- Chimera-dev - RBVI Mailing Lists

Center of rotation:
by Dougherty, Matthew T 24 Aug '15

24 Aug '15

I need to change the center of rotation at every frame. I am using from chimera import viewer cam = chimera.viewer.camera cmd = 'cofr fixed %s,%s,%s' %(cam.eyePos(0)) chimera.runCommand(cmd) which generates a message in the reply log Center of rotation: 564.31 -345.208 699.718 How can I disable this message in the reply log? Or is there another method I should use (eg, hack the cofr command)? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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Re: [chimera-dev] distance measurements
by Eric Pettersen 21 Aug '15

21 Aug '15

You run a python file simply by opening it, either with the “open” command or with File->Open. Another option here, since you aren’t creating images or doing anything graphical, is to run it entirely from the command line and not even bring up the graphical interface: chimera —nogui DistSing.py Looking at your script, it mostly looks good except the for the writing to the file. It looks like you give two ‘{}’s in the format string but then provide 4 arguments to the format() call. I think those have to match, though I’m no format() guru. —Eric > On Aug 21, 2015, at 11:18 AM, Feixia <feixia.chu(a)unh.edu> wrote: > > Thank you, Eric. > > I got a prototype program based on your suggestions (see attachment). But, I can't get it to run. I tried the 'Tools / General Controls / IDLE Python shell" by enter "import DistSing.py". The error message I got, "ImportError: No module named DistSing.py". > > I have Python27, and Chimera 1.7. Any suggestion to move forward? I ended PDB downloading at ~107,000 entires when most of the rest structures are gigantic ribosome, virus etc. Thanks. > > Feixia > > > On Thu, 20 Aug 2015 15:35:55 -0400, Eric Pettersen <pett(a)cgl.ucsf.edu> wrote: > > Probably the simplest way is to just see if you wound up with multiple models or not (i.e. len(openModels.list(modelTypes=Molecule)) > 1). If you just want to use one model per entry regardless of it being NMR or not, don’t loop over the model list but just use the first model in it, i.e. instead of: > > for mol in openModels.list(modelTypes=[Molecule]): > indented analysis code > > use: > > mol = openModels.list(modelTypes=[Molecule])[0] > unindented analysis code > > —Eric > >> On Aug 19, 2015, at 9:10 PM, Feixia <feixia.chu(a)unh.edu <mailto:feixia.chu@unh.edu>> wrote: >> >> Thank you, Eric! >> I am still downloading PDB files through Bio.python. I am just interested in the overall distance distribution of residues, say Lys alpha carbon. NMR entries might end up over-representing due to their multiple models. Thank you for pointing it out. Is there a quick way to distinguish crystal structures from NMR structures? >> >> Best, >> Feixia >> >> On Wed, 19 Aug 2015 14:17:35 -0400, Eric Pettersen <pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote: >> >> Hi Feixia, >> You could certainly use Chimera to do that. You need to know some Python. Take a look at the Programmer’s Guide: >> >> http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html <http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html> >> >> In particular, the “basic primer” discusses how to loop over files in a directory and do things to them one by one. >> Here’s some example code for printing the lysine CA-CA distances for a single open file. You could take that and move it into the loop described in the basic primer — customizing it as you wish… >> >> from chimera import openModels, Molecule >> # opening NMR files can produce multiple models, so use a loop... >> for mol in openModels.list(modelTypes=[Molecule]): >> lysCas = [a for a in mol.atoms if a.name == “CA” and a.residue.type == “LYS”] >> for i, ca1 in enumerate(lysCas): >> for ca2 in lysCas[i+1:]: >> print mol.name, ca1, ca2, ca1.coord().distance(ca2.coord()) >> >> —Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> >>> On Aug 18, 2015, at 8:36 AM, Feixia <feixia.chu(a)unh.edu <mailto:feixia.chu@unh.edu>> wrote: >>> >>> Hi there, >>> >>> I am interested in retrieving distance information from large dataset in an automatic fashion. For instance, can we use Chimera to get the distances between lysine alpha-carbons of current PDB entries. Presumably, we can download all PDB structures on our local desktop, and just call functions one structure at a time. I wonder if we can do that with Chimera. Your advice will be highly appreciated. >>> >>> Best, >>> Feixia >>> >>> >> _______________________________________________ >> 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 > > > > > -- > Feixia Chu, Ph.D. > Associate Professor > Molecular, Cellular & Biomedical Sciences > University of New Hampshire > Gregg Hall, Rm436 > 35 Colovos Rd > Durham, NH 03824 > Tel 603 862 2436 > <DistSing.py>

