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@uab.es ----- Missatge original ----- De: chimera-dev-request@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:
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)
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Message: 1 Date: Tue, 15 Dec 2009 10:55:42 -0800 From: Eric Pettersen <pett@cgl.ucsf.edu> To: chimera-dev@cgl.ucsf.edu Subject: Re: [chimera-dev] [Chimera-users] Programmer's Guide feedback.... Message-ID: <61EC3E93-8EE5-48E0-AB71-4705D5162EE4@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