- Chimera-dev - RBVI Mailing Lists

chimera import from unmodified python 2.5
by Ondrej Marsalek 12 Sep '08

12 Sep '08

hello everyone, first of all, i would like to say thank you for using vanilla python 2.5, i think this could be quite useful. unfortunately, there is one problem that keeps me from using chimera from a session of my regular python 2.5 installation (on ubuntu 8.04). after setting paths properly, an attempt to import chimera (or the binary module _chimera) produces the following exception: In [1]: import chimera --------------------------------------------------------------------------- <type 'exceptions.ImportError'> Traceback (most recent call last) /home/andy/<ipython console> in <module>() /home/andy/CHIMERA/share/chimera/__init__.py in <module>() <type 'exceptions.ImportError'>: /opt/chimera/lib/libwrappy2.so: undefined symbol: PyUnicodeUCS2_AsUTF8String In [2]: import _chimera --------------------------------------------------------------------------- <type 'exceptions.ImportError'> Traceback (most recent call last) /home/andy/<ipython console> in <module>() <type 'exceptions.ImportError'>: /opt/chimera/lib/libwrappy2.so: undefined symbol: PyUnicodeUCS2_AsUTF8String it seems that the python 2.5 provided with chimera is compiled with different unicode settings than the one in ubuntu. the shared chimera objects are compiled against that version of python and therefore can't be used from my normal python. the only way i see around this at the moment is to recompile chimera, but i wanted to leave that as the very last option. i would appreciate any suggestions, as a straightforward way to use chimera from my normal python would be really neat. i'll be glad to provide details if anyone is interested. regards, ondrej marsalek

3 6

structure analysis feature in UCSF Chimera
by Serge Gorelsky 08 Sep '08

08 Sep '08

Hello, would it be possible to add the two following features to the "Tools/Structure Analysis" menu of UCSF Chimera: the distance between atom A and a plane of other 3 atoms B,C,D ("the height of a trigonal pyramid with atoms B, C, D at the base ") and the angle between an axis (defined by atoms A and B) and the plane B-C-D ? Thank you very much in advance. -- Best regards, Serge Gorelsky (a Chimera user since 2005)

