- Chimera-users - RBVI Mailing Lists

adding CONECT records with nogui option
by shyamala 16 Mar '09

16 Mar '09

Hi Chimera users, I am sure there is a simple way to do this, but I need some help. I want to add CONECT records to a pdb file, given that the input file contains all necessary atom coordinate information. I need to do this within my shell script and I want to start chimera using the nongui option. Now, doing some google seach brought up this solution to add CONECT records (in the command line within CHIMERA gui) pdbrun nouser conect cat > filename.pdb where filename.pdb is the name of the output file with CONECT records added. the above mentioned command works when I pull up the file on GUI CHIMERA My question is then how would I use such a command when I want to use it in the nogui option. I have multiple files (>100) for which I need to add CONECT records and I want to do it with a script. Also, if someone could point me to a good resource for writing python scripts that can be then passed on to chimera, I would be grateful. Thanks, Shyamala Shyamala Iyer Graduate Student Department of Microbiology PO BOX 357242 University of Washington Seattle, WA, 98195

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Problem adjusting sphere quality in script
by Marhoefer, R (Richard) 16 Mar '09

16 Mar '09

Dear Chimera Users, I want to adjust the quality of spheres, cylinders and ribbons in a script. From the moviemaking tutorial script I learned that I must use some lines of Python. Therefore, I used the code as found in the example: import chimera chimera.LODControl.quality = 20 When I open this script like in the tutorial, the value of "subdivision quality" in the "Effects" panel is indeed set to 20. However, the quality of spheres and cylinders remains untouched. From that point in time any further modifications of the value in the "Effects" panel do not have any effect. If I change the value of "subdivision quality" in the "Effects" panel before opening the Python code, anything works fine. Did anybody succeed with changing the sphere quality in a script? Kind regards, Richard Mit freundlichen Grüßen / With kind regards Dr. Richard Marhoefer Senior Scientist BioChemInformatics Intervet Innovation GmbH Zur Propstei 55270 Schwabenheim, Germany E-Mail: richard.marhoefer(a)sp.intervet.com Phone: +49 (6130) 948 204 Fax: +49 (6130) 948 517 Mobile: +49 175 723 081 4 Home http://www.intervet.com Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 Geschäftsführer: Dr. Peter Schmid -------------------------------------- This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited -- please immediately and permanently delete. --------------------------------------

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command line
by Sirano Dhe-Paganon 16 Mar '09

16 Mar '09

After entering a command in the "command line" of UCSF-Chimera, I would like the command that I pasted to disappear. Currently, it does not disappear; how can I make it disappear after I press the enter button?

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Chimera needs your vote.
by Nir London 16 Mar '09

16 Mar '09

There is a poll going on at the macromolecular modeling blog "What is your favorite molecular viewer?" http://rosettadesigngroup.com/blog/284/what-is-your-favorite-molecular-view… PyMOL is currently at the lead, but you might make the difference, go ahead and show your support for Chimera (or choose one of the other viewers if you like them more) but most importantly drop a comment as to why YOUR viewer is the best. Disclaimer: for fairness, similar messeges are sent to the other competitors mailing lists as well, but we like yours the most ;) Nir London. Rosetta Design Group. http://rosettadesigngroup.com/blog/

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centering on an atom
by Sirano Dhe-Paganon 16 Mar '09

16 Mar '09

In UCSF-Chimera, I would like to center on an atom of a molecule without zooming-in towards the atom. I found the "focus" command, which centers the atom, but the command includes a zooming-in step; is there a "focus" or "center"-like option that does not zoom-in? Also, most visualization programs have a simple, one-click mouse-button to center on an atom; I cannot find this option in UCSF-Chimera. Sirano

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Re: [Chimera-users] window size
by Elaine Meng 13 Mar '09

