December 2013 - Chimera-dev - RBVI Mailing Lists

Re: [chimera-dev] [Chimera-users] keyboard shortcuts
by Tom Goddard 07 Jan '14

07 Jan '14

Hi Matt, I agree that difficulty of use kills interest in stereo -- needs to be as simple as binoculars, one knob. For recording transparent background animations currently you have to click the "Transparent background" button in the File / Save Image dialog. That switches Chimera rendering to use a frame buffer that includes transparency. You also will need to use PNG format for the movie recording images ("movie record format PNG") because that is the only recording format that handles transparency. Currently there is no command to set background transparency. We should add a "set backgroundTransparency true|false" command to do this so you can put it in a script. It will call the setBackgroundOpacity() routine in chimera/printer.py. Until that is added you could use a little Python script transpbg.py: from chimera import printer printer.setBackgroundOpacity(True) and call it from your movie command script with "open transpbg.py" The Chimera programming questions should go to chimera-dev(a)cgl.ucsf.edu to avoid spamming Chimera users who are not interested in programming issues. Tom On Dec 31, 2013, at 12:07 PM, "Dougherty, Matthew T" <matthewd(a)bcm.edu> wrote: > probably going to stick with the spreadsheet as my starting point for design and documentation. > Mapping the USB commands has to be hand crafted in concert with other non-chimera software manufacturer software. > The spreadsheet will allow me to deal with the mishmash, chimera commands, OS interactions, serial S3D serial/USB commands to projector. > > As for S3D, my analysis is that jumping through all the hoops is so awkward this is the main reason people don't mess with it. > One button to get in and out, turn a knob like a pair of binoculars. > Now that I got an 8ft rotating dome in my office, I am building a viz cockpit to push interactivity, s3D and volume rendering. > > just about finished with my first operational prototype, "UCP", user control panel. Will send it to chimera-dev for review. > it deals with a bunch of camera issues, particularly S3D so I can explore a range of interaxial distances. > It also gives me fine control of volume rendering, so I can accurately pull out stuff I would normally give up on. > Starting to feel pretty good about programming chimera extensions, at some point I plan to tackle the frame packing and a rework of space navigator. > > couple other things. > > 1) When I need to generate animations that have a transparent background I go to save image and set the transparency background. Sometimes I forget to do this and waste a lot of time on my rendering. > > I would like to add a new animation command to so I can set the transparency in my .com files. What is the chimera variable I need to set? > Also plan similar commands to set the screensize, screen distance and eye separation; but know how to do those. > > 2) These kinds of posts, should I be sending them to chimera-users or chimera-dev? > > > > Matthew Dougherty > National Center for Macromolecular Imaging > Baylor College of Medicine > ________________________________________ > From: Tom Goddard > Sent: Tuesday, December 31, 2013 1:36 PM > To: Dougherty, Matthew T > Subject: Re: [Chimera-users] keyboard shortcuts > > Ok. You might have your code use: > > for k in ('!001', '!002', '!003'): > add(k, 'HID', lambda: HID(k)) > > or if they really are just numbered > > for k in range(25): > s = '!