October 2015 - Chimera-dev - RBVI Mailing Lists

Chimera 2 input devices
by Dougherty, Matthew T 30 Oct '15

30 Oct '15

Under C1 accelerators and some other USB HID activity require the cursor to be on a graphics window. An exception would be the mouse or keyboard interacting with other gui windows such as button pushes or entering file names. For C2 it would be good to have a dedicated input channel independent of the cursor position like the 3dconnexion. The general trend I see with researchers is dual display. One handles graphics and the other gui controls. This gets tricky when s3d is used and the cursor. Is not exactly what. you think (2 visible cursors one active the other inactive) I manage this now with a dedicated chimera extension user gui buttons that rearrange the screens; and with controller mate I can have preconfigured-window-gui-location accelerator commands sent to activate the buttons, at the same time controller mate can set cursor positions and do button pushes. Works for Mac, not an option for PC or Linux. I guess I could set a frame trigger and check a dedicated tcp port, but I am hesitant creating a kludge, because of the underlying strategic design issue and messing with the event loop. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

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chimera2 S3D terminology
by Dougherty, Matthew T 29 Oct '15

29 Oct '15

recommend the follow changes to follow HDMI & S3D industry terminology wall-eye stereo ---> SBS-full DTI side by side stereo ---> SBS-half eye separation ---> interaxial distance Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

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chimera2 s3d
by Dougherty, Matthew T 27 Oct '15

27 Oct '15

can't remember I mentioned this. on the savepos, it would be good to save the s3d parameters, particularly the interaxial distance. been doing animations where the IA needs to change in order to optimize the S3D effect. sometimes I use unusual values for the parameters. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

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Linking Chimera with our molecular simulation tool-kit
by Lianheng Tong 22 Oct '15

22 Oct '15

Dear Chimera developers, I am a postdoc research associate working with Prof. Lev Kantorovich of King’s College London. I am currently a full time developer for the ab initio atomic simulation code CP2K, and as a part of our project funding, we are looking to develop a tool kit that would improve user friendliness that would allow the users to construct various bulk or molecular structures in an intuitive and graphically way. We currently have a quite extensive tool-kit (tetr) developed by Prof. Kantorovich for generating, modifying structures—especially tailored for periodic systems, as well as post processing utilities on volume data (such as generating STM images etc). It is written in FORTRAN, and currently is command based only, with the user input being either interactive or by a batch file. The goal, is to be able to link to a visualisation package like Chimera, so that: a) one is able to automatically update the visualisation when the user uses the tool interactively b) allow the user to select atoms and fragments and use these selections as an input to the tool-kit. Ideally, the took-kit can run as an independent code, with the extension providing an interface between Chimera and the tool-kit. The user would then control the tool-kit from within the Chimera command interface. I have used Chimera a lot during my PhD, however, I have not yet written any extension for it. I do, however, have quite a number of years experiences with code development, especially in Fortran and in Python. I am wondering: 1) If you would mind if we develop an extension to link our took-kit with Chimera 2) If the functionalities I mentioned above would be possible to achieve Any suggestions from you would be great. Thank you very much for your time, and I look forward to hearing from you soon. Best regards, Lianheng ==================================== Lianheng Tong Room S4.02, Strand Building Department of Physics Kings College London Strand, London WC2R 2LS, U.K. Tel: +44 20 7848 2064 Fax: +44 20 7848 2420 lianheng.tong(a)kcl.ac.uk ====================================

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binding handlers to SortableTable checkboxes
by Jan Kosinski 17 Oct '15

17 Oct '15

Hi again, How to attach handlers to checkboxes in the CGLtk SortableTable so the handler is invoked automatically when the checkbox is (un)checked? I get it working by subclassing and overriding _widgetCB as below but maybe you have sth more convenient? class ComponentSortableTable(SortableTable): def __init__(self,parent,*args,**kwargs): SortableTable.__init__(self,parent,*args,**kwargs) def _widgetCB(self, datum, column, newVal=None): SortableTable._widgetCB(self, datum, column, newVal=newVal) <my code if column.title == ‘show’: … > Thanks, Jan

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Model panel rename
by Dougherty, Matthew T 15 Oct '15

15 Oct '15

I would like to tie a USB foot pedal to the model panel rename button. I can get the foot pedal signal into my chimera extension. From an extension, what would be the easiest way to Python code the activation of the model panel button? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

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Chimera-dev October 2015