- Chimera-dev - RBVI Mailing Lists

event loop
by Dougherty, Matthew T 05 Feb '16

05 Feb '16

I am working on a human interface for volume rendering. The livid ds1 mixer uses midi through USB. http://lividinstruments.com/products/ds1/ I should be able to use python midi libraries for access. This leads to the problem of the midi implementation, and a question as to a similar implementation for chimera2. One implementation would insert into the event loop, another approach could be tied to a frame/trigger callback. Any suggestions? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= =================================================

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Volume Eraser: Recentering the eraser
by Mohan Sudabattula 07 Jan '16

07 Jan '16

Hello, My name is Mohan Sudabattula, I am fairly new at using Chimera so please excuse my lack of understanding the program. I am currently utilizing the Volume Eraser tool and am trying to employ it erase the internal structure of a viral capsid. Upon opening the Volume Eraser it always seems to orient itself to the "frontmost face of the current display region". This is problematic because it is now only partially erasing what I am needing to be erased. Instead I am looking to have it oriented so that it is in the center of my virus. Is there any way to reorient the eraser so that this may be the case? Thank you! Mohan Sudabattula confirm e2a44c6a1c2aa9063cccd37bee44a9add15bde48

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Could I ask some questions about Chimera?
by Archeries 05 Jan '16

05 Jan '16

Hi developers of Chimera, My name is Archeries Ye. I'm a undergraduate from Zhejiang University. These days I have been learning Protein Structure Prediction, and according to my advisor's suggestion, I'm going to study the protein structure prediction function of Chimera. I searched information of Chimera, but unfortunately have not got enough. I wonder if you could spare some time for my questions? 1. Which prediction algorithm does Chimera adapt? Is it independent from protein structure databases? And is it feasible to change the conformation by changing the electric charge of atoms? 2. Could the source code of Chimera be shared for uncommercial use? Thank you for spending your valuable time reading my letter. I will really appreciate for any reply from you. Archeries

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match API change
by Eric Pettersen 21 Dec '15

21 Dec '15

Just a heads up that as a side effect of now reporting both the full and pruned RMSD of an iterated match, the number of return values from Midas.match(), Midas.matchXform(), and MatchMaker.match() changed. The first two added the full RMSD just after the pruned RMSD in their tuple of return values, and the latter did a similar thing, though it returns a list of such (now larger) tuples. —Eric Eric Pettersen UCSF Computer Graphics Lab

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Re: [chimera-dev] Save the map after hide dust
by Tom Goddard 08 Dec '15

08 Dec '15

Hi Gary, I made it a bit easier to invert the shown portion of the map surface by adding an "sop invertShown" command. It will be in tonight's daily build. So to mask the dust on map #0 you could use sop hideDust #0 size 25 sop invertShown #0 mask #0 #0 invert true Would be nice to make this easier -- maybe in our next generation Chimera. Tom > On Dec 8, 2015, at 6:35 PM, Tom Goddard wrote: > > Hi Gary, > > Good to hear from you. The hide dust feature does not change the density map, it only hides the small connected surface pieces. You could set the map grid points to zero inside the dust blobs with the mask command. But first you need to be able to show only the dust and there is no command to do that. I've attached a Python script that does that. You select the map surface (ctrl-click) that you have done hide dust on, then open the surfinvert.py script to show only the dust. Then use the mask command > > mask #0 sel invert true > > to mask the density map (#0) to the selected surface (dust blobs only shown) and invert, since you want to keep everything outside the dust blobs, not everything inside the dust blobs. I tried it, works. But if you lower the threshold on the new map then of course you see more dust. > > Tom > > <surfinvert.py> > > The surfinvert.py script is also on the Chimera Python scripts page > > http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts> > > > >> On Dec 8, 2015, at 5:05 PM, Gang (Gary) Ren wrote: >> >> Hi Tom, >> >> I like the density map after hide density map, is there any way to save the >> density map after dust hide? Every time I save the density map, it saved the >> original map instead of density map after hidden dust. >> >> Thanks a lot >> Gary >> >> >> >> >

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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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