%03d' % k > add(s, 'HID', lambda: HID(s)) > > Tom > > > On Dec 31, 2013, at 11:29 AM, "Dougherty, Matthew T" wrote: > >> thx, I can generate that in a spreadsheet and paste it in. >> >> add( >> '!001', 'HID', lambda: HID('!001'), >> '!002', 'HID', lambda: HID('!002'), >> ... >> ) >> >> >> suggestion on chimera2, if you are going to use keyboard shortcuts I would recommend changing the ordering so the description is the last item. This makes it easier to read because the text and def tend to be 2-6 characters so the columns line up, and the descriptions lengths are hi;ghrange from 3-30 characters. >> >> Matthew Dougherty >> National Center for Macromolecular Imaging >> Baylor College of Medicine >> ________________________________________ >> From: Tom Goddard >> Sent: Tuesday, December 31, 2013 12:26 PM >> To: Dougherty, Matthew T >> Subject: Re: [Chimera-users] keyboard shortcuts >> >> There is no way to fetch the last keyboard shortcut typed. But you can achieve the same thing with the code I gave in the previous message. >> >> Tom >> >> >> On Dec 31, 2013, at 2:06 AM, "Dougherty, Matthew T" wrote: >> >>> Hi Tom, >>> >>> attached is what I am doing now. >>> >>> >>> Would like to do this instead >>> >>> def register_accelerators(): >>> accelerators = [ >>> ('!001',HID,'HID'), >>> ('!002',HID,'HID'), >>> ('!003',HID,'HID'), >>> ('!004',HID,'HID'), .... >>> >>> >>> def HID(): >>> get keyboard shortcut text string >>> call Matt's def passing the text string >>> matt's def is part of another chimera extension TBD >>> >>> >>> >>> >>> Matthew Dougherty >>> National Center for Macromolecular Imaging >>> Baylor College of Medicine >>> ________________________________________ >>> From: Tom Goddard >>> Sent: Monday, December 30, 2013 2:21 PM >>> To: Dougherty, Matthew T >>> Cc: chimera-users(a)cgl.ucsf.edu >>> Subject: Re: [Chimera-users] keyboard shortcuts >>> >>> Hi Matt, >>> >>> I don't understand your question. Is the idea that you want to register a single keyboard shortcut handler that handles many different shortcuts and takes the two-letter shortcut characters as an argument? You would still need to register that function for every set of shortcut keys it handles. You could do something like >>> >>> from Accelerators import add_accelerator as add >>> add('pq', 'Here is a description of what this shortcut does', lambda: myHandler('pq')) >>> >>> The "lambda" business is Python code that creates a function, in this case taking no arguments. And in this example it calls the funtion myHandler with argument "pq". >>> >>> Tom >>> >>> >>> >>> On Dec 27, 2013, at 4:56 PM, "Dougherty, Matthew T" wrote: >>> >>>> I am writing a bunch of USB-HID keyboard shortcuts for some extensions I am writing. >>>> >>>> Usually one shortcut per def. Since my decoding of HID is integrally tied to the extension, I would like to simplify all my shortcuts coming from one device to one def. >>>> >>>> As of now if I have 100 button commands I have to 1) register 100 shortcuts, 2) create 100 defs, 3) do corresponding stuff in my extension. >>>> I would prefer to call one def that passes the actual keyboard string to my extension, thereby simplifying my user accelerators to just registration. >>>> >>>> How do I get the string within my keyboard shortcuts python file? >>>> >>>> thanks, >>>> >>>> >>>> Matthew Dougherty >>>> National Center for Macromolecular Imaging >>>> Baylor College of Medicine >>>> _______________________________________________ >>>> Chimera-users mailing list >>>> Chimera-users(a)cgl.ucsf.edu >>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>> >>> >>> <USB-HID-D5.py> >> >> > >

