- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Chimera and secondary structure annotations
by Thomas Goddard 28 Oct '05

28 Oct '05

Hi Julio, The secondary structure calculation requires all peptide backbone atoms. In the Chimera docs it notes: "Ksdssp uses the coordinates of the backbone atoms (N, CA, C, O, and optionally H) of a protein to determine which residues are in alpha helices and beta strands." There is no way in Chimera to determine secondary structure from just CA positions. The error message you sent for pdb2mrc is a bug in the AIRS package which is developed and maintained by Matt Baker (mbaker(a)bcm.tmc.edu) at Baylor College of Medicine, not our group. It is a problem in file C:\Programme\EMAN\chimeraext\Airs\airsIO.py It occurs because you have a model open in Chimera which is neither a density map surface nor a PDB model (maybe a molecular surface or a solid volume rendering?). The airsIO.py code does not handle that correctly. You could try running it with only the PDB model open in Chimera to avoid this problem. Alternatively you could edit the airsIO.py file with a text editor changing near line 32 from: if str(model.__class__)=="VolumeViewer.surface.Surface_Model": path=str(volume_data_set(model).data.path) elif str(model.__class__)=="chimera.Molecule": modelfile=model.openedAs path=str(modelfile[0]) if filecheck.strip()==path: path=os.path.abspath(model.name) to if str(model.__class__)=="VolumeViewer.surface.Surface_Model": path=str(volume_data_set(model).data.path) elif str(model.__class__)=="chimera.Molecule": modelfile=model.openedAs path=str(modelfile[0]) else: path = "" if filecheck.strip()==path: path=os.path.abspath(model.name) Just two lines are added the "else:" and the "path = ""'. Make sure to use this indentation if you make the change since that is important in Python code. I'll send the error message to Matt Baker. Tom > Date: Sat, 29 Oct 2005 01:58:48 +0200 > From: "Dr .Julio Ortiz" <ortiz(a)biochem.mpg.de> > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Cc: meng(a)cgl.ucsf.edu > Subject: Re: Chimera and secondary structure annotations > > Dear Thomas and Elaine: > Thank you very much for your answers, I checked the ksdssp command and it works > for some pdbs, but not for those that I mentioned with the ribosomes. I think > that the problem is that some pdbs from ribosomes (like 1GIX and 1GIY) do not > have complete residues (just CAs). In the case of your images, you have use > 1PNS and 1PNU, and only those proteins in the 30S are complete. > I guess I need to contact some of the authors of the structures to see if the > complete coordinates are available. > > Another question: I installed the new version of Chimera and when using pdb2mrc > I received an error message: > ------------------------------ > Traceback (most recent call last): > File "C:\Programme\Chimera\share\__main__.py", line 59, in ? > value = chimeraInit.init(sys.argv) > File "C:\Programme\Chimera\share\chimeraInit.py", line 308, in init > tkgui.eventLoop() > File "C:\Programme\Chimera\share\chimera\tkgui.py", line 2725, in eventLoop > app.mainloop() > File "C:\Programme\Chimera\bin\Lib\lib-tk\Tkinter.py", line 965, in mainloop > self.tk.mainloop(n) > File "C:\Programme\Chimera\bin\Lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", > line 1751, in __call__ > _reporterror(self.func, args) > File "C:\Programme\Chimera\bin\Lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", > line 1814, in _reporterror > displayerror(msg) > File "C:\Programme\Chimera\bin\Lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", > line 1377, in displayerror > _errorReportFile.write(text + '\n') > File "C:\Programme\Chimera\bin\Lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", > line 1747, in __call__ > return apply(self.func, args) > File "C:\Programme\Chimera\share\chimera\baseDialog.py", line 229, in <lambda> > self.__buttonFuncName(txt))() > File "C:\Programme\EMAN\chimeraext\Airs\pdb2mrc.py", line 73, in Apply > targetPath=airsIO.getPath(target) > File "C:\Programme\EMAN\chimeraext\Airs\airsIO.py", line 32, in getPath > if filecheck.strip()==path: > UnboundLocalError: local variable 'path' referenced before assignment > > > ------------------------- > > I have already added the path of the EMAN in the tool menu. Could you tell me > what I am missing? > > > Thanks you very much, > Julio > > > > --------------------------------------------------------------------- > This message was sent using https://webmail.biochem.mpg.de > If you encounter any problems please report to rz-linux(a)biochem.mpg.de >

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Re: [Chimera-users] Chimera and secondary structure annotations
by Thomas Goddard 28 Oct '05