2 1

Re: [chimera-dev] headless chimera issues
by Eric Pettersen 20 Aug '08

20 Aug '08

Hi James, Yes, undoubtedly in nogui mode there is no Reply Log dialog for you to access. If you are using Python, there are far more direct ways to get an atom's coordinates than using getcrd and trying to parse the reply log anyway. Such as: from chimera.selection import OSLSelection sel = OSLSelection("#0:%s.%s@CA" % (snpPos, chain)) a = sel.atoms()[0] crd = a.coord() # or a.xformCoord() for transformed coordinates I've attached a PDF of a handout from a Chimera development class we just taught here at UCSF. It covers a bunch of handy resources and tips. The first resource it lists, the Programmer's Examples, is something you should look over. They cover how Chimera's molecular data is laid out, how to deal with selections, and so forth. --Eric On Aug 20, 2008, at 9:37 AM, James A. Cleland wrote: > Ok, I ran this in chimera (gui) and I see how it is working now, the > reply contains space-separated coordinates at the end of the string > and get_coords picks these off from the end (-1, -2, -3). Perhaps > this is another “headless” issue as there is no dialog? If so, maybe > there’s somewhere else I can pick off the reply information for > getcrd? > > Thanks! > > From: James A. Cleland [mailto:jcleland@jamescleland.com] > Sent: Wednesday, August 20, 2008 12:32 PM > To: 'Eric Pettersen' > Subject: RE: headless chimera issues > > This worked like a charm, thank you! I have run into another issue > that I thought you may be able to help with. > > We are attempting to draw a pointer indicating the alpha carbon for > a particular residue. This has been done in the past, but no longer > works. This may have been something that you helped with. > > The function that is currently failing is called “get_coords()”. > Here’s what I have: > > def _get_coords(): > from chimera import dialogs, Vector > coords = Vector(0,0,0) > r = dialogs.find('reply') > text = r.text.get('1.0', 'end') > coordString = text.splitlines()[-2] > coordString = coordString.split(' ') > print coordString > coords[2] = float(coordString[-1]) > coords[1] = float(coordString[-2]) > coords[0] = float(coordString[-3]) > return cords > > Prior to calling get_coords(), there is a command executed that > seems to provide the dialog information, if I’m understanding > correctly: > > runCommand("getcrd #0:%s.%s@CA" % (snpPos, chain)) > > The line that appears to be failing in get_coords() is the fourth in > the function, r.text.get(). It looks like dialogs.find() returned > None. > > Do you have any suggestions as to how I might get these coordinates > or what we might be doing wrong? > > Thanks! > James > From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] > Sent: Tuesday, August 19, 2008 7:41 PM > To: James A. Cleland > Cc: Tom Goddard > Subject: Re: headless chimera issues > > That's right -- the patch just prevents the error. It doesn't do > the coloring. Hopefully Tom Goddard will be able to help you with > that. > > --Eric > > On Aug 19, 2008, at 4:21 PM, James A. Cleland wrote: > > Thank you for the quick reply! I applied this patch manually by just > adding the import and the condition. I had commented the conditional > statements prior to writing you and this worked fine, but the > surface model didn’t appear to be colored according to the Delphi > output. Is it correct for me to assume that, after this patch is > applied, I’m still not seeing the electrostatic potential in the > surface coloring? > > Thanks again, > James > > From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] > Sent: Tuesday, August 19, 2008 6:56 PM > To: James A. Cleland > Cc: Tom Goddard > Subject: Re: headless chimera issues > > Hi James, > That exception would be a bug -- SurfaceColor should not > be trying to bring up a dialog if Chimera is running in nogui mode. > I've committed a fix for this and it will be in tomorrow's daily > build. Here's the diff if you want to correct your version: > > *** ChimeraExtension.py 6 May 2008 04:20:05 -0000 1.12 > --- ChimeraExtension.py 19 Aug 2008 22:51:36 -0000 > *************** > *** 50,56 **** > from VolumeViewer import open_volume_file > vlist = open_volume_file(path, ftype, open_models = False, > show_data = False, > show_dialog = False) > ! if len(vlist) > 0: > from SurfaceColor.gui import show_surface_color_dialog > d = show_surface_color_dialog() > d.use_electrostatics_colormap() > --- 50,57 ---- > from VolumeViewer import open_volume_file > vlist = open_volume_file(path, ftype, open_models = False, > show_data = False, > show_dialog = False) > ! import chimera > ! if len(vlist) > 0 and not chimera.nogui: > from SurfaceColor.gui import show_surface_color_dialog > d = show_surface_color_dialog() > d.use_electrostatics_colormap() > > I've cc'ed Tom Goddard on this mail since he is the > expert on Chimera's volumetric API and can hopefully provide advice > on coloring your map programmatically. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > > On Aug 19, 2008, at 1:32 PM, James A. Cleland wrote: > > > Hi Eric, > > My name is James Cleland and I am currently working with Dr. Rachel > Karchin at JHU. I had corresponded with Greg Couch over running > Chimera without an X server and he had directed me toward a build > designed to run headless. I have been using this for a couple of > weeks without problems, but I encountered an issue the other day. > > I am trying to import a surface for electrostatic potential that was > generated using Delphi. The trouble is, this is causing an error > (see below). > > Executing test.py...Opening pdb1a01.ent... > 1 model opened > > Traceback (most recent call last): > File "/home/pipeline/chimera/share/__main__.py", line 65, in > <module> > value = chimeraInit.init(sys.argv) > File "CHIMERA/share/chimeraInit.py", line 384, in init > chimera.openModels.open(a, prefixableType=1) > File "CHIMERA/share/chimera/__init__.py", line 1345, in open > File "CHIMERA/share/chimera/__init__.py", line 787, in _openPython > File "test.py", line 15, in <module> > runCommand("open 1a01.phi") > File "CHIMERA/share/chimera/__init__.py", line 2026, in runCommand > File "CHIMERA/share/Midas/midas_text.py", line 62, in makeCommand > File "CHIMERA/share/Midas/midas_text.py", line 918, in doOpen > File "<string>", line 1, in <module> > File "CHIMERA/share/Midas/__init__.py", line 1352, in open > File "CHIMERA/share/chimera/__init__.py", line 1345, in open > File "CHIMERA/share/SurfaceColor/ChimeraExtension.py", line 55, in > open_cb > File "CHIMERA/share/SurfaceColor/gui.py", line 613, in > show_surface_color_dialog > File "CHIMERA/share/chimera/dialogs.py", line 77, in display > File "CHIMERA/share/chimera/dialogs.py", line 62, in find > File "CHIMERA/share/chimera/baseDialog.py", line 435, in __init__ > File "CHIMERA/share/chimera/baseDialog.py", line 121, in __init__ > File "CHIMERA/share/chimera/tkgui.py", line 63, in <module> > ImportError: No module named Togl > Error while processing test.py: > ImportError: No module named Togl > (see reply log for Python traceback info) > > From what I can gather, the call to open is trying to present a > dialog for choosing surface colors and limits. I’ve seen this when > running Chimera with an X server. The trouble is, I need to skip > this dialog and, possibly, specify volume in some other fashion. > > We used to use the following python code in our Chimera script: > > from chimera import openModels, MSMSModel > runCommand("set bg_color black") > surf = openModels.list(modelTypes=[MSMSModel])[0] > from VolumeViewer.volume import Volume > vol = openModels.list(modelTypes=[Volume])[0] > from SurfaceColor import color_by_volume > color_by_volume(surf, vol, (-30, 0, 30), ((1,0,0,1.0), (1,1,1,1.0), > (0,0,1,1.0))) > > This was run using an older version of Chimera and used an X server. > We ran into problems using this version with –nogui, which is what > led me to the headless version. > > I have been playing around with SurfaceColor/ChimeraExtensions.py, > specifically line 55-56, trying to figure out how to at least get > color on the surface using the default volume. It appears that, by > commenting the aforementioned lines, I get no surface coloring at all. > > Can you provide some direction for me on this? Any help is > appreciated! > > Thanks, > > James A. Cleland > (w) 1(703)392-1357 > (c) 1(703)402-5447 > jcleland(a)jamescleland.com > > >