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writing in b-factor field
by MARIA VITTORIA CUBELLIS 30 Dec '13

30 Dec '13

Dear sir/madam, I have a file that associates to each amino acid of a protein A a given value v. I would like to transfer this value to the b-factor field of the protein A the value v. I have a single value for each aminoacid N1,N2... I would like to transfer the value to each atom let say N1 C v1 N1 CO v1 N1 N v1 .... .... N2 C v2 N2 CO v2 N2 N v2 and so on is it possible to this withe chimera? thank you mvcubellis

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volume rendering & histogram
by Dougherty, Matthew T 26 Dec '13

26 Dec '13

Hi, I was trying to develop an HID for volume rendering. How do I get access using python to the color and density values. I would like to read them and modify their values for color and threshold. I also would like to read the values for the histogram. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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Re: [chimera-dev] creating an extension
by Conrad Huang 09 Dec '13

09 Dec '13

Sorry for the terse message, Matt. The link is to how Chimera dialogs are initialized in extensions and the example only uses Tkinter widgets. For a new extension, I would follow the example template but use Pmw widgets in place of the Tkinter ones. Tkinter widgets tend to be very basic and you have to do a lot of work to get even simple layouts. Pmw widgets (built on top of Tkinter) have more options and require less coding. I really like their documentation (http://pmw.sourceforge.net/doc/index.html) and generally just use the reference manual pages which contain working example code at the bottom. Conrad On 12/9/2013 3:10 PM, Dougherty, Matthew T wrote: > Hi Conrad, > > Thanks for the link. Not clear on what is going here. You suggest > PMW, but the link involves tkinter. Not that familiar with pmw or > tkinter, their overlap or integration. Make sure I am correct on > this, the link is non pmw? My inclination is to go pmw, at the same > want to go with the overall programming methods. > > Matthew Dougherty National Center for Macromolecular Imaging Baylor > College of Medicine ________________________________________ From: > Conrad Huang [conrad(a)cgl.ucsf.edu] Sent: Monday, December 09, 2013 > 12:45 PM To: Dougherty, Matthew T; chimera-dev(a)cgl.ucsf.edu Subject: > Re: [chimera-dev] creating an extension > > Personally, I would just stick with a standard Python GUI like Pmw. > There's example code that work and it's well documented. Perhaps > http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/Main_Extensi… > > might help. > > Conrad > > On 12/7/2013 3:03 PM, Dougherty, Matthew T wrote: >> Hi, >> >> I am trying to create a simple extension that has a column of >> buttons (qty 10-20) having a corresponding column of user defined >> text blocks. When I push a button, the corresponding text string >> will be read and processed as a command string (eg, "reset >> default", "rock X 3", "move Z 2000") >> >> I started with VolumePlanes and whittled it down to the nub to >> figure out what it was doing relative to what I want; below. I am >> realizing the buttons defined by this example extension uses some >> specific chimera GUI strategies. My going with a row of buttons >> would work as in this volumeplanes example, but is second >> preference on layout. More visually intuitive to have it side by >> side. Not sure this is possible with another dozen lines of code, >> or if I would need to go about it another route using different >> CGLTk api's and scrap using this volumeplane extension as a boiler >> plate. >> >> >> So I am realizing that this is putting me into the intricacies of >> CGLtk. An alternate would be to go with std python gui code. I >> also know you are reinventing chimera, one reason being the tk >> libraries, which opens up a third approach. So I am at a crossroad >> as to how to proceed. Because the code is relatively small, a >> rewrite for chimera2 does not seem an issue. Also there are some >> issues with parenting I am unfamiliar with (eg, t.withdraw(), >> columnconfigure). >> >> I am thinking this might be a good example of an extension for a >> beginner, so writing it as such might be useful for others. >> Particularly for new developers trying to sort out the boundaries >> between python, chimera, tk, and the extension linkages. >> >> Need some direction as to which way to go for the least amount of >> work of coding. >> >> thanks, >> >> Matthew Dougherty National Center for Macromolecular Imaging >> Baylor College of Medicine >> >> >> =========== >> >> # >> ----------------------------------------------------------------------------- >> >> > >> import chimera >> from chimera.baseDialog import ModelessDialog import >> ButtonCommands >> >> # >> ----------------------------------------------------------------------------- >> >> > >> class Button_Commands_Dialog(ModelessDialog): >> title = 'Button Commands' name = 'button commands' buttons = >> ('C1', 'C2', 'C3','Close',) >> >> # >> --------------------------------------------------------------------------- >> >> > >> # > --------------------------------------------------------------------------- >> > def fillInUI(self, parent): t = parent.winfo_toplevel() >> self.toplevel_widget = t t.withdraw() >> >> parent.columnconfigure(2, weight = 2) >> >> from CGLtk import Hybrid >> >> ps = Hybrid.Scale(parent, 'Cmd1', 0, 10, 1, 0) ps.frame.grid(row = >> 2, column = 0, sticky = 'ew') >> >> ps.callback(self.change_plane_cb) >> ps.entry.bind('<KeyPress-Return>', self.change_plane_cb) self.plane >> = ps >> >> def change_plane_cb(self, full_size = False): return >> >> # >> --------------------------------------------------------------------------- >> >> > >> # > --------------------------------------------------------------------------- >> > def C1(self): c_1='echo c1' chimera.runCommand(c_1) >> >> def C2(self): c_2='echo c2' chimera.runCommand(c_2) >> >> def C3(self): c_3='echo c3' chimera.runCommand(c_3) >> >> # >> ----------------------------------------------------------------------------- >> >> > >> def Button_Commands_dialog(create = False): >> from chimera import dialogs return >> dialogs.find(Button_Commands_Dialog.name, create=create) >> >> # >> ----------------------------------------------------------------------------- >> >> > >> def show_button_commands_dialog(): >> from chimera import dialogs return >> dialogs.display(Button_Commands_Dialog.name) >> >> # >> ----------------------------------------------------------------------------- >> >> > >> from chimera import dialogs >> dialogs.register(Button_Commands_Dialog.name, >> Button_Commands_Dialog, replace = True) >> >> _______________________________________________ Chimera-dev >> mailing list Chimera-dev(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev >> >

