- Chimera-dev - RBVI Mailing Lists

modify the menu bar
by Elisabeth Ortega 21 Jan '11

21 Jan '11

Dear Chimera Dev Team, I'm trying to put other option in the menu bar (File, Select, Actions, ... , myOption, Help) to store my own scripts. I'm doing a deep search on your python and C++ codes but I don't find which is the code that I have to modify. I know that is easy to store my scripts in the Tools menu, but I prefer to put my scripts in a new option of the menu bar. Thanks a lot for taking the time to reply. Elisabeth Ortega Autonomous University of Barcelona (UAB)

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Creating graphics objects from Python code
by Konrad Hinsen 12 Jan '11

12 Jan '11

Hi everyone, I would like to add non-molecular graphics objects to my molecules for illustration. The obvious way to do so is to load a BILD or VRML file, but since I create these objects in Python scripts, I'd prefer to a direct Python interface rather than write a temporary file and load it. Is there a reasonably stable interface for doing this? Thanks in advance, Konrad. -- --------------------------------------------------------------------- Konrad Hinsen Centre de Biophysique Moléculaire, CNRS Orléans Synchrotron Soleil - Division Expériences Saint Aubin - BP 48 91192 Gif sur Yvette Cedex, France Tel. +33-1 69 35 97 15 E-Mail: research AT khinsen DOT fastmail DOT net ---------------------------------------------------------------------

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Coloring
by Hajeung Park 21 Dec '10

21 Dec '10

Hello, I want to color "C" to a certain color. The manual is not very clear bout it. My understanding is Color green byatom ,a @C But it give me error. Thanks.

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chimera.openModels.listids()
by Darren Weber 09 Dec '10

09 Dec '10

From 'help(chimera.openModels): | listIds(...) | listIds(hidden: bool = false, all: bool = false) -> list of tuple(int, int) Why does it return a tuple of two ints for each element? Could you answer this by enhancing the help documentation on that method? Thanks, Darren -- Darren L. Weber, Ph.D. Programmer/Analyst Resource for Biocomputing, Visualization, and Informatics University of California, San Francisco N453 Genentech Hall, Mission Bay Campus 600 16th Street, M/S 2240 San Francisco, CA 94158-2517 Tel: +1 415 847-3127 www: http://psdlw.users.sf.net/

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Chimera Use
by Bill Gleason 04 Dec '10

04 Dec '10

http://chronicle.com/blogs/brainstorm/hic-haec-hype-little-green-men-or-ars… Thanks, and my best, Bill -- William B. Gleason, PhD Associate Professor, Department of Laboratory Medicine & Pathology, University of Minnesota Medical School Fellow, University of Minnesota Supercomputer Institute http://ptable.blogspot.com/ ( Periodic Table blog) http://blog.lib.umn.edu/bgleason/pt/ (UThink blog)

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Headtracking software
by Tamás Borsos 17 Nov '10

17 Nov '10

Hi, first of all I would like to thank You all for your work on this project, because we are using your software regularly for short three dimensional presentations to our students at Lorand Eotvos University, Hungary. I am working at the Faculty of Natural Sciences as a software engineer and we have a large stereoscopic projection system and we are just about to finish the development of our head tracking system, which is already able to measure the position and orientation of the viewers head. This way we will be able adapt the viewpoint of the three dimensional software to the viewpoint of the user. In order to completely interface our system with your software we need to modify it or write an additional module. Would you be so kind to help me find a sophisticated (or maybe easy) way to upload/adjust the cameraposition (world transformation) through an interface to your software? Thank you very much in advance. Regards, Thomas Borsos

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Read a file from script
by Elisabeth Ortega 04 Nov '10

04 Nov '10

Dear all, I need to read some parameters that are write in the same file that I have opened. For exemple, I had a python script that parses the author of the PDB file and I want to run it in a chimera script to use it in other part of the script. To open the file I use: from openSave import osOpen f=osOpen("/home/eortega/data.pdb") code .... I want to do that more "polite". I mean, without write the entire route of the file. Saying to chimera that reads the same file that it has open and appears in the screen. Could anyone help me? Thanks Best Elisabeth Ortega Universitat Autonoma de Barcelona

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Programming a Table
by Elisabeth Ortega 03 Nov '10

03 Nov '10

Dear all, I'm trying to do a script that shows in a table an array of numerical values. One little script that shows what I'm trying to do is: from chimera import runCommand as run run("sel") b=[] for a in chimera.selection.currentAtoms(): b=a.serialNumber from CGLtk.Table import SortableTable t=SortableTable(b) t.addColumn("serial", "Serial", format=None) t.setData(b) t.launch() With this little script I'm trying to show in a column of the table the serial number of the atoms of my system. But when I execute that, I got a message in the Python Shell that says: Traceback (most recent call last): File "/home/eortega/intento-tabla.py", line 11, in <module> t=SortableTable(b) File "CHIMERA/share/CGLtk/Table.py", line 489, in __init__ File "CHIMERA/lib/python2.5/lib-tk/Tkinter.py", line 2442, in __init__ Widget.__init__(self, master, 'frame', cnf, {}, extra) File "CHIMERA/lib/python2.5/lib-tk/Tkinter.py", line 1923, in __init__ BaseWidget._setup(self, master, cnf) File "CHIMERA/lib/python2.5/lib-tk/Tkinter.py", line 1901, in _setup self.tk = master.tk AttributeError: 'int' object has no attribute 'tk' And I don't understand it. How can I build successfully my table? Thank you very much Best Elisabeth Ortega Universitat Autònoma de Barcelona

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raw_input
by Victor Muñoz 06 Oct '10

06 Oct '10

Hi, I've been doing different scripts in python for chimera UCSF, but recently I'm having problems using the raw_input() function. I've been using this functions for a long time and I haven't had any problem until now. The error I have when using it is: Traceback (most recent call last): File "/users/victor/Desktop/Doctorat/Python/Scripts/rmsd_aro_screen.py", line 51, in <module> aref=input() File "/users/victor/bin/chimera/lib/python2.6/idlelib/PyShell.py", line 1007, in readline self.top.mainloop() # nested mainloop() File "/users/victor/bin/chimera/share/Idle/__init__.py", line 82, in mainloop origListedTopLevel.mainloop(self) NameError: global name 'origListedTopLevel' is not defined I don't know where the error comes from, but I have the same error in both mi computer and my laptop. Thanks for all in advance. Kind regards, Victor Muñoz Robles --

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some questions
by Gentile, Maria Antonietta 04 Oct '10

04 Oct '10

Hi, I would have some information about CHIMERA. Is it possible to obtain the topology of a protein structure by using CHIMERA? How? And the second question is about the secondary structure representation of a protein, in my case wiht CHIMERA I am not able to visualize all secondary structure elements, how can I modify the settings for this problem? Thank you

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