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Re: [Chimera-users] other/2169
by conrad＠cgl.ucsf.edu 16 Jan '07

16 Jan '07

Synopsis: interface with QPACK State-Changed-From-To: open->closed State-Changed-By: conrad State-Changed-When: Tue Jan 16 10:18:12 2007 State-Changed-Why: QPACK interface available as experimental feature. See http://www.cgl.ucsf.edu/chimera/experimental/experimental.html for more information. http://www.cgl.ucsf.edu/cgi-bin/gnatsweb.pl?cmd=view&pr=2169&database=chime…

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Re: [Chimera-users] Select atom by serial number.
by Jean Didier Pie Marechal 16 Jan '07

16 Jan '07

Hi Elaine and thank you very much for your help. I am pleased to see the selection specifications are OK. Coming back from the WE, I retried this selection on my structure and... it works perfect... For once, it seems I needed a reboot more than my desktop... My apologies for your waste of time. Regards, JD Dr. Jean-Didier Maréchal Professor Lector Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdonyola (Barcelona) Tel: +34.935814988 e-mail: JeanDidier.Marechal(a)uab.es ----- Missatge original ----- De: Elaine Meng <meng(a)cgl.ucsf.edu> Data: Dijous, Gener 11, 2007 8:59 pm Assumpte: Re: [Chimera-users] Select atom by serial number. > > Hi JD, > We also tested Chimera 1.2309 on Windows, and these specifications > > work correctly. Example: > Command: sel @/serialNumber=232 > will select NZ of Lys 27 in chain A of the PDB entry 1zik. The > only > other thing I can think of (besides what was in the previous > message) > is to check if your PDB file is correctly formatted. The > ATOM/HETATM > serial number is supposed to be in columns 7-11 and right-justified. > Best, > Elaine > > On Jan 11, 2007, at 11:39 AM, Elaine Meng wrote: > > > Hi JD, > > You are using the correct specifications - both of your examples > > > should work. I tested both approaches in Chimera 1.2304 on Mac > OSX > > and they worked correctly. We'll have to look into your > specific > > version/platform and get back to you. If you want, you could > send > > me the PDB file you are using so I could test if there is some > > issue specific to that structure. To be clear: the serial > number > > is the number shown in the column after ATOM (or HETATM) in the > PDB > > file, regardless of what order the atoms are really in. That > is, > > if the first ATOM has 2 in that column, its serial number is 2 > and > > not 1. > > Best, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu > > UCSF Computer Graphics Lab and Babbitt Lab > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > http://www.cgl.ucsf.edu/home/meng/index.html > > > > > > > > > > On Jan 11, 2007, at 10:47 AM, Jean-Didier Maréchal wrote: > > > >> Hi Everyone, > >> > >> > >> > >> > >> > >> I am desperately trying to select an atom of my pdb by its > serial > >> number. > >> > >> Looking at the archives, it seems that I should put something > like > >> @/serialNumber=525 > >> > >> I tried “sel #0@/serialNumber=525” in the commandl ine and “@/ > >> serialNumber=525” in the Atom Specifier. None of these > selections > >> worked. Can someone tell me the right way to do this, please ? > >> > >> > >> > >> Cheers > >> > >> JD > >> > >> > >> > >> Current running chimera: version 1 build 2309 > >> > >> OS: windows > >> > >> > >> > >> _______________________________________________ > >> Chimera-users mailing list > >> Chimera-users(a)cgl.ucsf.edu > >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > >

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Numeric/numpy revisited
by Randy Heiland 11 Jan '07

