Hi Eric,
> >
> > The case I have been burned by many times is where all globals
> of
> > ChimeraExtension.py are deleted. In both the ChimeraExtension.py
>
> > case and opening a *.py file with File / Open the trouble is that
> if
> > the Python code registers a callback and the callback function
> tries
> > to use a name in the global name space like calling another
> function
> > defined in the same file or a global import then it fails. This
> is
> > extremely confusing when it happens.
> >
> > Tom
> >
> >
> > -------- Original Message --------
> > Subject: Re: [chimera-dev] [Chimera-users] Programmer's Guide
> > feedback....
> > From: Eric Pettersen
> > To: chimera-dev
> > Date: 12/15/09 10:55 AM
> >> On Dec 15, 2009, at 9:36 AM, Tom Goddard wrote:
> >>
> >>> 4. The ToolbarButton.py doesn't work unless the "import re"
> and
> >>> "import chimera" are in the function body. This is because
> >>> Chimera deletes all globals after loading a file. This has
> often
> >>> been a headache for me and Chimera should not delete globals.
> >>
> >> This is a behavior of Python. We load scripts into their own
> >> temporary module to avoid pollution of the Chimera main
> namespace
> >> (e.g. if the script defined globals named "id" or "sum" or
> "type"
> >> they would override built-in functions of the same name for all
> >> future script executions!). When Chimera unloads the temporary
> >> module, Python nulls out it's global namespace (to give garbage
> >> collection a shot at working).
> >>
> >> Now perhaps Chimera shouldn't unload the module. I think this
> >> would be a reasonable change. Perhaps it could be discussed at
> our
> >> next internal Chimera developers' meeting to ensure that I'm not
>
> >> forgetting any other ramifications that the change might have.
> >>
> >> --Eric
> >>
> >> Eric Pettersen
> >> UCSF Computer Graphics Lab
> >> http://www.cgl.ucsf.edu
> >>
> >>
> >>
> >> _______________________________________________
> >> Chimera-dev mailing list
> >> Chimera-dev at cgl.ucsf.edu
> >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev
> >>
> >
> > _______________________________________________
> > Chimera-dev mailing list
> > Chimera-dev at cgl.ucsf.edu
> > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev
>
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