March 2013 - Chimera-dev - RBVI Mailing Lists

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

4 3

3dconnexion
by Dougherty, Matthew T 03 Apr '13

03 Apr '13

Hi, I am starting to build a matrix of USB HID devices using controllermate on a mac. I am planning to use two 3dconnexion devices. one to handle 6D translation/rotation, and the other to manage color/lighting; or maybe left hand for trans and right for rotation, etc. . The current driver in chimera only sees one device. If I touch the first USB 3dconnexion device plugged in, it behaves as expected. Touching the second device, chimera acts as though it is the first device. So the driver is not keeping track of the number of devices. In controllermate I can see both devices and can program them independently. For example, I will be able to remap these signals to my choosing and pass it on to a chimera extension I am developing. The second problem I am having is when chimera starts up it exclusively grabs the low level driver, ignoring the the high level driver which incorporates context management. Consequently controllermate is unable to intercept and modify the signal before passing it on. A good reason to do this would be creating deadband zones, or a user defined response curve, or integration with multibutton panel like the logitech g13 so that I can modulate the response (eg, 0.1x,1x,10x,100x, etc). How do I disable 3dConnexion so that it will not load in chimera? I could wipe out the code, but would prefer minimally screwing with chimera base code which is a headache for daily builds and has a risk factor of unforeseen consequences. Something in preferences would be helpful. In a related question on preferences, the scroll wheel is tied to camera zoom. I would like to remap that as a movement in z. Generally I like to keep my scale factor at 1; I find heavy or casual use tends to get me into camera problems. Is this possible? at the moment I disable the scroll wheel. Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine

3 6

changing position for a residue using python
by Jean-Didier Maréchal 27 Mar '13

27 Mar '13

Hi all, I have a problem with a prot and it seems that renumbering could help. I'd like to automatically add 230 to the residue number of the aa of my second chain. As I feared, when looping other residue to change res.id.position, my script fails as position can not be modified. How could I do this? Should I delete position and re-create it? Best JD

4 3

Re: [chimera-dev] [Chimera-users] Import Chimera Modules
by Tom Goddard 18 Mar '13