13 Mar '09

Hi Jean-Paul, For a more reliable response, please send questions to chimera- users(a)cgl.ucsf.edu rather than to me directly -- I might be out (sick or vacation), or others may know the answer when I don't! There is no preference for window sizes and locations. However, there is a startup option "--geometry" for the main window (but not other tools, sorry): <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html#geometry> How to specify startup options depends on your type of computer: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/startup.html> Some related things... After you start Chimera, you can use the "windowsize" command to specify the pixel dimensions of the main window. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/window.html> If you save a session, it should restore with the same main window size. I don't think the location is saved, however. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/sessions.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Mar 13, 2009, at 11:16 AM, Jean-Paul Armache wrote: > hello, > i have a question. is there a way of saving the window sizes and > windows positions in chimera ? whenever i start chimera the default > all the windows have always the same position and sizes. i always > adjust it to the same position and size, but maybe there is a way to > save it as a preference ? i checked the preferences file, nothing > there. > thank you, > best regards, > jean-paul armache

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chimera help
by Terrance Chiang 11 Mar '09

11 Mar '09

Hi, I've been trying to make an electrostatic potential map for the protein that I'm working on, but there seems to be some error with the file when I try to open it. I was wondering if you could help me with this. The error says: Missing "object 1 class gridpositions counts <l><m><n>" header line I also need help with using the pdb2pqr service that can convert files from pdb into apbs. Perhaps my error lies there. Thanks, Terrance Chiang

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Atoms outside volume
by Tom Goddard 10 Mar '09

10 Mar '09

Hi Tsutomu, I guess you want the atoms outside a given contour level of the volume. There is a Chimera keyboard shortcut "oa" (outside atoms) to select those atoms. If you don't use shortcuts (Tools / General Controls / Keyboard Shortcuts) you can run them as ordinary Chimera commands using the "ac" command: volume #0 level 2.5 select #1 ac oa These 3 commands set the contour level for map #0, select all the atoms in PDB model #1, then run keyboard shortcut oa which changes the selection to just those outside the contour. If you have multiple maps open, the "oa" shortcut is using the highlighted one in the volume dialog. You can write the selected atoms to a file if desired with menu entry Actions / Write List.... If you really want atoms outside the volume bounding box, then just use a threshold less than the smallest data value (range shown in volume dialog). Tom Tsutomu Matsui wrote: > Dear Tom, > > My name is Tsutomu Matsui, a postdoc in Jack Johnson Lab at Scripps > Resaerch Institute. I love Chimera very much. I would like to select > all atoms inside or outside a volume file (density map). Is it possible? > > Thank you very much, > Tsutomu >

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center of the molecule
by Bala subramanian 10 Mar '09

10 Mar '09

Dear Friends, How can i get the x,y,z of the center of the loaded molecule in chimera. While i do box generation generation for DOCK program, i want to tell the script to construct box by considering the x,y,z center of the molecule. Thanks, Bala

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Copy a pdb display configuration to another pdb model
by Tom Goddard 10 Mar '09

10 Mar '09

Hi Xiangan, I've added a new Chimera command "mcopy" to copy colors, display styles, coordinates and other settings from one molecule to another. mcopy #0 #1 will copy the colors, display styles (ribbon, stick, sphere, ...), and visibility (which atoms/residues shown) from molecule #0 to molecule #1. To copy other attributes such as atom coordinates, molecule placement (transform), or labels use the "settings" option: mcopy #0 #1 settings lxp copies just atom/residue labels, atomic coordinates and placement. The recognized settings are: c = color, s = style, v = visibilty, l = labels, x = coords, p = placement, a = all. The default is "csv". This command will be in tonight's Chimera builds. http://www.cgl.ucsf.edu/chimera/alpha-downloads.html Tom Xiangan Liu wrote: > Tom, > I asked you a question in BPS meeting regarding the implementation of > copying a display configuration of a pdb file to anoth pdb with the > same sequences. Did you get chance to implement it into chimera daily > release? If yes, what is the command. If not, can you send me the > corresponding python codes to me? > Thanks, > > Xiangan >

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Atom Replacement
by Warren Menezes 10 Mar '09

10 Mar '09

** High Priority ** Hi! I was wondering if it is possible to replace a Selenium atom in a protein with a Sulfur atom? The reason is because Sulfur has parameters. Thanks! Warren M Chicago