11 Jan '07

I'll post this long-winded thing to the users list although it's really for the developers... I'm revisiting the issue of wanting to have access to the numpy pkg (numpy.scipy.org) for a Chimera plugin - a delayed continuation of the problem discussed here: http://www.cgl.ucsf.edu/pipermail/chimera-users/2006-April/000743.html Here's my situation: I installed chimera-1.2304-osx_x11.dmg. I then built the numpy pkg (from svn) using my system's python (2.4) via 'python setup.py build' and copied the resulting /numpy dir into the chimera /share dir. I then discover/verify 2 things: 1) using my system's python, I can successfully import both Numeric and numpy - Numeric coming from chimera and the numpy that I just built and copied into chimera's /share dir 2) using the python2.4 bundled with chimera, I cannot import both Numeric and numpy. I can always import one (either one), but then get a bizarre error when trying to import the other. --------------------------- More verbosely: I set PYTHONPATH to /Applications/Chimera.app/Contents/Resources/lib/python2.4/site-packages/Num eric:/Applications/Chimera.app/Contents/Resources/share Then check the system python: [macmini:~] heiland% pwd /Users/heiland [macmini:~] heiland% which python /usr/local/bin/python [macmini:~] heiland% ll /usr/local/bin/python lrwxr-xr-x 1 root heiland 68 Jul 27 06:19 /usr/local/bin/python@ -> ../../../Library/Frameworks/Python.framework/Versions/2.4/bin/python [macmini:~] heiland% python Python 2.4.3 (#1, Apr 7 2006, 10:54:33) [GCC 4.0.1 (Apple Computer, Inc. build 5250)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import Numeric >>> import numpy >>> from numpy.core.multiarray import typeinfo >>> Then check the chimera python: /Applications/Chimera.app/Contents/Resources/share [macmini:Contents/Resources/share] heiland% ../bin/python2.4 Python 2.4.3 (#1, Oct 16 2006, 09:43:37) [GCC 4.0.1 (Apple Computer, Inc. build 5247)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import Numeric >>> import numpy Traceback (most recent call last): File "<stdin>", line 1, in ? File "/Applications/Chimera.app/Contents/Resources/share/numpy/__init__.py", line 36, in ? import core File "numpy/core/__init__.py", line 8, in ? import numerictypes as nt File "numpy/core/numerictypes.py", line 83, in ? from multiarray import typeinfo, ndarray, array, empty, dtype ImportError: cannot import name typeinfo ----------------------------- OK, it then dawns on me that probably what I really should be doing is building numpy using chimera's python. So, after downloading the chimera (1.2318) OSX headers (http://www.cgl.ucsf.edu/chimera/sourcecode.html ), putting the /include in the /Resources dir, and doing: /Applications/Chimera.app/Contents/Resources/bin/python2.4 setup.py build It all builds fine, but then I have the same bizarre error when trying to import both Numeric and numpy as before. Crap. So I then use 'ldd' to see the dependencies in the different python executables: ldd /Applications/Chimera.app/Contents/Resources/bin/python2.4 /Applications/Chimera.app/Contents/Resources/bin/python2.4: /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 71.1.3) /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 7.3.0) /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libmx.A.dylib (compatibility version 1.0.0, current version 47.1.0) [macmini:~] heiland% ldd /Library/Frameworks/Python.framework/Versions/2.4/bin/python /Library/Frameworks/Python.framework/Versions/2.4/bin/python: /usr/lib/libmx.A.dylib (compatibility version 1.0.0, current version 47.1.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 88.1.3) Note the different versions on the libSystem.B.dylib. Some more poking... [macmini:~] heiland% locate libgcc_s.1.dylib /Developer/SDKs/MacOSX10.3.9.sdk/usr/lib/libgcc_s.1.dylib /Developer/SDKs/MacOSX10.4u.sdk/usr/lib/libgcc_s.1.dylib /usr/lib/libgcc_s.1.dylib [macmini:~] heiland% ldd /Developer/SDKs/MacOSX10.4u.sdk/usr/lib/libgcc_s.1.dylib /Developer/SDKs/MacOSX10.4u.sdk/usr/lib/libgcc_s.1.dylib: /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 88.3.3) [macmini:~] heiland% ldd /Developer/SDKs/MacOSX10.3.9.sdk/usr/lib/libgcc_s.1.dylib /Developer/SDKs/MacOSX10.3.9.sdk/usr/lib/libgcc_s.1.dylib: /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 71.1.3) [macmini:~] heiland% ldd /usr/lib/libgcc_s.1.dylib /usr/lib/libgcc_s.1.dylib: /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 88.1.2) ----------------------------- One thing worth noting is the different gcc builds (my system python used a later build, 5250, cf 5247 for chimera's python). I also installed the latest xcode (2.4.1) before doing all this. If you've stayed with me to the end, I congratulate you :) Basic question - any ideas? Would it be possible for the Chimera OSX developers to verify they have the latest xcode? And secondly, do you know how one can the chimera python have the dependency on libSystem.B.dylib v.88.1.2 instead of 71.1.3 ? Thanks, -Randy Fwiw, this link http://mail.python.org/pipermail/pythonmac-sig/2006-April/017310.html seems related to this thread also.

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Select atom by serial number.
by Jean-Didier Maréchal 11 Jan '07

11 Jan '07

Hi Everyone, I am desperately trying to select an atom of my pdb by its serial number. Looking at the archives, it seems that I should put something like @/serialNumber=525 I tried sel #0@/serialNumber=525 in the commandl ine and @/serialNumber=525 in the Atom Specifier. None of these selections worked. Can someone tell me the right way to do this, please ? Cheers JD Current running chimera: version 1 build 2309 OS: windows

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secondary structure assignment
by nurul 10 Jan '07

10 Jan '07

hello i'm a student from malaysia and i'm using chimera in my studies, i have one question regarding this software, how does it assign the secondary structure? is it using dssp or stride or any other secondary structure assignment program? thank you

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Chimera benchmarks in both OSX and WinXP on same hardware
by Jeff Speir 08 Jan '07