28 Oct '05

Hi Julio, The "ksdssp" command in Chimera will compute secondary structure for proteins. This uses the Kabsch and Sander algorithm. As far as I know you do not need any secondary structure info for the ribosomal RNA to make a nice ribbon. To use this command use Chimera menu entry Favorites / Command Line and then type ksdssp in the command entry at the bottom of the Chimera window. More details are in the Chimera manual: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html Here are some ribosome pictures I made with Chimera a few months ago. http://www.cgl.ucsf.edu/chimera/complexes05/bakeoff-talk.html Tom > Date: Fri, 28 Oct 2005 21:21:44 +0200 > From: "Dr .Julio Ortiz" <ortiz(a)biochem.mpg.de> > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: Chimera and secondary structure annotations > > Hi Thomas: > It is time for a couple of new questions about Chimera. > I am trying to generate some nice representations of the 70S ribosome showing > its proteins as ribbons, but the PDBs do not have annotations of secondary > structure. In many papers that I have seen the people use the program "Ribbons" > and a collegue suggested me also "DSSP" to generate the annotations and > visualize the results in "PyMOL". I am still fighting with some installation > problems, so I have not succeed yet in my original goal. > > The question for you is if Chimera, or some assotiated tool can generate the > annotations for secondary structure from a PDB file. In particular, do you have > some suggestions for the ribosome structures (large file with also RNA?). > > Thanks, > Julio > > > > -- > Max-Planck Institut für Biochemie > Abteilung Molekulare Strukturbiologie > Am Klopferspitz 18 > D-82152 Martinsried > Germany > Tel: +49 (89) 8578 2032 > fax: +49 (89) 8578 2641 > > --------------------------------------------------------------------- > This message was sent using https://webmail.biochem.mpg.de > If you encounter any problems please report to rz-linux(a)biochem.mpg.de

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list index out of range
by Paula Petrone 25 Oct '05

25 Oct '05

Hi, I am trying to load in an MD-ensemble, using a pdb and an X-plor file .dcd. For some reason, it gives me "IndexError: list index out of range". I generated the .dcd file myself (with Fortran). VMD program seems to have no problem with it. Is it a format problem? Is it a bug? Any suggestion? Thanks a lot! (I attach the files) paula

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Error when making Covalent bonds
by David Chenoweth 25 Oct '05

25 Oct '05

Hi! I am trying to pull up two molecules in chimera and link them by forming a covalent bond between a N and C atom. I am selecting only the N of one molecule and the C of the other. When I go to command line and use the bond sel command I get the following error message. Type error: Cannot form covalent bond joining two molecules. Does anyone know how to get around this. Thanks, David C.

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Benchmarks
by Mingfeng Yang 24 Oct '05

24 Oct '05

Just realized there must be some benchmarks on chimera's webpages, and I found them. :) Glad to provide the benchmarks from my systems. Benchmark 1: Computer: IBM T41 Graphics Card: ATI Radeon mobility M7 (32M?, not 100% sure) CPU: pentium-m 1.4GHz System Memory: 512M OS: Ubuntu GNU/LINUX 5.10 Driver for video card: the built-in open-source radeon driver from Xorg-x11 6.8.2 Chimera: version 1 build 2176 Benchmark scores: surface 147 mesh 127 contour 133 solid 128 recolor 68 Benchmark 2: Computer: HP XW5500 workstation Graphics Card: ATI FireGL 8800 (128M memory) CPU: pentium-4 2.4GHz System Memory: 512M OS: Gentoo GNU/LINUX Driver for video card: ATI fglrx driver 8.14.30 Chimera: version 1 build 2176 Benchmark score: surface 234 mesh 227 contour 142 solid 256 recolor 107 Something is confusing me. As you see that scores from benchmark 2 are higher than scores from benchmark 1. But in case that I want to save a protein structure as a png file, the rendering in system 1 is nearly two times faster. How can this happen? Best, Mingfeng Yang

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preferences file
by Boaz Shaanan 22 Oct '05

22 Oct '05

Hi, After upgrading to a new version, is it advisable to use a preferences file from the previous version (which is set up to turn on all sorts of things tuned to my liking) with the new one or are there possible issues of versions incompatibility which should rather be avoided ? I'd appreciate your advice. Thanks, Boaz Boaz Shaanan, Ph.D. Associate Professor Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone:972-8-647-2220 Fax: 972-8-647-2992 972-8-646-1710 E-mail:bshaanan@bgu.ac.il

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1.2180 on Windows
by Eric Pettersen 20 Oct '05

20 Oct '05

We are now aware that the 1.2180 release still doesn't work on some people's XP installations -- so don't rush out to try it! Seems fine on non-Windows platforms. I'll post something when I think we have a fixed version. Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Bug?
by Mingfeng Yang 19 Oct '05

19 Oct '05

Chimera version 1 build 2176, 1. start chimera, load in a protein 2. from help-->user guide, open firefox webbrowser to read help information 3. chimera main window becomes dead (black screen, not respond to mouse click and keyboard.) 4. close firefox browser, chimera goes back to normal OS: Gentoo linux, kernel-2.6.10 Firefox: version 1.07, build from gcc-3.4.4

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exporting ribbon models to vrml
by Doug Huff 18 Oct '05

18 Oct '05

Hello I work at Arkitek studios. We create rendered 3D for the science and technology crowd. I am a animator and have been charged with creating a rendering of a ribbon model in 3DS max (our software package). Your Chimera program displays the type of geometry I need and I can import vrml into my application. I can't seem to find the method to export ribbon models to vrml. When I use the multiscale models tools I always wind up with a surface model. Please remember I am not a scientist :) Thanks in advance for your help. Doug Huff 206 286 0337 http://www.arkitek.com

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ATI-Driver & Chimera hangs OS
by Mingfeng Yang 16 Oct '05

16 Oct '05

I am using Chimera build version 1 build 2176 on my Gentoo Linux platform, with ati firegl 8700 graphic card. After I upgraded the ati-drivers from 8.14.13 to 8.16.20, chimera will hang the whole system, everything dead, including the keyboard. I can only see the chimera window frame (the border), nothing else. What could be the problem? Thanks. Yang

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