18 Mar '13

Hi Jon, I'm switching this discussion to the chimera developer mailing list since it is so technical. I'm wondering why you want to run Chimera in your own Python. Often people want that so they can install their own custom Python modules and use them with Chimera. We recommend just using the Chimera Python for that and installing your other modules into the Chimera Python. That saves you a lot of grief trying to do what you did -- set up the environment to get Chimera to start in another Python. Tom -------- Original Message -------- Subject: Re: [Chimera-users] Import Chimera Modules From: Jonathan Williams To: Tom Goddard Date: 3/18/13 2:37 PM > Hi Tom, > > Good news: I got the chimera modules to import! > > I think that you were correct about having an older > libfreetype.6.dylib that was being used instead of Chimera's version, > probably from my Enthought Python Distribution . Overall I believe > that my EPD was making things harder for me. So I removed the EPD > from my system, set all of the environment variables per the Chimera > IDLE, added ~/Resources/lib and ~/Resources/share to PYTHONPATH, and > now I'm in business. > > Thank you for your help and suggestions! > > Jon > > > On Mar 18, 2013, at 12:49 PM, Tom Goddard <goddard(a)sonic.net > <mailto:goddard@sonic.net>> wrote: > >> Hi Jon, >> >> Chimera includes the version of libfreetype.6.dylib it needs. The >> error must mean you have another older libfreetype.6.dylib on your >> system that Chimera is getting instead of its own version. The first >> thing would be to try to locate where the other libfreetype.6.dylib >> is. I guess Chimera starts on your machine, so somehow it gets the >> right library. That suggests that you do not have the environment >> variables that control library loading setup in the same way as >> Chimera does. I'd suggest you start Chimera, open the IDLE shell >> window (Tools / General Controls) and print all the environment >> variables seen by the running Chimera using for example >> >> import os >> for k,v in os.environ.items(): >> print k,v >> >> and see if those differ from what you are trying outside Chimera. >> >> Tom >> >> >> >> -------- Original Message -------- >> Subject: Re: [Chimera-users] Import Chimera Modules >> From: Jonathan Williams >> To: Tom Goddard >> Date: 3/18/13 8:05 AM >>> Hi Tom, >>> >>> Thanks for the response. I set the DYLD_FALLBACK_LIBRARY_PATH >>> variable, and I think this took care of my original problem. >>> However I have encountered a new error: >>> >>> ImportError: >>> dlopen(/Applications/Chimera.app/Contents/Resources/lib/_chimera.so, >>> 2): Library not loaded: @executable_path/../lib/libfreetype.6.dylib >>> Referenced from: >>> /Applications/Chimera.app/Contents/Resources/lib/_chimera.dylib >>> Reason: Incompatible library version: _chimera.dylib requires >>> version 15.0.0 or later, but libfreetype.6.dylib provides version 13.0.0 >>> >>> This seems like I just need to update my FreeType libraries, but I >>> have not had a chance to try this yet. If you have any other >>> suggestions, those would be appreciated, otherwise I'll send an >>> update when I get a chance. >>> >>> Thanks again, >>> >>> Jon >>> >>> >>> On Mar 15, 2013, at 7:02 PM, Tom Goddard <goddard(a)sonic.net >>> <mailto:goddard@sonic.net>> wrote: >>> >>>> Hi Jon, >>>> >>>> Maybe the trick is Chimera uses environment variable >>>> DYLD_FALLBACK_LIBRARY_PATH instead of LD_LIBRARY_PATH or >>>> DYLD_LIBRARY_PATH. Here's the Chimera Mac start-up C++ code that >>>> sets the environment variables >>>> >>>> http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/dist/mac/chimera-aqua.… >>>> >>>> and a comment on this code change says "Use >>>> DYLD_FALLBACK_LIBRARY_PATH instead of DYLD_LIBRARY_PATH, so >>>> system frameworks will get system versions of shared libraries." >>>> >>>> Tom >>>> >>>> >>>> >>>> On Mar 15, 2013, at 2:49 PM, Jonathan Williams wrote: >>>> >>>>> Hello, >>>>> >>>>> I am currently trying to import Chimera modules into a non-Chimera >>>>> python installation. I have referenced previous messages from >>>>> this mailing list >>>>> (http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003620.html) >>>>> and have added the relevant paths to Chimera in the >>>>> LD_LIBRARY_PATH, PYTHONPATH, and CHIMERA environment variables. >>>>> >>>>> However when I try to import Chimera, Midas or "import >>>>> chimeraInit" followed by "chimeraInit.init([])" I receive the >>>>> following error: >>>>> >>>>> >>> import chimeraInit >>>>> >>> chimeraInit.init([]) >>>>> Traceback (most recent call last): >>>>> File "<stdin>", line 1, in <module> >>>>> File >>>>> "/Applications/Chimera.app/Contents/Resources/share/chimeraInit.py", >>>>> line 594, in init >>>>> import chimera >>>>> File >>>>> "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", >>>>> line 16, in <module> >>>>> from _chimera import BBox, Camera, Color, ColorGroup, >>>>> DirectionalLight, LODControl, Lens, LensViewer, Light, Material, >>>>> MaterialColor, Model, NoGuiViewer, OGLFont, OSLAbbreviation, >>>>> OpenModels, OpenState, PathFinder, PixelMap, Plane, Point, >>>>> PositionalLight, Selectable, SharedState, SpotLight, Sphere, >>>>> Texture, TextureColor, TrackChanges, Vector, Viewer, X3DScene, Xform >>>>> ImportError: >>>>> dlopen(/Applications/Chimera.app/Contents/Resources/lib/_chimera.so, >>>>> 2): Symbol not found: __cg_TIFFClientOpen >>>>> Referenced from: >>>>> /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO >>>>> Expected in: >>>>> /Applications/Chimera.app/Contents/Resources/lib/libTIFF.dylib >>>>> in /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO >>>>> >>> >>>>> >>>>> I am using MacOSX 10.8.2, Python 2.7.3, and Chimera 1.7 (build >>>>> 38197) for 64bit Mac. >>>>> >>>>> Any help or advice would be greatly appreciated, >>>>> >>>>> Jon Williams >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Chimera-users mailing list >>>>> Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>>> >>> >> > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