08 Jan '07

Dear Chimera developers, By request from my lab mates I've run Chimera's built-in benchmark routine under both OSX and Windows XP Pro SP2 for comparison. Attached is an MSWord document with the results. Hope they are useful. Of note, OSX falls behind in the ribbon graphics compared to WinXP, especially with large molecules. The test was done on an Apple Mac Pro (hardware details in attached document) with Windows XP Pro installed via Boot Camp. Both operating systems were fully updated with all available patches. Please let me know if you have any questions. Best Regards, Jeff Jeffrey A. Speir, Ph.D. The Scripps Research Institute Dept. of Molecular Biology 10550 North Torrey Pines Rd. La Jolla, CA 92037 Phone: (858) 784-8646 Fax: (858) 784-8660 E-mail: speir(a)scripps.edu

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OSX headers
by Randy Heiland 04 Jan '07

04 Jan '07

Hi gang, Would it be possible to get the latest OSX (10.4) headers posted at http://www.cgl.ucsf.edu/chimera/sourcecode.html ? -Randy

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command line zone selection?
by Kenward Vaughan 02 Jan '07

02 Jan '07

I'm putting together a demo for my students this next semester, and was hoping to be able to do a zone selection about the ligand. Is this possible with the command line? I haven't been able to pull out a reference for such, yet. Certainly I could pull together the list of residues myself, but thought it'd be nice to have the command available. Some students might like to create a demo file for their reports, and this would become a pivotal tool for a subset of those. If not directly available, then a wishlist addition, perhaps? Something like: zonesel [within|beyond] [+/- angstroms] [atom-spec] where the sign of the angstrom value denotes whether to include (+) or exclude (-) the atoms in atom-spec. Cheers, Kenward Vaughan -- .'^~;,_ Dr. Kenward Vaughan `:,'~~~~~ Professor of Chemistry \;:/ Bakersfield College |,;| 1801 Panorama Drive / ', \ Bakersfield, CA 93305 / o O \ http://www2.bc.cc.ca.us/kvaughan (oOoOOoOo) ---========--- ???$$MM$$???

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how to change the color and thickness of the unit cell outline
by Sabuj Pattanayek 02 Jan '07

02 Jan '07

Hi, How do I change the color and thickness of the unit cell outline? Thanks, Sabuj

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Re: [Chimera-users] chimera and my ATI card
by Thomas Goddard 29 Dec '06

29 Dec '06

Hi Jeff, The system crash on your laptop indicates it is a graphics driver problem. Unfortunately these are very common -- maybe 1 in 20 driver version / graphics card combinations have Chimera crashing or system crashing bugs. I intend to make a web page that includes all the bad combinations we have encountered -- hopefully I'll get to it in January. The reason Chimera is particularly susceptible to these bugs is that it uses many capabilities of the OpenGL 3-d graphics library -- some that are seldom used by video games and other 3-d applications. There are only 4 practical solutions: 1) update the driver, 2) use an older driver, 3) set driver options to use less OpenGL acceleration, or 4) use a different machine. I use solution 2 on my home machine with an Nvidia Quadro driver that is a dozen versions behind the current one and over a year old. New drivers come out fairly often for both Nvidia and ATI cards and usually do not offer better performance -- only a new set of bugs (old ones fixed, new ones introduced). If you could send us a Chimera bug report by starting Chimera and use menu entry Help / Report a Bug this will send us your graphics driver version so we can include it on our bad drivers page. And if you find another driver version that works I would of course like to know which version. Sorry to offer so little help on this. Tom From: Jeff To: "'Thomas Goddard'" <goddard(a)cgl.ucsf.edu> Subject: chimera and my ATI card Date: Thu, 28 Dec 2006 23:59:26 -0800 hi Tom, on my laptop (IBM T43p), chimera is crashing the machine. I have the latest release installed in WinXP (as of 12/21), and a fairly recent release (within 2006) installed on Linux (also on same machine, different drive). this occurs with both really small volumes (100 cubed) and larger ones (600x400x100 or so), doing common tasks like rotating a surface rendering. in XP, it froze with a required reboot; with Linux, I got the screen that I have attached. the GPU is an 'ATI MOBILITY FireGL V3200', which was one of the GPUs you could get on a 'workstation laptop' back in June '05. I am pretty sure the drivers are current (within '06) and I use the ATI proprietary drivers in both XP and Linux - there is a standard ATI driver package that you download and then it just installs the proper version for your card. On an older laptop (prior to '05) I had similar issues with crashing, also on an ATI card, but different generation (was a Dell purchased in feb. '02). on my desktop workstation with an NVidia card, it works fine, although sometimes surfaces get rendered in the wrong place (something in background looks more in foreground, etc) - but I don't have problems with chimera getting killed (or killing the OS). any thoughts on having it run on my laptop? this machine is the only one I have access to outside of the lab, and was originally bought for this purpose (reconstructions and processing). thanks, -jeff

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