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Re: [chimera-dev] apple events
by Tom Goddard 09 Dec '13

09 Dec '13

Maybe Apple events can be used to pass events between apps. I don't know. We do cross-platform code development (Windows, Mac, Linux), so we rarely are interested in mechanisms only available on Mac, and we know little about those. Tom On Dec 9, 2013, at 2:51 PM, "Dougherty, Matthew T" wrote: > Hi Tom, > > Just surveying possibilities. > > Thought apple events may be a way to pass events between apps. Currently using keyboard short cuts, thought this might be useful as another conduit of control. > > > > Matthew Dougherty > National Center for Macromolecular Imaging > Baylor College of Medicine > ________________________________________ > From: Tom Goddard [goddard(a)sonic.net] > Sent: Monday, December 09, 2013 4:41 PM > To: Dougherty, Matthew T > Cc: chimera-dev(a)cgl.ucsf.edu > Subject: Re: [chimera-dev] apple events > > Hi Matt, > > The Apple event code in Chimera I believe handles when a user drags a file onto Chimera. That is received as an Apple event and Chimera opens the file in response. Don't know what other Apple events might be interesting to handle. > > Tom > > > On Dec 6, 2013, at 11:34 AM, "Dougherty, Matthew T" wrote: > >> I was nosing around the code and I noticed something about an apple events handler. >> >> Wondering if this be applied to some of my development. >> >> Could you elaborate on its current use and potential application? >> >> >> Matthew Dougherty >> National Center for Macromolecular Imaging >> Baylor College of Medicine >> _______________________________________________ >> Chimera-dev mailing list >> Chimera-dev(a)cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev >> > >

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apple events
by Dougherty, Matthew T 09 Dec '13

09 Dec '13

I was nosing around the code and I noticed something about an apple events handler. Wondering if this be applied to some of my development. Could you elaborate on its current use and potential application? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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creating an extension
by Dougherty, Matthew T 09 Dec '13