1 0

Re: [chimera-dev] making a python package
by Eric Pettersen 14 Aug '08

14 Aug '08

Hi Bill, Greg is the real expert here, but he's at SIGGRAPH right now so I'll put out what little I know and let Greg correct anything I get wrong when he has time. Yeah, compiling/linking can be a nightmare when you are trying to use libs you have no control over and that may have been compiled with options you didn't anticipate or from modified sources. That's why we cheat and include everything we depend on (which is one reason Chimera is such a huge download). In particular, we include Tk and Tcl libraries. If you look in Chimera's "foreign" source directory, there is a TclTk subdirectory there. So no worries about out-of-date/incompatible versions and all that. We have another layer of control in that we're not (currently) trying to provide a package that other people can easily compile on their own system. So therefore we don't need a configure step. Our makefiles have conditionals based on the OS to get the right flags for linking and compiling and whatnot for the systems that we ourselves compile on. A lot of that makefile logic is concentrated in the "includable" makefiles found in the mk directory, so that individual makefiles only have to include the appropriate mk makefile and then customize a few variables themselves. We try to use "foreign" source with as little patching as possible so that we can easily incorporate updated versions, so many of the foreign packages (e.g. Tcl/Tk) do have their "native" configure step. Nonetheless, the Chimera makefile that initiates the foreign package build may supply arguments to the configure so that the final build uses the right compiler flags, uses the right build/install location, and so forth. I don't know how much help this has been, but feel free to ask more questions and maybe I'll know the answers. :-) --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Aug 14, 2008, at 11:54 AM, William Baxter wrote: > Hello Eric, > > I'm trying to make an installation package like Chimera's, in which > our > software installs its own Python. Can you explain how your > installation > package is set up? I have a script that goes through the usual > configure, make, and make install commands, but it encounters > different > problems on each platform (for us, Linux and Irix). How does the > Chimera > install make sure everything is linked together properly? > > Any help is greatly appreciated. > > Thanks, > Bill Baxter > > -- > William T. Baxter, Ph.D. > Wadsworth Center > Empire State Plaza, PO Box 509 > Albany, NY 12201-0509 > > > Subject: Re:[chimera-dev] making a python package > From: William Baxter > Date: 02:42 PM > To: Greg Couch > > > Greg, > thanks for your description. I have another couple of questions. > > My script goes through the usual configure, make, make install > commands, > but Chimera seems to go straight to compilation. How do you set it > up to > be so fast? > > Also, finding Tcl/Tk for Tkinter is a headache that seems to be > different on each platform. How do you ensure that Python finds that > right Tcl libs? > > The Chimera installation is really admirable and efficient. I'd like > to > emulate it as far as possible. > > Any advice you can give is greatly appreciated. > > Thanks, > Bill B. > > Greg Couch wrote: >>> On Wed, 30 Jul 2008, William Baxter wrote: >>> >>>>> Hello, >>>>> >>>>> we would like to package our software, Spire >>>>> (www.wadsworth.org/spider_doc/spider/docs/spire/) the way >>>>> Chimera is >>>>> packaged, with its own Python, Tcl/Tk, and other libraries. Do >>>>> you have >>>>> some documentation, or can you point me toward some resources that >>>>> explain how to go about creating such an installation package? >>>>> >>>>> Thanks, >>>>> Bill Baxter >>> >>> We don't have any documentation, but here's a quick description of >>> what we do binary distributions for chimera: >>> >>> On Windows, we use the Inno Setup program, >>> <http://www.jrsoftware.org/isinfo.php>. >>> >>> For Mac OS X, we build a disk image using the hdiutil program. >>> And we >>> modify the name all of the shared libraries with something like: >>> install_name_tool -id @executable_path/$(LIBNAME) >>> >>> On Linux and other Unix systems, we use a modified self-extracting >>> zip >>> archive where an installation program is run after the files have >>> been >>> extracted. >>> >>> In all cases, when chimera starts up, we set up the environment to >>> get >>> our shared libraries (and clear the environment of things that would >>> hurt us, like PYTHONHOME). >>> >>> Hope this helps, >>> >>> Greg Couch >>> UCSF Computer Graphics Lab > > > -- > William T. Baxter, Ph.D. > Wadsworth Center Empire State Plaza, > PO Box 509 Albany, NY 12201-0509

1 0

making a python package
by William Baxter 01 Aug '08

01 Aug '08

Hello, we would like to package our software, Spire (www.wadsworth.org/spider_doc/spider/docs/spire/) the way Chimera is packaged, with its own Python, Tcl/Tk, and other libraries. Do you have some documentation, or can you point me toward some resources that explain how to go about creating such an installation package? Thanks, Bill Baxter -- William T. Baxter, Ph.D. Wadsworth Center Empire State Plaza, PO Box 509 Albany, NY 12201-0509 IMPORTANT NOTICE: This e-mail and any attachments may contain confidential or sensitive information which is, or may be, legally privileged or otherwise protected by law from further disclosure. It is intended only for the addressee. If you received this in error or from someone who was not authorized to send it to you, please do not distribute, copy or use it or any attachments. Please notify the sender immediately by reply e-mail and delete this from your system. Thank you for your cooperation.

