- Chimera-users - RBVI Mailing Lists

save mol2 command
by Huang, Shengyou 22 Jan '07

22 Jan '07

Hi, Does anybody know a COMMAND which can save a mol2 format file in Chimera? Thanks! Shengyou Huang

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yet another chimera question...
by Jeff 19 Jan '07

19 Jan '07

good morning Tom, there isn't by chance a way to output the orientation/location of a given model (or, likewise, its corresponding per-model clipping plane) so that I can write down particular views that are useful, without having to re-save chimera sessions with unique IDs (my kludge as of right now). and a related follow-up - if so, how do I re-input the orientations by command line in chimera (if possible?) thanks, -jeff

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clarification regarding the application of chimera...
by harini senthil 19 Jan '07

19 Jan '07

I am a final year b.tech industrial biotech student working on docking studies between a polymer and membrane proteins of e.coli. I would like to know whether chimera can be utilised for performing polymer protein docking studies. Thanking you --------------------------------- Heres a new way to find what you're looking for - Yahoo! Answers

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Re: [Chimera-users] chimera to rebuild crystal
by Elaine Meng 18 Jan '07

18 Jan '07

Maybe a more integrated solution would be to put the additional option(s) in Unit Cell - easy for me to say, however! 8-) Elaine On Jan 12, 2007, at 2:15 PM, Thomas Goddard wrote: > Hi Elaine, > > Brady Bernard wanted to output multiple unit cells, more than 3x3x3 > in > fact (which is what multiscale can do). The script lets you set the > number > of unit cells along each axis. That isn't supported in Unit Cell. > > Sorry the Brady email wasn't posted to chimera-users. Nag Eric about > that since the original email went directly to him. Of course, I too > now > have personal email messages from Brady that should have gone to > chimera-users. > I am still figuring out how to forward the mail and have the original > sender's name appear in the chimera-users archive summary. > > Tom

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Re: [Chimera-users] Export idatmType
by Eric Pettersen 18 Jan '07

18 Jan '07

On Jan 17, 2007, at 10:47 PM, Brady Bernard wrote: > is there a way to do this with --nogui so that i can automate it in > a script? > > thanks, > brady It's pretty easy to make a Python script that opens a file, loops through open molecules and then their atoms, and prints our the atom identifier and IDATM type to that file. Here's an example: import chimera f = open("types.txt", "w") for m in chimera.openModels.list(modelTypes=[chimera.Molecule]): for a in m.atoms: print>>f, a, a.idatmType f.close() If you save the above into a file with a ".py" suffix (e.g. types.py), then you could save all the types of 1gcn with "chimera -- nogui pdb:1gcn types.py", which would create a file named "types.txt" (in the same folder as types.py) with the types listed. BTW, you need to preserve the indentation of the Python code above -- it matters to Python. If you're automating this in a shell script, it may be simpler to just print the info to standard output and redirect that into a file, rather than open the file in the Python script. The command would then be "chimera --nogui --nostatus pdb:1gcn types.py > 1gcn_types.txt" (note the "--nostatus" flag so that status messages don't get mixed into the output). The Python script becomes: import chimera for m in chimera.openModels.list(modelTypes=[chimera.Molecule]): for a in m.atoms: print a, a.idatmType --Eric > ----- Original Message ----- > From: Eric Pettersen > To: Brady Bernard > Cc: Thomas Goddard ; Elaine Meng > Sent: Tuesday, January 16, 2007 4:40 PM > Subject: Re: Export idatmType > > Hi Brady, > Tom forwarded your mail to me. There almost is a way. In the > 1.2318 snapshot, the Render By Attribute tool allows you to save > attribute values to a file using that tool's "File->Save > Attributes..." menu item (saved in the format that Define Attribute > accepts). So, why "almost"? The idatmType attribute is screened > out of the list of available attributes since it can be expensive > to compute the values -- and since you could already select by > IDATM type using the regular selection menu. But now that save > exists I will have to improve Render By Attribute so that it can > know that idatmType values are strings ahead of time (so it doesn't > have to ask for any values to figure that out). > Anyway, for your purposes it is not too hard to force Render By > Attribute to show you idatmType. First, get the 1.2318 release. > Then edit the file <your Chimera>/share/ShowAttr/__init__.py (on a > Mac: Chimera.app/Contents/Resources/share/ShowAttr/__init__.py) > and edit line 24. It will look like this: > > 'name': False, 'idatmType': False, 'idatmIsExplicit': False, > > change it to: > > 'name': False, 'idatmIsExplicit': False, > > Save the file and thereafter Render By Attribute should show you > the idatmType attribute. > > --Eric > >> hi tom - is there a quick way to save the atom types from >> idatmType to a text/log file along with the atom name or number? > >