09 Dec '13

Hi, I am trying to create a simple extension that has a column of buttons (qty 10-20) having a corresponding column of user defined text blocks. When I push a button, the corresponding text string will be read and processed as a command string (eg, "reset default", "rock X 3", "move Z 2000") I started with VolumePlanes and whittled it down to the nub to figure out what it was doing relative to what I want; below. I am realizing the buttons defined by this example extension uses some specific chimera GUI strategies. My going with a row of buttons would work as in this volumeplanes example, but is second preference on layout. More visually intuitive to have it side by side. Not sure this is possible with another dozen lines of code, or if I would need to go about it another route using different CGLTk api's and scrap using this volumeplane extension as a boiler plate. So I am realizing that this is putting me into the intricacies of CGLtk. An alternate would be to go with std python gui code. I also know you are reinventing chimera, one reason being the tk libraries, which opens up a third approach. So I am at a crossroad as to how to proceed. Because the code is relatively small, a rewrite for chimera2 does not seem an issue. Also there are some issues with parenting I am unfamiliar with (eg, t.withdraw(), columnconfigure). I am thinking this might be a good example of an extension for a beginner, so writing it as such might be useful for others. Particularly for new developers trying to sort out the boundaries between python, chimera, tk, and the extension linkages. Need some direction as to which way to go for the least amount of work of coding. thanks, Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine =========== # ----------------------------------------------------------------------------- import chimera from chimera.baseDialog import ModelessDialog import ButtonCommands # ----------------------------------------------------------------------------- class Button_Commands_Dialog(ModelessDialog): title = 'Button Commands' name = 'button commands' buttons = ('C1', 'C2', 'C3','Close',) # --------------------------------------------------------------------------- # --------------------------------------------------------------------------- def fillInUI(self, parent): t = parent.winfo_toplevel() self.toplevel_widget = t t.withdraw() parent.columnconfigure(2, weight = 2) from CGLtk import Hybrid ps = Hybrid.Scale(parent, 'Cmd1', 0, 10, 1, 0) ps.frame.grid(row = 2, column = 0, sticky = 'ew') ps.callback(self.change_plane_cb) ps.entry.bind('<KeyPress-Return>', self.change_plane_cb) self.plane = ps def change_plane_cb(self, full_size = False): return # --------------------------------------------------------------------------- # --------------------------------------------------------------------------- def C1(self): c_1='echo c1' chimera.runCommand(c_1) def C2(self): c_2='echo c2' chimera.runCommand(c_2) def C3(self): c_3='echo c3' chimera.runCommand(c_3) # ----------------------------------------------------------------------------- def Button_Commands_dialog(create = False): from chimera import dialogs return dialogs.find(Button_Commands_Dialog.name, create=create) # ----------------------------------------------------------------------------- def show_button_commands_dialog(): from chimera import dialogs return dialogs.display(Button_Commands_Dialog.name) # ----------------------------------------------------------------------------- from chimera import dialogs dialogs.register(Button_Commands_Dialog.name, Button_Commands_Dialog, replace = True)

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Re: [chimera-dev] Chimera/Python sparse matrices
by Greg Couch 06 Dec '13

06 Dec '13

On 8/13/2010 12:06 PM, Forbes J. Burkowski wrote: > What are the steps that need to be taken if the Python used in Chimera is > to have the ability to import functions from SciPy or PySparse? > > Thanks for any advice that you can provide. > > Cheers, > Forbes Burkowski If you want to use prebuilt SciPy binaries with chimera, you need one that is compatible with the version of chimera that chimera is using. Chimera 1.4.x uses Python 2.5, and the daily builds use Python 2.7. You would add those packages to chimera by either (1) given the '--pypath dir' command line option, (2) setting your CHIMERAPTH environment variable (instead of PYTHONPATH, PYTHONPATH is ignored so chimera won't be accidentally broken by other installed Pythons), or (3) add the installation directory to sys.path in Python. If you're not using a daily build on Linux, then you should edit CHIMERA/share/chimeraInit.py and comment out or remove the part that sets the RTLD_GLOBAL flag -- it appears to be no longer needed and its presence breaks SciPy. If you're going to compile from source, which you'll need to do if you're using a daily build, I'd recommend trying PySparse first, since it is a smaller package. Python packages that incorporate C (or C++ or Fortran) code are more difficult than prebuilt binaries because (a) you need a compiler, and (b) if the code calls the Python C API, you need a compatible compiler, ideally the same one as what the rest of Chimera was build with. PySparse needs BLAS and LAPACK libraries and optionally wants UMFPACK and/or SuperLU. On on Redhat and Fedora Linux, you can get the first three libraries by installing the blas-devel, lapack-devel, and suitesparse-devel packages. Chances are you'll be able to install PySparse into chimera's python by running "CHIMERA/bin/pythonXXX setup.py install" in the pysparse source tree (where CHIMERA is the path to where chimera was installed). On Linux, you might have to set the LD_LIBRARY_PATH environment variable to CHIMERA/lib. On Mac OS X, the path to the chimera binary is CHIMERA/Contents/Resources/bin/pythonXXX and the environment variable is DYLD_LIBRARY_PATH. Or you could install PySparse into another Python and use the --pypath/CHIMERAPATH/sys.path approach as given above. Hope this helps, Greg

