January 2014 - Chimera-dev - RBVI Mailing Lists

cd command
by Dougherty, Matthew T 24 Jan '14

24 Jan '14

can you tell me where the chimera command "cd" python code is located? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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session callback
by Dougherty, Matthew T 24 Jan '14

24 Jan '14

I was wanting to execute some code during quit session, close session, and save session; priority on quit. Is this going to be straight forward, such as registering a callback? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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Moving atoms from HETATM to ATOM entries
by Jean-Didier Maréchal 24 Jan '14

24 Jan '14

Dear all, I am working with some chemically modified residues. For consistency with MMTK, I have to move non-natural atoms in the ATOM list of the pdb. I would like to do that directly from chimera and not editing the pdbfile. I thought that I could alter the heteroatom value of chimera's residues to get there. But whether this is not the right attribute or I miss something. What I do is: build my system, select the atoms of the non-natural and natural part of the residue. Make a new residue and then, having selected it: atoms=chimera.selection.currentAtoms() for a in atoms: a.residue.isHet=False This indeed changes the isHet attribute but when saving the pdb, the residue is in the HETATM field. Any pointer? Best, JD **************************** Dr. Jean-Didier Maréchal Associate Professor The Computational Biotechnological Chemistry Team Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es www: http://g <http://asklipio.qf.uab.es>ent.uab.cat/jdidier<http://ent.uab.es/jdidier>

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pointers
by Dougherty, Matthew T 13 Jan '14

13 Jan '14

Hi, I am trying to track down some variables to develop some methods, and need some direction as to locations and practical options. 1) where do I find the name of the session variable? I want to build in organizational structure for the session files and data files in regards to project management. 2) the pull down menus change depending on the dialog that is the focus. Usually it is volume viewer and main window. Is there a way to lock in the main viewer pull down menu? would prefer that to be constant. 3)sometimes I need to transfer a session, or receive a session from somebody. If the session only uses pdb files I am ok. If there are mrc files involved, then they have to be located, bundled, transferred, and linkages repaired. I would like to get a list of all the extraneous data files that the session uses, and copy all those files into a single folder, that is usually on a thumb drive. So I would need to develop sw to locate those files, copy them as an aggregate along with the session file. 4) for S3D, is the focal plane the same thing as the convergence plane, or is it the screen plane? Is everything that is close to the camera is negative parallax, focal plane is zero parallax, everything behind is positive parallax? 5) I have a number of related animations using different session files. Usually I will create a core session, with the other files having small variants (eg, inclusion of different pdb or vrml files). Each session file produces a clip, each session file has a corresponding command file that sequences the positions, and other animation components. The end of clip1 is the beginning point for clip2, etc. Passing positions between session files is the problem. How do I export a position so as to import it into another session file? 6) I need to animate the lighting. I get the impression lighting is relative to the camera, but it could be to the origin, or to the aggregate of the models, or to the clipping planes, etc. not sure on this. It does not appear to be saved as part of the savepos command. I have dug into the lighting code and can move the lights around using the HID tools I am creating. What would be the best or viable or quickest approach to animate the lights? Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

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Re: [chimera-dev] Chimera python packaging
by Tom Goddard 08 Jan '14

08 Jan '14

Hi Thomas, Packaging all the libraries needed by PyTom like Chimera does it is a lot of work. For Chimera we build from source and include about 40 third-party libraries and programs (like Python, numpy, hdf5, PIL, ffmpeg, …) on Windows, Mac and Linux in 32-bit and 64-bit versions. The Chimera build and packaging system is just Makefiles we wrote, a system that has probably taken about 1 programmer-year to develop and maintain. Even though it is a lot of work, if you want to people to use your software you have to package it for an easy install. Requiring people to compile or install a dozen required packages will reduce your number of users I'd say by 10 to 100-fold. It looks like for PyTom you have about 10 required libraries and support Linux and Mac but not Windows. Probably distributing just 64-bit would be fine -- since that is needed for big data sets. There are plenty of problems trying to package these all up. Here are a few that come to mind. Your build machine may have libraries that your users will not have and when you compile third party libraries they may link against those. For instance, fftw might see that you have a blas system library and compile for it. So you often have to tell packages not to use such libraries. Sometimes no configure flag is available and we patch the third party build scripts. On Linux we only rely on Linux Standard Base (LSB) libraries. Common libraries like tiff, zip, jpeg are ones to look out for. On both Linux and Mac you'll need to tell your executables where to find the included shared libraries. We use environment variables (LD_LIBRARY_PATH, DYLD_LIBRARY_PATH on Mac) which means are exectutables shell scripts that set the environment variables and then start the real executable. The paths have to be relative paths since the user could install your package anywhere. On the Mac there are also Frameworks to worry about. We build Python as a Mac Framework, but maybe you would find it easier to instead use the non-framework version since that will be like Linux. You of course have to build on old versions of Mac and Linux operating systems if you want compatibility with older operating systems. For instance we build Mac Chimera on Mac OS 10.6 even though 10.9 is the current release. It is a pain to keep machines with old operating systems running. It is possible to compile on a newer operating system targeting an older operating system but we find it easier just to use the old operating system. Even with that compatibility among different Linux distributions was a bit of a nightmare in the past. I'm not sure if is still troublesome. You should make sure the licenses for the libraries you want to redistribute allow that. You'll have trouble using GPL libraries if you distribute any libraries that are not open source. This only scratches the surface of the long list of problems we have dealt with in building third-party libraries, packaging and distributing them. Tom On Jan 8, 2014, at 10:59 AM, Thomas Hrabe wrote: > Hi Tom, > > I am looking for ways to ship my old software pytom (pytom.org) in a way similar to chimera. > > Meaning that I want to add all required dependencies such as python, numpy, … to the whole package and ship the compiled version. > Is there anything I have to look out for, especially for the python? > How do you automate daily builds and all that? Do you use an integration server like jenkins? > > Thank you for your support, > Thomas > > > ---------------------------------- > > Thomas Hrabe (Ph.D.) > Sanford-Burnham > Medical Research Institute > 10901 North Torrey Pines Road > La Jolla, CA 92037, USA > +1 858 646 3100 ext 4070 > > > > > >

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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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Chimera-dev January 2014