- Chimera-dev - RBVI Mailing Lists

savepos
by Dougherty, Matthew T 12 Jun '15

12 Jun '15

This relates to a previous email exchange. I would like to add a description parameter to the import of midas positions. The reason is that I would like to keep the position names brief when I am doing scripting, but would like to put detailed information in the description, for example a flag indicating that the research group has picked particular positions to be used in an animation after proofing through a pool of 50 saved positions. I would also like to use the field to indicate other things such as which animation is is to be used in, number of seconds I should hold the position before moving on, date it was created, etc. I think there are two ways to add a description field into position 1) something in the chimera build that I could access with python, 2) something I would add through my python code. If I did this I would have concern that the description parameter gets included in the session save, or could create incompatibilities in the session files down the road on later chimera builds. Which method would you recommend? In a related s/w dev comment, I am now connecting an ipad via wifi, to my laptop. This is allows me to pass the ipad around as a control surface in a collaborative conference room/dome environment. As the conductor of the collaborative viz, I would have buttons on the laptop that would alter the gui on the ipadbased on the needs of the moment (e.g., color, stereo3D, threshold). This part of overall HID toolbox of multiple gamespads, contour shuttle dialbox, 3dconnection, and master control button boxes, where I am remapping variables (e.g., translation/rotation) to an HID such that a user can make a preference as to which HID is more intuitive. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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Opening a *.py file on Windows, Chimera has issues with spaces in name
by Bernard Lieberman 08 Jun '15

08 Jun '15

Hello, I'm writing an application that calls a relevant python file and opens it in Chimera. I've gotten the program working just fine on the majority of systems but one of my clients attempted to use the application and noticed it's having a breaking point or issue (on his particular Windows Vista system) when the application tries to open the python file. Windows itself recognized the exact path and location and can open the file on other computers just fine. Any assistance or advice on what I'm missing (if there's a chimera-specific setting) or if this is a known issue with particular OS'es etc., please let me know. Best regards, Bernard

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VolumeEraser
by yes sir 06 May '15

06 May '15

Dear Sirs, I recently started using chimera, please apologise my lack of knowledge. In order to erase a surfnet volume I am trying to use the Erase volume module, but it doesn't work. Are the surfnet objects available to be used in VolumeEraser functions? Is there another way to study volume intersections? If you know, please point out the article which describes the procedure for this kind of volume calculation. Best regards, Alex

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User interface
by Dougherty, Matthew T 04 May '15

04 May '15

I have been writing some extensions and maxed out my real estate for my control panel buttons, widgets, etc. I figure I need to rewrite it to be more like the viewer tool, having tabs at the top to select different gui menus. Can you offer me some ideas for a organizational strategy along with code ideas? Eg, getting menu items to save/restore as part of a session file. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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Re: [chimera-dev] PS3 controller/Chimera2
by Tom Goddard 29 Apr '15

29 Apr '15

I am using the same polling space navigator code in Chimera 2 which uses the wxWidgets window toolkit. Again the right approach would be to generate wx events, but there are too many other higher priority problems to solve in Chimera 2. Tom > On Apr 29, 2015, at 5:59 PM, Dougherty, Matthew T wrote: > > Hi Tom, > > How do you plan to implement spacenav into chimera2. > Will you be using Tk? > > Matthew Dougherty > National Center for Macromolecular Imaging > Baylor College of Medicine > =========================================================================== > From: Tom Goddard > Sent: Wednesday, April 29, 2015 5:56 PM > To: Dougherty, Matthew T > Cc: chimera-dev(a)cgl.ucsf.edu <mailto:chimera-dev@cgl.ucsf.edu> > Subject: Re: [chimera-dev] PS3 controller > > Hi Matt, > > Here is the Mac spacenavigator C++ code used by Chimera > > http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/_spacenavigator/s… <http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/_spacenavigator/s…> > > The Linux spacenavigator code instead uses the Python ctypes module to get events. > > http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/SpaceNavigator/sn… <http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/SpaceNavigator/sn…> > > and the Windows spacenavigator code uses a Python COM interface to get the events. > > http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/SpaceNavigator/sn… <http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/SpaceNavigator/sn…> > > Each of these allow Chimera to get the most recent Space Navigator position before each frame is drawn using the Chimera “new frame” trigger. This technique for processing the events is called “polling” and is bad. The right way to do it would be to get the space navigator events when they occur and put them in the Tk event queue so they are handled when Chimera processes the Tk event queue. That is how Chimera gets mouse and keyboard events. I didn’t do that because the integration with the Tk window toolkit is harder. > > Tom > > >> On Apr 29, 2015, at 12:56 PM, Dougherty, Matthew T wrote: >> >> >> I have written an extension that uses a PS3 game controller. >> >> To make the hardware work and generate the keyboard accelerators text strings, I am using controllermate s/w on a Mac. >> >> To make it work generically across platforms, like spacenav, I am going to have to write a driver that can load with chimera. >> >> Any thoughts? >> Can you point me to the c code for spacenav? >> >> Matthew Dougherty >> National Center for Macromolecular Imaging >> Baylor College of Medicine >> =========================================================================== >> _______________________________________________ >> Chimera-dev mailing list >> Chimera-dev(a)cgl.ucsf.edu <mailto:Chimera-dev@cgl.ucsf.edu> >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev>