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distance measurements
by Feixia 20 Aug '15

20 Aug '15

Hi there, I am interested in retrieving distance information from large dataset in an automatic fashion. For instance, can we use Chimera to get the distances between lysine alpha-carbons of current PDB entries. Presumably, we can download all PDB structures on our local desktop, and just call functions one structure at a time. I wonder if we can do that with Chimera. Your advice will be highly appreciated. Best, Feixia -- Feixia Chu, Ph.D. Associate Professor Molecular, Cellular & Biomedical Sciences University of New Hampshire Gregg Hall, Rm436 35 Colovos Rd Durham, NH 03824 Tel 603 862 2436

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extracting statistics from an existing fitlist
by Dan Lin 11 Aug '15

11 Aug '15

Hello: I'm trying to extract the statistics from a previously run fitmap global search to a text file. Is there a way to find the objects that all the information is stored in so I can write a script to write it out? I've been trying to dig through the code to find out where it is stored, but have not had any luck. Thanks for the help!

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Enhancing the command-line
by Tom Goddard 15 Jul '15

15 Jul '15

Hi Joshua, We are ahead of you. In Chimera 2 which is not yet released we have put in support for command completion, command keyword completion, it should be able to give you the whole syntax of the command in the status line. It doesn’t do this yet but it is supposed to have those capabilities. We haven’t discussed improved command history search but I agree that would be handy, to for instance bring back your last command starting with “surf”. Could these features be put in Chimera 1? I don’t think we will do it because we are putting all effort on Chimera 2 and plan a first release with very minimal capabilities this Fall. We’d be happy to help you add these things to Chimera 1. The command-line user interface is in chimera/share/Midas/midas_ui.py and uses the Tk window toolkit. This would be the place where you would bind the tab key or other special keys that for instance do history search. We don’t have detailed Chimera 1 programming API documentation, just a few tutorials http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html <http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html> and nothing that describes command-line code. A basic problem is that Chimera 1 only knows the command names. There is no table of keyword arguments that a command takes so you couldn’t provide any detailed help on tab completion. It doesn’t seem very useful to complete just the command name. To get programming help use the chimera-dev mailing list. The Chimera developers here, Eric, Conrad, Greg and I will answer any technical questions through that list. Tom > On Jul 15, 2015, at 10:40 AM, Broyde, Joshua E. wrote: > > Dear Tom, > I hope you are well. I have a general question/issue regarding the Chimera user interface that I wanted to discuss with you. > The Chimera GUI user interface is extremely intuitive and well done, but I was wondering if it would be possible to beef up the command-line user interface? For example, it would be nice if there was tab completion within the command-line interface For example, if a user typed "mat" and then a tab, the command line could show "match", "matchmaker", "matrixcopy" ,""matrixget", and "matrixset". Other features could include a more robust history search, for example. > > These kind of things are implemented in other command-line interfaces for other resources, such as Bash, iPython, and Rstudio. > > This is something that I was thinking of doing myself to make my work more efficient, except that I don't know where to begin from a programatic perspective. Are there any files/directories or things I should know about how the command-line works internally in Chimera that would help for implementing this? Is there a point person at RBVI I could contact to ask questions regarding this? I need to generally know more about the internal guts of the CLI of Chimera before beginning. > > Of course, if I produce something useful, I will share it with you so you can share it with the general Chimera community. > > Sincerely, > Joshua Broyde

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chimera extensions
by Dougherty, Matthew T 06 Jul '15

06 Jul '15

How can I reload an extension when chimera is running? At the present, after I modify python code I restart chimera for the s/w changes to take effect. Is there a way through idle, etc, that I can cause user code modifications to load without restarting chimera? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ===========================================================================

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Packaging an extension... Error
by MARYAM ARAB 15 Jun '15