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Numpy multiarray import problem
by Mateusz Dobrychłop 05 Dec '13

05 Dec '13

Dear Chimera Team, I am working on my own Chimera Extension. After succesful installation of BioPython using Chimera's Python copy, I've encountered another BioPython - related problem, that is also related to the numpy library. I'm trying to import something from the BioPython library, and BioPython is trying to import from numpy. I recieve a following error: RuntimeError: module compiled against API version 8 but this version of numpy is 7 ... File "/home/mateusz/pyry4.4/Modules/Trans/ComponentRepresentation.py", line 6, in <module> from Bio.PDB import PDBParser, PDBIO, NeighborSearch File "/home/mateusz/.local/UCSF-Chimera64-1.8.1/lib/python2.7/site-packages/Bio/PDB/NeighborSearch.py", line 10, in <module> from Bio.KDTree import KDTree File "/home/mateusz/.local/UCSF-Chimera64-1.8.1/lib/python2.7/site-packages/Bio/KDTree/__init__.py", line 10, in <module> from KDTree import KDTree File "/home/mateusz/.local/UCSF-Chimera64-1.8.1/lib/python2.7/site-packages/Bio/KDTree/KDTree.py", line 20, in <module> from Bio.KDTree import _CKDTree <type 'exceptions.ImportError'>: numpy.core.multiarray failed to import I tried to install numpy the same way I installed BioPython (using Chimera's Python copy), but this does not solve the problem. I also tried to import numpy.core.multiarray directly in Chimera's IDLE and it did import. I'm using Chimera 1.8.1 on Ubuntu 12.10 (64 - bit). Is there anything I can do to make it work? Best wishes, Mateusz

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Re: [chimera-dev] camera positions
by Tom Goddard 05 Dec '13

05 Dec '13

Hi Matt, Take a look at the _savePosition() routine in chimera/share/Midas/__init__.py that defines the contents of each position: return ( viewer.scaleFactor, viewer.viewSize, cam.center, cam.nearFar, cam.focal, xforms, clips, om.cofrMethod, cofr, viewer.clipping, cam.fieldOfView, ) These are the fields you see in the session file. Notice it has the camera focal plane position (cam.focal) but no eye separation parameter. Tom On Dec 5, 2013, at 5:09 AM, "Dougherty, Matthew T" wrote: > Hi Tom, > > I was looking at a typical savepos as it is saved as a session file, below > > Can you tell me how to interpret it contents? Trying to understand what parameters are kept. > > > Matthew Dougherty > National Center for Macromolecular Imaging > Baylor College of Medicine > > > > def restoreMidasBase(): > formattedPositions = {'cPos': (1.0, 5.706403395613076, (105.314, 50.822, 41.951), (43.72859999036789, 40.17340000963211), 41.951, {(0, 0): ((0.0, 0.0, 0.0), (0.0, 0.0, 1.0, 0.0))}, {(0, 0, 'Molecule'): (False, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, False, 5.0)}, 4, (105.314, 50.822, 41.951), False, 7.8352333034904085)} > import Midas > Midas.restoreMidasBase(formattedPositions) >

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Chimera-dev December 2013