2 1

cElementTree broken in latest production release
by Mark Moll 10 Jul '08

10 Jul '08

Minimal example: from xml.etree.cElementTree import XML XML('<fail>') If you execute this code, you get this error: "cannot load dispath table from pyexpat" -- Mark

2 1

problem with solvate
by Jean-Didier Maréchal 19 Jun '08

19 Jun '08

Hi Guys, I tried the solvate module on the alpha build of the 15/06/2008 on windows. And I have the following error: Running sleap command: C:\Archivos de programa\Chimera2\bin\amber10\exe\sleap -f d:\docume~1\jd\config~1\temp\tmpi8eph7\solvate.cmd (solvate) [gtkleap]$ source leaprc.ff03 (solvate) Error: can not find file leaprc.ff03 in all the search path. Failure running sleap Check reply log for details I made a search of the mentioned file and it does not pop up. Cheers JD -----Mensaje original----- De: chimera-users-bounces(a)cgl.ucsf.edu [mailto:chimera-users-bounces@cgl.ucsf.edu] En nombre de chimera-users-request(a)cgl.ucsf.edu Enviado el: miércoles, 18 de junio de 2008 21:00 Para: chimera-users(a)cgl.ucsf.edu Asunto: Chimera-users Digest, Vol 62, Issue 18 Send Chimera-users mailing list submissions to chimera-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimera-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..." Today's Topics: 1. Find contour level to enclose a specified volume (Thomas Goddard) 2. Re: Find contour level to enclose a specified volume (Tom Goddard) ---------------------------------------------------------------------- Message: 1 Date: Tue, 17 Jun 2008 15:44:57 -0700 From: Thomas Goddard <goddard(a)cgl.ucsf.edu> Subject: [Chimera-users] Find contour level to enclose a specified volume To: "'Chimera BB'" <chimera-users(a)cgl.ucsf.edu> Message-ID: <48583E69.5090608(a)cgl.ucsf.edu> Content-Type: text/plain; charset="iso-8859-1" Ed Brignole asked about setting a volume contouring level so that the resulting surface encloses a desired volume (cubic Angstroms). Attached is a Python script that does this in two ways. The first way is fast but approximate finding the level such that the number of enclosed grid points times the voxel volume equals the requested volume. Estimating the enclosed volume of the surface this way can give a much different result than actually computing analytically the volume within the surface. The second approach computes surfaces at different contour levels and calculates analytically the volume. It uses bisection to find the correct contour level. This approach can be slow, about 30 seconds for a 256^3 volume (sfv.mrc virus map) with ~2.5e6 surface triangles. Most of that time (80%) is actually computing the enclosed volume. That should be very fast but the code is checking for holes in the surface in a rather slow way. Both methods use the step size (subsampling) set in the volume dialog. Tom

2 1

Re: [chimera-dev] [Chimera-users] displacing atoms following a given vector
by Eric Pettersen 22 May '08