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Re: [Chimera-users] Movie resolution
by Zoghbi, Maria 18 Jan '07

18 Jan '07

Now it works perfectly! Thanks Maria Elena Zoghbi UMass Medical School Maria.Zoghbi(a)umassmed.edu -----Original Message----- From: Thomas Goddard [mailto:goddard@cgl.ucsf.edu] Sent: Wednesday, January 17, 2007 5:04 PM To: Zoghbi, Maria Cc: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] Movie resolution Hi Maria, Sorry the code I suggested was not correct. The new lines should have images = ... instead of image = ... Otherwise your change looks correct. Tom

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For Chimera mac users
by Eduardo Sanz-Garcia 17 Jan '07

17 Jan '07

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Re: [Chimera-users] Movie resolution
by Zoghbi, Maria 17 Jan '07

17 Jan '07

I made the change (please, see document attached to be sure I did it right). When I restarted Chimera and tried to record a movie there was an error message (see reply log attached). Maria Elena Zoghbi UMass Medical School Maria.Zoghbi(a)umassmed.edu -----Original Message----- From: Thomas Goddard [mailto:goddard@cgl.ucsf.edu] Sent: Wednesday, January 17, 2007 4:16 PM To: Zoghbi, Maria Cc: chimera-users(a)cgl.ucsf.edu Subject: Re: [Chimera-users] Movie resolution Hi Maria, Ok, so the bug is not fixed in Chimera version 1.2304. I made a note of that in our bug database. Here is a suggestion from the original bug report that solved the problem in that case: Edit the file in you Chimera 1.2304 distribution chimera/share/MovieRecorder/RecorderHandler.py using any text editor to change line 97 from image = chimera.viewer.pilImages() to width, height = chimera.viewer.windowSize image = chimera.viewer.pilImages(width, height, supersample = 1, opacity = False) Make sure to use the same indentation as the original code since this is important in the Python language. Then restart Chimera and try movie recorder again. Let me know if that fixes the problem. Tom

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Re: [Chimera-users] Movie resolution
by Zoghbi, Maria 17 Jan '07

17 Jan '07

I see. Thanks. I am using the version 1.2304, and the platform is Windows XP. Maria Elena Zoghbi UMass Medical School Maria.Zoghbi(a)umassmed.edu -----Original Message----- From: Thomas Goddard [mailto:goddard@cgl.ucsf.edu] Sent: Wednesday, January 17, 2007 1:45 PM To: Zoghbi, Maria Subject: Re: [Chimera-users] Movie resolution Hi Maria, This is a bug. The movie capture should work for any window size without artifacts. This Chimera bug was reported earlier: http://www.cgl.ucsf.edu/cgi-bin/gnatsweb.pl?cmd=view&pr=3151&database=ch imera Pressing the "view audit trail" button on that bug report page gives more info -- more than you want to konw. Supposedly that bug was fixed in Chimera version 1.2297. If you are using a newer version of Chimera than that and you still have this problem, then send me email with your Chimera version number and platform (Windows, Linux, Mac). Tom

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bond rotation buglet
by Eric Pettersen 17 Jan '07

17 Jan '07

I just found out that the current release has a bug where it sometimes claims that a bond is terminal (and therefore won't let you rotate it) when it isn't. This occurs when there is already an active bond rotation adjacent to the desired new rotation, and the atom in common would have all its bonds in rotations. You can work around the problem by deactivating the other rotation (in the panel showing the rotations, click on the label for the rotation (under "Bond") which brings up a menu of actions, one of which is Deactivate). I also have a code fix that I could send to people that need it -- just drop me an email. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Movie resolution
by Zoghbi, Maria 17 Jan '07

17 Jan '07

Hello, I'm trying to make a movie, but the only format that I have been able to make work is the VCD (Video Compact Disc), which produces a low resolution movie (457x240). As soon as I change to a different standard format the recorded images are totally wrong (rotated, shifted, wear lines, etc). I have tried to choose my own resolution and the only one that has worked is when high=3/2width, but only when high ≤ 300. Are these restrictions for the resolution of the movies normal or am I doing something wrong? How can a make a higher resolution movie? I appreciate any help. Thanks Maria Elena Zoghbi UMass Medical School Maria.Zoghbi(a)umassmed.edu

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Re: [Chimera-users] Export idatmType
by Eric Pettersen 16 Jan '07