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Re: [Chimera-users] converting a pdb to surface, then to obj
by Tom Goddard 10 Mar '09

10 Mar '09

Hi Dave, Yes, exporting surfaces from Chimera in Wavefront OBJ format does not include colors for multi-color surfaces. You have to export VRML, X3D, Povray, or Renderman formats for that. I know some people export to VRML then convert to OBJ with other software for import into Maya, but I have not seen any case where they carried the Chimera colors into Maya. If you figure out how to do that I'd like to hear about it. Tom Dav Tom wrote: > Daer Thomas Goddard, > > I recently saw your reply to export feature to obj. > > Is it true that there is no current support to export vertex color > (e.g. electronic potential surface color) through obj export format. > Only the vrml and x3d export include vertex color. > > thank you > > Dave. > > "Hi, I am trying to use pdb files to generate surface models (using > multiscale models) to convert to .obj files for use with Maya software. > I keep getting the same error and can't decide if I'm just not using the > command appropriately or if the is something else wrong with the files. > Any ideas?" >

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Re: [Chimera-users] Renaming chain directly in Chimera
by Elaine Meng 10 Mar '09

10 Mar '09

Hi Damien, For a more reliable response, please send mail to chimera-users(a)cgl.ucsf.edu rather than to me directly -- sometimes the others know the answer when I don't, and sometimes I'm away from work. Chimera doesn't provide a way to just choose some set of residues and give them any chain ID you want. It can reassign chain IDs if you are merging models, for example if you had two models that were both chain A, it could combine them into another model with chains A and B. However, I can't think of how that process could be used to do what you want in this situation. I've come across a few PDB-editing web servers, but I don't know which of these might do what you want. You may need to use SPDBV for pre- processing in this case. Here are the web servers in case they are of general interest: <http://www.igs.cnrs-mrs.fr/Caspr2/magicPDB.cgi> <http://dicsoft2.physics.iisc.ernet.in/pdbgoodies/inputpage.html> 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 Feb 27, 2009, at 9:40 AM, Damien Larivière wrote: > Dear Elaine, > > If a PDB structure contains 2 chains A and B, is it possible to > rename chain B as for example chain A directly in Chimera in order > to get one only chain ? Also, is it possible to rename part of > residues of a chain A (residues 256 to 312 for example) as chain B ? > > I ask this question because I often export low resolution surfaces > (obtained with Multiscale Models tool) in the vrml format or obj > format. However, I often have to color all the model (chains A and > B) in only one color and highlight a set of residues in another color. > > I know that I can do this by selecting the residues of interest, > coloring them by using Color zone, but the result is not exportable > in VRML (problem of vertex color or something like that). To avoid > export problem, it is very simple to rather rename chains and/or > reassign a letter to part of chain, which I do by using > SwissPDBviewer. So, can I do this in Chimera ? > > Thanks for your help > > Damien >

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WriteDMS with cofactors?
by Walter Novak 10 Mar '09

10 Mar '09

Hi All, I seem to have trouble with the dock prep procedure for molecules with cofactors, specifically NADP+. I cannot figure out how to write out the surface of both the protein and cofactor together. I can do this with the standalone DMS program using the "-a" flag. Am I missing something? I am using pdb 1el3 as a test and trying to redock the inhibitor I84 back into the complex. I completed the tutorial using 1abe and this was very valuable in learning how to prep molecules with DOCK. Thanks, Wally Walter R.P. Novak, Ph.D. Postdoctoral Fellow Rosenstiel Basic Medical Research Center Brandeis University 415 South St. MS 029 Waltham, MA 02454-9110 Phone: (781) 736-4944 Fax: (781) 736-2405

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program loading problem
by John Means 09 Mar '09

09 Mar '09

I previously had the latest release version of Chimera running on RedHat. Last week I ran the RedHat updater, and now Chimera will not load. When I run the program executable, the splash screen comes up, saying "Loading Tix" then the splash screen goes away. I've tried removing the Chimera directory and reinstalling the program, to no avail. Any suggestions or assistance would be greatly appreciated. -John Means