22 May '08

Hi JD, You would displace the atoms of molecule 'm' by the vector (1,2,3) like so: v = chimera.Vector(1,2,3) for a in m.atoms: a.setCoord(a.coord() + v) --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On May 22, 2008, at 1:12 PM, Jean-Didier Maréchal wrote: > Dear All, > > I have been flying through the developer's guide but can't find what I > look for, sorry. > > I have a given molecule and a vector in cartesian coordinates (e.g. a > normal mode but not necessarily) indicating a direction of > displacement > for the different atoms of the molecules. I would like to write a > script > that displaces the atoms following this vector. I am prettysure that > some modules of chimera should allow me to do that, but I can't find > which ones. Could you give me a hand on this please? > > ALl the best > JD > > > El jue, 22-05-2008 a las 12:00 -0700, chimera-users- > request(a)cgl.ucsf.edu > escribió: >> Send Chimera-users mailing list submissions to >> chimera-users(a)cgl.ucsf.edu >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> or, via email, send a message with subject or body 'help' to >> chimera-users-request(a)cgl.ucsf.edu >> >> You can reach the person managing the list at >> chimera-users-owner(a)cgl.ucsf.edu >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Chimera-users digest..." >> >> >> Today's Topics: >> >> 1. Stereo projection (Magali Cottevieille) >> 2. Stereo projection (Steven Ludtke) >> 3. Re: Stereo projection (Greg Couch) >> 4. Re: findhbond/5750 (FindHBond failure) (Eric Pettersen) >> >> >> --------------------------------------------------------------------- >> - >> >> Message: 1 >> Date: Wed, 21 May 2008 16:06:07 -0400 >> From: Magali Cottevieille <mc3077(a)columbia.edu> >> Subject: [Chimera-users] Stereo projection >> To: chimera-users(a)cgl.ucsf.edu >> Message-ID: <483480AF.9020604(a)columbia.edu> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> Hi, >> >> Is there any way, with two projectors piloted by two graphic >> cards, to >> send from Chimera the stereo left eye view onto one, and the stereo >> right eye view onto the other one ? These two projectors are meant >> to be >> used with filters and special glasses to create a 3D view. >> Thanks for your help! >> >> -- >> Magali Cottevieille, Ph.D. >> Howard Hughes Medical Institute, >> Department of Biochemistry and Molecular Biophysics, >> 630 W 168th St, P&S Black Building 2-221 >> New York, NY 10032 >> >> Ph: (+1) 212-305-9521 >> Fax: (+1) 212-305-9500 >> >> Email: mc3077(a)columbia.edu >> magali.cottevieille(a)gmail.com >> >> >> >> ------------------------------ >> >> Message: 2 >> Date: Wed, 21 May 2008 16:18:26 -0500 >> From: Steven Ludtke <sludtke(a)bcm.edu> >> Subject: [Chimera-users] Stereo projection >> To: chimera-users(a)cgl.ucsf.edu >> Cc: mc3077(a)columbia.edu >> Message-ID: <0F963AC8-7667-4B76-B8E2-0DC9855E406C(a)bcm.edu> >> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes >> >> Yes, we have done this before, though I don't remember with absolute >> certainty if we >> did it with chimera. You don't use 2 video cards normally, but rather >> 1 card with 2 >> outputs. Also, you will need one of the 'professional' cards where >> the >> driver supports >> stereo in a window ie- NVidia Quadro (we didn't try ATI). The NVidea >> stereo drivers then >> have a mode for this type of stereo, or at least that's my memory, it >> was a year or two >> ago when we demonstrated this. You need: >> >> 2 identical projectors which permit geometry correction so their >> corners can be exactly aligned >> 2 polarizer plates. we got (http://www.3dstereo.com/viewmaster/pj- >> pfilt-3x3.html >> ) for $20 a pair >> linear polarizing glasses (from the same site) >> Quadro or similar GFX card >> >> Note that with this type of stereo, you could technically make this >> work with any old dual >> output 3-D card, but you would have to write the visualization >> software so it would open >> 2 display windows with slightly different orientations that you could >> then manually (or >> automatically) position on each of the 2 projectors. >> >> We did this just as an initial proof of concept, and haven't managed >> to get back to it again, >> though we keep meaning to, as it is MUCH cheaper than the commercial >> solutions. Oh, one warning, >> the polarizer plates mentioned above are plastic, and the light >> energy >> put out by your typical >> projector is quite substantial. We actually melted one of the >> polarizers on our first attempt, >> despite using much of it's 3x3 inch surface area. ie - use a low >> power >> projector, or put the >> polarizer between thick glass plates or somesuch... >> >>> From: Magali Cottevieille <mc3077(a)columbia.edu> >>> Date: May 21, 2008 3:06:07 PM CDT >>> To: chimera-users(a)cgl.ucsf.edu >>> Subject: [Chimera-users] Stereo projection >>> >>> Hi, >>> >>> Is there any way, with two projectors piloted by two graphic >>> cards, to >>> send from Chimera