15 Jun '15

Dear Developers, Hi, I have a C++ program and I want to package it under the tools menu. I made a dll from my program. My dll gets two input ( pdb name and volum density level ,) and generate the output. when I save the python codes to execute my dll in the chimera IDLE, every thing works well and my program starts working and generates the output. here is the code that I ran in the IDLE: import ctypes dll = ctypes.CDLL('tracer_v2.dll') dll.calc.argtypes = [ctypes.c_char_p, ctypes.c_double] dll.calc.restype = ctypes.c_int print(dll.calc('1733_H',3)) The problem that I faced is that when I add an extension button to the chimera and wants to call my function (calc('1733_H', 3) ) from there, I get an error: WindowsError Exception in Tk callback Function: <function command at 0x0D1A89B0> (type: <type 'function'>) Args: () Traceback (innermost last): File "C:\Program Files (x86)\Chimera 1.10.1\bin\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "C:\Program Files (x86)\Chimera 1.10.1\share\chimera\baseDialog.py", line 449, in command getattr(s, buttonFuncName(txt))() File "Z:\Tracer_Chimera\GUI\TracerUI\gui.py", line 43, in Apply TracerUI.mainchain() File "Z:\Tracer_Chimera\GUI\TracerUI\__init__.py", line 9, in mainchain dll = ctypes.CDLL('tracer_v2.dll') File "C:\Program Files (x86)\Chimera 1.10.1\bin\lib\ctypes\__init__.py", line 365, in __init__ self._handle = _dlopen(self._name, mode) WindowsError: [Error 126] The specified module could not be found Would you please help me know how I can fix it? Thanks, Maryam Arab Research Assistant Old Dominion University

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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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Get value of 'measure distance' command
by Hoai Thu NGUYEN 24 Mar '15

24 Mar '15

Hi, I need to calculate the minimum distance between 2 residues but It seems that I can't find the correct way to use the 'measure distance' command in python script. I tried: import Measure temp = Measure.measure_command('distance', 'distance :628.a :20.b') but it gave me the error: "No target atoms or surface" Can you please precise the correct syntax of this command? Thank you! Thu

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Re: [chimera-dev] volume display in my gui
by Tom Goddard 06 Mar '15