16 Jan '07

Hi Brady, Tom forwarded your mail to me. There almost is a way. In the 1.2318 snapshot, the Render By Attribute tool allows you to save attribute values to a file using that tool's "File->Save Attributes..." menu item (saved in the format that Define Attribute accepts). So, why "almost"? The idatmType attribute is screened out of the list of available attributes since it can be expensive to compute the values -- and since you could already select by IDATM type using the regular selection menu. But now that save exists I will have to improve Render By Attribute so that it can know that idatmType values are strings ahead of time (so it doesn't have to ask for any values to figure that out). Anyway, for your purposes it is not too hard to force Render By Attribute to show you idatmType. First, get the 1.2318 release. Then edit the file <your Chimera>/share/ShowAttr/__init__.py (on a Mac: Chimera.app/Contents/Resources/share/ShowAttr/__init__.py) and edit line 24. It will look like this: 'name': False, 'idatmType': False, 'idatmIsExplicit': False, change it to: 'name': False, 'idatmIsExplicit': False, Save the file and thereafter Render By Attribute should show you the idatmType attribute. --Eric > hi tom - is there a quick way to save the atom types from idatmType > to a text/log file along with the atom name or number?

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Fwd: chimera to rebuild crystal
by Eric Pettersen 16 Jan '07

16 Jan '07

Hi Tom, Brady's question below seems more up your alley somehow. It also seems like one of those things that should be cross-posted to the chimera-users or -dev lists for "community building" purposes, though I'll leave that up to your discretion. --Eric Begin forwarded message: > From: "Brady Bernard" <bradyb(a)u.washington.edu> > Date: January 11, 2007 5:06:21 PM PST > To: "Eric Pettersen" <pett(a)cgl.ucsf.edu> > Subject: chimera to rebuild crystal > > hi, > > i am interested in using distance-dependent statistics in a scoring > function and i would like more than the default 3x3x3 repeating units > to rebuild a crystal using cryst1 data in pdb files. how can i do > this with chimera? i will need to do this for thousands of files and > am familiar with scripting and using the -nogui option with cmd files, > etc. > > thanks in advance for your help, > > brady bernard > uw bioengineering

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Chimera doesn't display AMBER molecular dynamics trajectories with periodic boundary condition.
by juyong Lee 16 Jan '07

16 Jan '07

Hi, I'm using chimera 1.2309 version. And I found out that MD movie module in chimera doesn't display AMBER trajectory file with periodic condition correctly. I works well only with non-periodic condition trajectory file. Another visualization program, VMD, has two seperated options for AMBER trajectory file: with periodic condition and not. I prefer display style of chimera. So, I really hope to see my AMBER trajectory with Chimera. Do you have any tips for this problem? or have plan to add the format, with periodic boundary condition. :-) Thanks again for your great program and have a nice day! ============================================= Lee, juyong Ph.D student, Department of chemistry, Seoul National University, Korea. drfaust23(a)gmail.com

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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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Flickering graphics
by Thomas Goddard 22 Dec '06

22 Dec '06

Hi Murali, What kind of flickering do you see when moving maps in Chimera? Does the surface appear shattered? One nvidia graphics driver bug I have seen causes the surface to appear broken into many triangles instead of smooth while it is moved. Or is it tearing that you see? That is when the top half of the screen momentarily shows one position for the map but the bottom shows a different one. That happens because you are moving the model and the redraw is not synchronized to the vertical refresh of the display. That is a graphics driver setting problem. Or does flicker mean it appears like every other frame is black? Every possibility I can think of points to a graphics driver problem, not a Chimera problem. You can check on Linux what graphics driver you are using with the glxinfo command: % glxinfo ... OpenGL vendor string: NVIDIA Corporation OpenGL renderer string: Quadro4 500 GoGL/AGP/SSE2 OpenGL version string: 1.5.2 NVIDIA 66.29 ... The OpenGL renderer and version lines tell you the driver. If it says "Mesa" this means you have no driver installed and it is using software rendering (no hardware acceleration). Usually a new Linux system does not have a graphics driver installed by default so you have to get the driver from the NVidia web site. http://www.nvidia.com/content/drivers/drivers.asp The latest Nvidia GeForce driver version is 9746. The first step to try to fix your problem is update to the newest driver. Tom > Date: Fri, 22 Dec 2006 09:42:43 -0600 > From: "Murali Ayaluru" <mayaluru(a)gmail.com> > To: goddard(a)cgl.ucsf.edu > Subject: flickerings in model > > Hi, > > Greetings! > > I am using Chimera (chimera-1.2304-linux.exe) in Linux (FC-6) environment. > Basically I use this > for visualizing the structures generated from EM. While moving the model > (either vertical or horizontal) and also while rendering the volumes, I saw > lot of flickering in the model. Is there some parameter I have to change > to fix this problem? The graphic card we use is nVidia GeForce 7300 LE. I > don't have much experience in linux OS. Any suggestions to fix the problem > will be highly appreciated. > > Thanks and have a nice day. > > Regards, > Murali

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