the stereo left eye view onto one, and the stereo >>> right eye view onto the other one ? These two projectors are meant >>> to be >>> used with filters and special glasses to create a 3D view. >>> Thanks for your help! >>> >>> -- >>> Magali Cottevieille, Ph.D. >>> Howard Hughes Medical Institute, >>> Department of Biochemistry and Molecular Biophysics, >>> 630 W 168th St, P&S Black Building 2-221 >>> New York, NY 10032 >>> >>> Ph: (+1) 212-305-9521 >>> Fax: (+1) 212-305-9500 >>> >>> Email: mc3077(a)columbia.edu >>> magali.cottevieille(a)gmail.com >>> >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users(a)cgl.ucsf.edu >>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >> --------------------------------------------------------------------- >> ------- >> Steven Ludtke, PhD | Baylor College of Medicine >> sludtke(a)bcm.tmc.edu | Associate Professor & Co- >> Director >> stevel(a)alumni.caltech.edu | National Center For Macromolecular >> Imaging >> V: (713)798-9020 | Dept of Biochemistry and Mol. >> Biol. >> F: (713)798-1625 | >> | Those who Do, Are >> http://ncmi.bcm.edu/~stevel | The converse also applies >> >> >> >> >> >> ------------------------------ >> >> Message: 3 >> Date: Wed, 21 May 2008 14:25:09 -0700 (PDT) >> From: Greg Couch <gregc(a)cgl.ucsf.edu> >> Subject: Re: [Chimera-users] Stereo projection >> To: Magali Cottevieille <mc3077(a)columbia.edu> >> Cc: chimera-users(a)cgl.ucsf.edu >> Message-ID: <Pine.OSF. >> 4.63.0805211409520.1818353(a)guanine.cgl.ucsf.edu> >> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed >> >> On Wed, 21 May 2008, Magali Cottevieille wrote: >> >>> Hi, >>> >>> Is there any way, with two projectors piloted by two graphic >>> cards, to >>> send from Chimera the stereo left eye view onto one, and the stereo >>> right eye view onto the other one ? These two projectors are >>> meant to be >>> used with filters and special glasses to create a 3D view. >>> Thanks for your help! >> >> Chimera supports stereo using workstation graphics cards, i.e., >> NVidia >> Quadro FX and ATI/AMD FireGL cards. We don't have a recent FireGL >> card >> (and driver), so the rest of this email will be about the NVidia >> Quadro FX >> cards and driver. >> >> The Quadro FX graphics cards have two video outputs and the driver >> lets >> you display the left eye on one output and the right eye on the >> other. >> The higher end cards have SLI support (on FireGL it's called >> CrossFire) >> which lets you use two matched graphics cards together. It is >> unclear to >> me how or if SLI/CrossFire and stereo work together, but I would >> expect >> them to. >> >> Greg >> >> >> ------------------------------ >> >> Message: 4 >> Date: Thu, 22 May 2008 10:51:29 -0700 >> From: Eric Pettersen <pett(a)cgl.ucsf.edu> >> Subject: Re: [Chimera-users] findhbond/5750 (FindHBond failure) >> To: Tyler Arbour <tyler.arbour(a)gmail.com> >> Cc: Chimera BB <chimera-users(a)cgl.ucsf.edu> >> Message-ID: <A4A9CFED-F357-4943-AB11-43D644C07DF0(a)cgl.ucsf.edu> >> Content-Type: text/plain; charset="us-ascii" >> >> Hi Tyler, >> The problem is that Chimera "knows" the atom types of standard >> residues and doesn't try to compute them from scratch. Therefore it >> assigns ND1 in HIS a sp2 type, which throws a monkey wrench into the >> find-hbond computation as it looks for the planarity of the ND1 and >> sees it bonded to nothing! >> For what you want to do, you want to get that atom's residue >> changed. Do this: >> >> 1) Control-double click on the ND1 atom >> 2) Chose "Modify Atom" from the resulting popup menu. >> 3) Change the "Element" to "N"; leave "Geometry" as "tetrahedral" >> 4) Change "Bonds" to 3 >> 5) In the "Residue Name" section, use the "new residue" option with >> "NH3" as the name and chain "het" >> 5) Click the Change button >> >> That should give you what you want. >> >> --Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> http://www.cgl.ucsf.edu >> >> On May 22, 2008, at 10:25 AM, Tyler Arbour wrote: >> >>> Wow, I didn't expect a response for this...great! I was actually >>> just trying to create a figure representing a computational model >>> that I am using. Starting from the crystal structure, I wanted to >>> actually change the histidinal N to a simple NH3 molecule. I am >>> just trying to get familiar with Chimera--I usually use DS >>> Viewerpro for modifying structures, and it doesn't seem like >>> Chimera is well-suited to this type of modification. If you have >>> any advice on an easy way to make this conversion so that I have a >>> nice figure, I'd greatly appreciate it! Thanks. >>> >>> Tyler >>> >>> On May 22, 2008, at 11:17 AM, Eric Pettersen wrote: >>> >>>> Hi Tyler, >>>> Your structure seems to have a histidine residue (residue 159 in >>>> chain A) that consists solely of an ND1 atom! How did you manage >>>> that? >>>> >>>> --Eric >>>> >>>> >>>> Eric Pettersen >>>> UCSF Computer Graphics Lab >>>> http://www.cgl.ucsf.edu >>>> >>>> >>> >> >>