06 Mar '15

You can get a PIL (Python Image Library) image of the Chimera graphics window with import chimera image = chimera.viewer.pilImages()[0] You can supply optional width and height arguments in pixels otherwise the image size will match the graphics window size. An example using pilImages is the Chimera image saving code in the saveImage() routine share/chimera/printer.py Chimera moves the models and the Chimera always points along the -z axis. So to change the viewing angle you would rotate the models, for example: import chimera axis = chimera.Vector(1,0,0) angle = 30 r = chimera.Xform.rotation(axis, angle) chimera.openModels.setXform(r) The openModels code is in C++ and you can see the C++ header file for the OpenModels class which has equivalent Python methods here http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/_chimera/OpenMode… <http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/_chimera/OpenMode…> This stuff is all pretty hard to figure out. Unfortunately we do not have adequate programming documentation for Chimera. We are remedying this in our next generation Chimera 2 which is not yet released. Tom > On Mar 6, 2015, at 4:15 PM, hy liao wrote: > > Hi Tom: > > Thanks for the great details! A snapshot on the main Chimera window is good enough! I actually do not need interaction but just the correct display. In other words, given a volume data (density map) and a viewing angle (azimuthal and elevation angles), how do I get the corresponding 2D snapshot (a surface rendering) of the volume? Once I have this snapshot, I guess I can place it in my window by assigning it to my canvas object. > > Thanks again! > Stu > > > On Friday, March 6, 2015 6:27 PM, Tom Goddard wrote: > > > Hi Stu, > > The gui.py file I mentioned is shown with Chimera menu entry Tools / Volume Data / Values at Atom Positions. It does not embed volume images though. > > Chimera is not designed to handle multiple interactive 3-d renderings, so you cannot in any simple way embed the Chimera graphics in your own Tk window. The graphics is shown as a Togl widget (Tk OpenGL widget) that is drawn by Chimera C++ code. Why do you want do that? Why not just manipulate the view in the main Chimera graphics window? The only example of embedding 3d data display in another window is the Chimera side view (menu Favorites / Side View) which has Python code in > > chimera/share/chimera/viewing.py > > But it uses C++ code to handle the drawing. > > If your aim is to make a custom app with Chimera graphics and your own set of controls you could modify the Chimera main window with Python code in > > chimera/share/chimera/tkgui.py > > All of this is quite hard. Another route is to take a snapshot image from the main Chimera window to put it in your own window, but then you could not rotate it. > > Tom > > > >> On Mar 6, 2015, at 3:11 PM, hy liao wrote: >> >> Hi Tom: >> >> Thank you for your prompt reply. Sorry for my ignorance, but how can I run the script chimera/share/AtomDensity/gui.py and see the gui it actually produces? >> >> Alternatively, this might be another way of formulating my question: to display a picture in a gui using tkinter, one can create a frame object, then a canvas object, then set the position of the canvas, then create a photoimage object, and then indicate that the picture goes in the canvas. Now, instead of a picture, how do I do the same for a chimera type of volume display? Do I have to also go through creating a frame, a canvas, and then indicate that the volume must reside in the just created canvas. It would be great if you know of any example out there. I have been relying on examples so far. >> >> Thanks again! >> >> Stu >> >> >> On Friday, March 6, 2015 4:26 PM, Tom Goddard wrote: >> >> >> >> Hi Stu, >> >> To find out about Python functions that control volume display in Chimera that you could use from your Tkinter gui take a look at the Chimera Python scripts web page: >> >> http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts> >> >> for example the readvol.py example shows how to access volume data values. In Python you can make use of commands that would be normally typed at the Chimera command-line in the following way >> >> from chimera import runCommand >> runCommand(‘volume #0 level 12.5 color pink’) >> >> or you could directly call functions in Python that change volume display, for example, >> >> import VolumeViewer as vv >> v0 = vv.volume_list()[0] >> v0.set_parameters(surface_levels = [12.5], surface_colors = [(1,.5,.5,1)]) >> >> To find those functions you can look at the Chimera Volume class Python code in your Chimera distribution >> >> chimera/share/VolumeViewer/volume.py >> >> (on Mac in Chimera.app/Contents/Resources/share/VolumeViewer/volume.py), and you can look at how the Chimera “volume” command does it >> >> chimera/share/VolumeViewer/volumecommand.py >> >> For making a Tk GUI look at a simple example in the Chimera distribution, for example, the values at atom positions dialog >> >> chimera/share/AtomDensity/gui.py >> >> >> Tom >> >> >> >>> On Mar 6, 2015, at 12:16 PM, hy liao wrote: >>> >>> Hi, I am developing a GUI with Tkinter, using anaconda's python 2.7.9. I like how chimera displays volumes (density maps), so I would like to a chimera-volume-display in my GUI. I am now disregarding anaconda and developing all within chimera's IDLE. However, I do not know which chimera commands I could use for my purpose; could you please point to some choices? >>> >>> I am new with developing chimera extension and tkinter, and I mostly look for code examples. I had a look at http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/ <http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/>, "Working with the Chimera Extension Manager," but I do not know which commands I could use to have chimera display a volume in a grid of my GUI. >>> >>> Thanks! >>> Stu >>> _______________________________________________ >>> 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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Re: [chimera-dev] volume display in my gui
by Tom Goddard 06 Mar '15