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Displaying a dimer from a monomer
by Eric Pettersen 09 Mar '09

09 Mar '09

(extracted from a bug report...) Dear Folks, How do I display a dimer, such as for 6RHN? So far I have been able to call up the monomer only, whereas the structure (and other evidence) shows it to be a dimer. Thanks, Sincerely, John Lowenstein

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converting a pdb to surface, then to obj
by Cheri Hampton 09 Mar '09

09 Mar '09

Hi, I am trying to use pdb files to generate surface models (using multiscale models) to convert to .obj files for use with Maya software. I keep getting the same error and can't decide if I'm just not using the command appropriately or if the is something else wrong with the files. Any ideas? Thanks, Cheri > <type 'exceptions.AttributeError'> Exception in Tk callback > Function: <function command at 0x1a44ab90> (type: <type 'function'>) > Args: () > Traceback (innermost last): > File > "CHIMERA/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line > 1747, in __call__ > None > File "CHIMERA/share/chimera/baseDialog.py", line 244, in command > None > File "CHIMERA/share/OpenSave/__init__.py", line 210, in Save > None > File "CHIMERA/share/chimera/baseDialog.py", line 453, in OK > None > File "CHIMERA/share/OpenSave/__init__.py", line 161, in Apply > None > File "/home_local/cheri_local/chimera/share/ExportOBJ/__init__.py", > line 177, in write_surfaces_cb > write_surfaces_as_wavefront_obj(paths[0]) > File "/home_local/cheri_local/chimera/share/ExportOBJ/__init__.py", > line 184, in write_surfaces_as_wavefront_obj > mlist = surface_models() > File "/home_local/cheri_local/chimera/share/ExportOBJ/__init__.py", > line 147, in surface_models > mlist = chimera.openModels.list(modelTypes = [_surface.Surface_Model, > <type 'exceptions.AttributeError'>: 'module' object has no attribute > 'Surface_Model' -- `~: `~: `~: `~: `~: `~: `~: `~: `~: Cheri M. Hampton, Ph.D Howard Hughes Medical Institute Columbia University Medical Center 650 W 168th St. P&S Black 2-221 New York, NY 10032 (212)305-9524 ch2674(a)columbia.edu `~: `~: `~: `~: `~: `~: `~: `~: `~:

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Gap between C=O mainchain bond and supersmooth ribbon
by Dr. Jean-Didier Maréchal 09 Mar '09

09 Mar '09

Dear all, I want to represent the C=O bond that chelates an ion in my structure and the rest of the prot in ribbon (supersmooth). I don't want the carbon explicitly represented but yes the bond and the oxygen with a ball and stick representation. Following a previous post, I have two copies of my model. One is represented in ribbon. In the other one, I have the oxygen in bs and for the bond I did "bonddisplay always #1:22@C,O". It does pretty much what I want but I see that in many cases I have a empty gap between the end of the bond and the ribbon. Something I don't want. Is there a way to remove this gap? Or should I always represent the carbon also (something I find less esthetic that the other option). All the best, 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: viernes, 06 de marzo de 2009 5:16 Para: chimera-users(a)cgl.ucsf.edu Asunto: Chimera-users Digest, Vol 71, Issue 6 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. (no subject) (Du, Sean) 2. Re: (no subject) (Elaine Meng) 3. Re: (no subject) (Eric Pettersen) 4. Re: Issue with surface modelling using Chimera (Elaine Meng) 5. saving a rotated map (Scott Stagg) 6. Re: saving a rotated map (Gabriel Lander) ---------------------------------------------------------------------- Message: 1 Date: Thu, 5 Mar 2009 14:08:39 -0800 From: "Du, Sean" <Sean.Du(a)maxygen.com> Subject: [Chimera-users] (no subject) To: <chimera-users(a)cgl.ucsf.edu> Message-ID: <3A581C9EE7D7DF43ACE4FAA43592FAEC07B3542B(a)rc-ga-mail-1.mxygn.com> Content-Type: text/plain; charset="us-ascii" Dear Chimera developers and sophisticated users, I have trouble to show the surfaces of serveral crystal structures, including 1rzk and 2b4c. Whenever I select: Action/Surface/Show, I would get pop-up error window and the following message in my Reply Log: C:\Program Files\Chimera\bin\mscalc.exe 1.400000 2.000000 0 Surface calculation failed, mscalc returned code 5 C:\Program Files\Chimera\bin\mscalc.exe 1.400000 2.000000 0 Surface calculation failed, mscalc returned code 5 Since I don't have problem with other pdb files, such as 3dnn, I wonder if this problem is simply associated with some particular pdb files? If anyone out there knows a few tricks to overcome this, I'd really appreciate it. Many thanks in advance, Sean ---------------------------------------------- Sean Du, Ph.D. Senior Scientist, Project Leader Maxygen, Inc. 515 Galveston Drive Redwood City, CA 94063 Office: (650) 298-5380 Cell: (510) 366-3586 -----------------------------------------------