1 0

Code source for Multi-touch
by Gergely Nagy 20 May '08

20 May '08

Dear Chimera Dev Team, I am referring to my email that I wrote in the beginning of April where I told about our diploma work. Just to sum it up in a couple of lines, we have a multi-touch screen (30") and we would like to make Chimera work with it. We would like to work with Chimera, because at the Center of Integrative Genomics at the University of Lausanne and at the Swiss Institute of Bioinformatics people use this software so this adaptation would even be useful besides that it would be our diploma work. So a couple of questions arise. Would it be possible to have the entire source code? We are ready to sign an NDA or any other contract if necessary. I am asking this because I am having difficulties to imagine how we could make the changes without being able to check how it works in the program. If there is a way to do it rapidly then of course we won't need the entire code source. The library that handles the touch events (touchDown, touchUpdate, touchRemove) is written in C++ (would wrap it of course). It gives basically the coordinates of the touches and updates the coordinates when dragging the finger. So we would need to replace mouse events with those and make zooming, translating and rotating functions available by using only the fingers. We would also make a new menu bar with only a couple of functions to be able to demonstrate the concept. So please tell us what would be possible and what wouldn't so we can evaluate the situation and make the right decisions immediately. Thanks a lot for taking the time to reply. Best regards, Gergely Nagy Marco Pambianchi

3 2

Error on command-line startup: OSX 10.5
by Bernard Heymann 05 May '08

05 May '08

When I start up Chimera from the command line under Leopard, I get a lot of messages such as: The process has forked and you cannot use this CoreFoundation functionality safely. You MUST exec(). Break on __THE_PROCESS_HAS_FORKED_AND_YOU_CANNOT_USE_THIS_COREFOUNDATION_FUNCTIONALITY___YOU_MUST_EXEC__ () to debug. Chimera still runs, but I thought this is probably something to be dealt with sooner than later. I did some digging and came across the following technical note from Apple: http://developer.apple.com/technotes/tn2005/tn2083.html The reference to the fork message is at the bottom of the page. I also found on another site the following advice for an X11 application: "I've updated the OSX Readme TclTk build example to include an extra configure option: --disable-corefoundation Since the example is for an X11 TclTk build, CoreFoundation isn't really necessary, so this is OK." Because Chimera uses Tk, I thought this might be something to try to avoid these error messages and possible instability down the line. Bernard Heymann Rm 1515, 50 South Dr, NIH, Bethesda, 20892-8025 Tel 301-451-8241, Fax 301-480-7629

3 2