1 0

Following on new atom types (again)
by Elisabeth Ortega 18 Mar '13

18 Mar '13

Dear Chimera dev. Team, I'm trying to do the same as JD. The message that I receive is when I try to minimize is "Element Pt (atom #0.1.A@PT1) is not currently supported". As Mr Pettersen told me before, I defined the parameters of PT in heme-iron.frcmod file in ../bin/amber/dat/leap/parms and I also defined the "pt" atom in the MMTK Database. Then I added the charges without the covalent bond between the PT and its neighbours and finally I try to minimize with and without the bonds. Nothing happens. Probably I'm modifying the wrong files... Then, I have other question to you regarding the IDAM Type. When I minimize, the N3 atoms become N3+. How can I change it? Thank you so much for your time and your patience. -- Elisabeth Ortega Carrasco, Ph.D. Student Molecular Modelling of Transition Metal Systems Group Lab. C7/153, Chemistry Department Universitat Autonoma de Barcelona Tel.: +34935812857 email.: ortega.elisabeth(a)qf.uab.cat

3 2

Following on new atom types.
by Jean-Didier Maréchal 15 Mar '13

15 Mar '13

Hi, I am following on Elisabeth's question on the 23rd of january regarding setting up new atoms. I have added platinum (for cisplatinum) as a new atom type and proceed as you recommended (calculate the charge on isolated species and generate the covalent bond for the first coordination sphere of the metal). I have though two questions: 1. when running the minimization I have the following message: Atom whose IDATM type has no equivalent Sybyl type: #-2147483648.-2147483648:1@PT1-CPT (type: Pt) Although the minimization still proceed, I'd like to do things right. Could you tell me where I could change the sybyl atomtype. I looked with the idle the idatmType of this atom and it gives me Pt+. I don't understand what is wrong. 2. I'd like to rapidly change the charges of the cisplatinum using charges calculated with ab initio calculations. I was thinking to change these values from the idle changing the charge attribute previous to minimization. Does it sound correct? What would be the easiest way you would reckon? Best regards, JD **************************** Dr. Jean-Didier Maréchal Associate professor The Computational Biotechnological Chemistry Team Unitat de Química Física 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>

3 3

Chimera binary code issue
by jupiter 13 Mar '13

13 Mar '13

Hi, I have been reading Chimera document on Chimera web site and I am understanding that Chimera is better to run with hardware accelerator, but we don't have GPUs in our virtual machines, we have to use mesa and we are using xlib-glx driver for remote VNC connection. One major issue I am currently investigating is that the binary Chimera code can perform 3D rotation in mesa DRI driver, but very poor performance when using mesa xlib-glx driver on CentOS 6. Please correct me my following assumptions and options to rectify the problem: (1) Binary code could be hard linked with mesa DRI driver, the solution is to remove the hard link, or replace some libraries. (2) Chimera may not be able to run on mesa xlib-glx driver at all, no possible workarounds, no solution. (3) Chimera can be used with xlib-glx driver if we can build Chimera source code with mesa xlib-glx driver. I understand you don't encourage people to build Chimera from source code, nor do I wish. But if that is the only choice which can fix the problem, would you please point me instructions and procedures how to build the source code on Linux? I've looked at README.bootstrap from svn source code, but Thank you. Kind regards. Jupiter

3 7

neighbors
by Elisabeth Ortega 12 Mar '13

12 Mar '13

Dear Chimera Dev. Team, There is any way to select the neighbors of a selected atom without drawing the bond? If it is not possible... could you tell me how draw and erase bonds using a python function? Thank you for your time. -- Elisabeth Ortega Carrasco, Ph.D. Student Molecular Modelling of Transition Metal Systems Group Lab. C7/153, Chemistry Department Universitat Autonoma de Barcelona Tel.: +34935812857 email.: ortega.elisabeth(a)qf.uab.cat

2 1

2-D projection of volume in Chimera
by Jesus Montoya 04 Mar '13

04 Mar '13

Hi, Is there a way to project a 3-D volume into a single 2-D image plane in Chimera? For example, I want to load a volume twice into Chimera and view the two copies side by side in an identical orientation (manually set by rotating the volumes with the mouse). Then, I want to view one of them as a 2-D projection along the axis that comes out of the screen. While a "solid" representation of the volume is similar, it is not exactly what I need... Thanks!

3 2