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PS3 controller
by Dougherty, Matthew T 29 Apr '15

29 Apr '15

I have written an extension that uses a PS3 game controller. To make the hardware work and generate the keyboard accelerators text strings, I am using controllermate s/w on a Mac. To make it work generically across platforms, like spacenav, I am going to have to write a driver that can load with chimera. Any thoughts? Can you point me to the c code for spacenav? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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visualizing lines between atoms
by Mathilde LE BOUDIC-JAMIN 24 Apr '15

24 Apr '15

Dear all, We're creating a chimera entension and we want (among other things) to ask Chimera to draw a line between pairs of selected atoms. Would you by chance have an idea about how to program it? I'm sorry but I'm not comfortable with the chimera modules yet. Thanks, Regards Mathilde

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stereo3D focal plane
by Dougherty, Matthew T 23 Apr '15

23 Apr '15

I am using S3D regularly, and developed a USB user interface that allows me to adjust S3D parameters such as focal plane using a contour express dial. I have stopped using scale factor by disabling the keyboard scroll, and switching to z translation. I am finding that I need to adjust the focal plane a lot.? Usually it is between the clipping planes, but when I do z translations it normally gets between the camera and the near clipping plane, or out past the far clipping plane. For S3D animations I can work around it. For interactive use, people are having major eye strain. I would like to modify the chimera code to automatically adjust the focal plane as the clipping planes change. Can you point me to the area of code where I could make the change? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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pull down menus
by Dougherty, Matthew T 13 Apr '15

13 Apr '15

When I am using chimera I am frequently using it with two monitors. One monitor has the 3D graphics maximized. The other monitor has the dialog boxes and various control GUI. Thing get messy when I use the graphics in stereo3D, particularly DTI SBS-half; such as save session. The cursor does not track easily to the pull down menus of the 3D graphics window. I would like to copy all the pulldowns (not changing the originals) onto some gui on my other monitor. Is there an easy way I replicate these pulldowns using an python extension I would write? Is there one place in the chimera code that sets up the pulldowns? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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Using Chimera to display family shuffling information.
by Matthew Tiffany 13 Apr '15

13 Apr '15

To Whom It May Concern: I am interested in displaying results from DNA shuffling experiments on a crystal structure. Here is a graphical tool that I have found to do this: http://qpmf.rx.umaryland.edu/XoverDemo.html What I would like to do is input an alignment of parental sequences and separately a chimeric protein that is derived from the parental sequences by domain shuffling. Then color code a related structure based upon which domain of a parent the chimeric protein came from. The Xover program does this in a graph, but I would like to be able to do this in 3D space. It is similar to color coding by conservation in MultiAlign, but not exactly. Is there any existing plugin that you may be aware of that does this already or a potential backbone plugin that I can use as a starting point to try and code it myself. Regards, Matthew Tiffany Postdoctoral Fellow Mark A. Kay Laboratory Stanford University 269 Campus Drive CCSR 2110 Stanford, CA 94305

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