06 Mar '15

Hi Stu, The gui.py file I mentioned is shown with Chimera menu entry Tools / Volume Data / Values at Atom Positions. It does not embed volume images though. Chimera is not designed to handle multiple interactive 3-d renderings, so you cannot in any simple way embed the Chimera graphics in your own Tk window. The graphics is shown as a Togl widget (Tk OpenGL widget) that is drawn by Chimera C++ code. Why do you want do that? Why not just manipulate the view in the main Chimera graphics window? The only example of embedding 3d data display in another window is the Chimera side view (menu Favorites / Side View) which has Python code in chimera/share/chimera/viewing.py But it uses C++ code to handle the drawing. If your aim is to make a custom app with Chimera graphics and your own set of controls you could modify the Chimera main window with Python code in chimera/share/chimera/tkgui.py All of this is quite hard. Another route is to take a snapshot image from the main Chimera window to put it in your own window, but then you could not rotate it. Tom > On Mar 6, 2015, at 3:11 PM, hy liao wrote: > > Hi Tom: > > Thank you for your prompt reply. Sorry for my ignorance, but how can I run the script chimera/share/AtomDensity/gui.py and see the gui it actually produces? > > Alternatively, this might be another way of formulating my question: to display a picture in a gui using tkinter, one can create a frame object, then a canvas object, then set the position of the canvas, then create a photoimage object, and then indicate that the picture goes in the canvas. Now, instead of a picture, how do I do the same for a chimera type of volume display? Do I have to also go through creating a frame, a canvas, and then indicate that the volume must reside in the just created canvas. It would be great if you know of any example out there. I have been relying on examples so far. > > Thanks again! > > Stu > > > On Friday, March 6, 2015 4:26 PM, Tom Goddard wrote: > > > Hi Stu, > > To find out about Python functions that control volume display in Chimera that you could use from your Tkinter gui take a look at the Chimera Python scripts web page: > > http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts> > > for example the readvol.py example shows how to access volume data values. In Python you can make use of commands that would be normally typed at the Chimera command-line in the following way > > from chimera import runCommand > runCommand(‘volume #0 level 12.5 color pink’) > > or you could directly call functions in Python that change volume display, for example, > > import VolumeViewer as vv > v0 = vv.volume_list()[0] > v0.set_parameters(surface_levels = [12.5], surface_colors = [(1,.5,.5,1)]) > > To find those functions you can look at the Chimera Volume class Python code in your Chimera distribution > > chimera/share/VolumeViewer/volume.py > > (on Mac in Chimera.app/Contents/Resources/share/VolumeViewer/volume.py), and you can look at how the Chimera “volume” command does it > > chimera/share/VolumeViewer/volumecommand.py > > For making a Tk GUI look at a simple example in the Chimera distribution, for example, the values at atom positions dialog > > chimera/share/AtomDensity/gui.py > > > Tom > > > >> On Mar 6, 2015, at 12:16 PM, hy liao wrote: >> >> Hi, I am developing a GUI with Tkinter, using anaconda's python 2.7.9. I like how chimera displays volumes (density maps), so I would like to a chimera-volume-display in my GUI. I am now disregarding anaconda and developing all within chimera's IDLE. However, I do not know which chimera commands I could use for my purpose; could you please point to some choices? >> >> I am new with developing chimera extension and tkinter, and I mostly look for code examples. I had a look at http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/ <http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/>, "Working with the Chimera Extension Manager," but I do not know which commands I could use to have chimera display a volume in a grid of my GUI. >> >> Thanks! >> Stu >> _______________________________________________ >> 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 > > >

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volume display in my gui
by hy liao 06 Mar '15

06 Mar '15

Hi, I am developing a GUI with Tkinter, using anaconda's python 2.7.9. I like how chimera displays volumes (density maps), so I would like to a chimera-volume-display in my GUI. I am now disregarding anaconda and developing all within chimera's IDLE. However, I do not know which chimera commands I could use for my purpose; could you please point to some choices? I am new with developing chimera extension and tkinter, and I mostly look for code examples. I had a look at http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/, "Working with the Chimera Extension Manager," but I do not know which commands I could use to have chimera display a volume in a grid of my GUI. Thanks!Stu

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UnitCell.molecule_center(): Attribute does not exist
by Alejandro Virrueta 11 Feb '15

11 Feb '15

Hello all, I'm trying to execute the script to fill out the crystal unit cell found here: http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q13 However, I get the error that UnitCell does not have the 'molecule_center' attribute (code line ~12). I checked with dir(), and yeah, it's not there: ['ModelessDialog', 'Unit_Cell_Dialog', '__builtins__', '__doc__', '__file__', '__name__', '__package__', '__path__', 'chimera', 'dialogs', 'find_model_by_name', 'outline_box', 'place_molecule_copies', 'remove_extra_copies', 'show_unit_cell_dialog'] Where did the attribute go? Is there some other module I could use? Could someone explain (or direct me to some webpage that explains) the process of expanding the ASU and I can write my own script. Any help is greatly appreciated! Thanks! Alex

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Re: [chimera-dev] [Chimera-users] Find subsequence programatically
by Thomas Hrabe 22 Jan '15

22 Jan '15

Hi Eric , I have an algorithm that returns some subsequences of a structure and i want to color the corresponding structure segment automatically. Thanks Thomas from the road Am 22.01.2015 um 16:37 schrieb Eric Pettersen <pett(a)cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>>: On Jan 22, 2015, at 4:21 PM, Thomas Hrabe <thrabe(a)sanfordburnham.org<mailto:thrabe@sanfordburnham.org>> wrote: Hi Chimera Team, How can I automate the Sequence View -> Edit -> Find Subsequence Tool programmatically with the Chimera shell or better within python? I don't know what your context is here exactly, but if you have a Sequence object you can use its regexMatch or prositeMatch methods to find subsequences. They return lists of (start, end) tuples. If you need more info, provide some more detail about your usage context and I can help better. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Re: [chimera-dev] [Chimera-users] Ringer/Chimera/IDLE
by Greg Couch 21 Jan '15

21 Jan '15

(This question is a developer question and not a user question, but since it was asked on chimera-users, the response is there as well. Followups should go to chimera-dev(a)cgl.ucsf.edu.) The "ValueError: missing default material" means that the script was not run by chimera, which we don't support. We also don't support using an IDLE other than the one you get by running chimera and using Tools / General Tools / IDLE. We only support using chimera's Python code in scripts that are invoked by chimera. That is why the ringer shell script is: "$CHIMERA_HOME"/bin/chimera --nogui --silent --script "$RINGER"/ringer/main.py -- "$@" In the same vein, if you replaced "$RINGER"/ringer/main.py with the following 2 line script: import chimera print chimera.MaterialColor(1, 1, 1) Everything works. Long ago, we considered what it would take to get chimera's Python code working in a different application. In that scenario, you would need to: 1. Set the CHIMERA environment variable to the root of the Chimera installation 2. Set other environment variables that are set in CHIMERA/bin/chimera for your platform 3. Add $CHIMERA/share to your Python's sys.path 4. import chimeraInit; chimeraInit.init([], nogui=True, eventloop=False, exitonquit=False) But since chimera uses a modified Python, that is insufficient. For example, chimera changes Python's default string to unicode conversion to use utf-8 instead of ASCII. We've also backported some of Python 3's unicode support that chimera depends on. If you are lucky, your use of chimera's Python code will not be affected by those changes. HTH, Greg P.S. Your immediate problem might be fixed by calling chimera.initializeColors(), but that is a hack that is not guaranteed to keep working. On 01/16/2015 12:20 PM, Alejandro Virrueta wrote: > Hello, > > I am modifying some Ringer files for my own needs, but I am running > into a weird issue. If I run Ringer via typical means: > > $RINGER/ringer/ringer -i ringer_in_${pdb_ID}.txt -o > ringer_out_${pdb_ID}.txt > > it works fine. However, when I step through it in what I think is my > version of IDLE ("$CHIMERA_HOME/bin/chimera --nogui --nostatus > --script `which idle2.7` > /usr/bin/idle2.7", with `which idle2.7` returning "/usr/bin/idle2.7"), > I run into this error: > > Traceback (most recent call last): > File "/Users/av376/ringer-2.0/ringer/main_copy.py", line 233, in > <module> > main() > File "/Users/av376/ringer-2.0/ringer/main_copy.py", line 161, in main > move_set, pdb = structureFile(parameters, path) > File "/Users/av376/ringer-2.0/ringer/main_copy.py", line 65, in > structureFile > pdb = chimera.openModels.open(parameters.pdbfileName) > File > "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", > line 1817, in open > checkForChanges=False, noprefs=noprefs) > File > "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", > line 1644, in add > makePseudoBondsToMetals(realMolecules) > File > "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", > line 1961, in makePseudoBondsToMetals > cmPBG = mol.metalComplexGroup(issueHint=True) > File > "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", > line 119, in _getMetalPbg > am.color = preferences.get(MOLECULE_DEFAULT, MOL_COMPLEX_COLOR) > File > "/Applications/Chimera.app/Contents/Resources/share/chimera/preferences/base.py", > line 608, in get > forPrefSave=forPrefSave) > File > "/Applications/Chimera.app/Contents/Resources/share/chimera/preferences/base.py", > line 179, in get > return self._options[name].get(forPrefSave=forPrefSave) > File > "/Applications/Chimera.app/Contents/Resources/share/chimera/preferences/base.py", > line 80, in get > return self.prefToVal(self.value) > File > "/Applications/Chimera.app/Contents/Resources/share/chimera/tkoptions.py", > line 1229, in _prefToColor > return getColorByName(pref) > File > "/Applications/Chimera.app/Contents/Resources/share/chimera/colorTable.py", > line 87, in getColorByName > color = chimera.MaterialColor(r/255.0, g/255.0, b/255.0) > ValueError: missing default material > > Any suggestions? > > Cheers, > Alex > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Alternate conformations in residues
by Alejandro Virrueta 21 Jan '15

21 Jan '15

Hello all, Is there a way to get the all the information for an alternate conformation from a residue object? I have res.altLocs resulting in set([a,b]), but how can I get chi1-4 for conformation b for example? Thanks! Alex

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