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D-amino acids
by Francesco Pietra 06 Mar '09

06 Mar '09

Hi Elaine: As I was interested in inverting the configuration at the alph carbon of amino acids in a peptide, I came across (between ==) ========================= Elaine Meng meng at cgl.ucsf.edu Mon Jun 30 10:53:33 PDT 2008 Hi Yasser, Sorry, mutation with the Rotamers tool (or swapaa command) is only to L-amino acids. Some less convenient alternatives: - use Build Structure (under Tools... Structure Editing) to build out the D- side chain manually. Note the resulting bond lengths and angles are approximate. - open another structure that contains the D- amino acid, match the backbone atoms of the residue you wish to substitute, write out coordinates "relative to" the first structure, then manually edit the PDB file to substitute that sidechain for the one originally in the structure. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at 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 Jun 27, 2008, at 12:33 PM, Yasser Almeida Hernández wrote: > Can Chimera mutate by D-residues? If this is possible, how i can do > it? > > Thanks... > -- > Yasser Almeida Hernández > Estudiante, 4to Año Bioquímica > Facultad de Biología > Universidad de la Habana ================================ What about doing that with a molecular mechanics package? Most such packages have the capability of enantiomerize. Then, back to Chimera. Your view? thanks francesco pietra

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saving a rotated map
by Scott Stagg 06 Mar '09

06 Mar '09

Hello all, I would like to save a rotated density map after using the fit map in map feature, but I can't figure out how to save the transformed map. Does anyone have any suggestions? Thanks, Scott -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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(no subject)
by Du, Sean 06 Mar '09

06 Mar '09

Dear Chimera developers and sophisticated users, I have trouble to show the surfaces of serveral crystal structures, including 1rzk and 2b4c. Whenever I select: Action/Surface/Show, I would get pop-up error window and the following message in my Reply Log: C:\Program Files\Chimera\bin\mscalc.exe 1.400000 2.000000 0 Surface calculation failed, mscalc returned code 5 C:\Program Files\Chimera\bin\mscalc.exe 1.400000 2.000000 0 Surface calculation failed, mscalc returned code 5 Since I don't have problem with other pdb files, such as 3dnn, I wonder if this problem is simply associated with some particular pdb files? If anyone out there knows a few tricks to overcome this, I'd really appreciate it. Many thanks in advance, Sean ---------------------------------------------- Sean Du, Ph.D. Senior Scientist, Project Leader Maxygen, Inc. 515 Galveston Drive Redwood City, CA 94063 Office: (650) 298-5380 Cell: (510) 366-3586 -----------------------------------------------

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Issue with surface modelling using Chimera
by Leiah Luoma 06 Mar '09

06 Mar '09

Hi there, I'm in the middle of using Chimera to analyze my protein model and want to look at the predicted surface. I cannot get it to show the whole surface: a few tracts of ribbon structure pepper the model. I selected all from the drop down menu, and waited until the whole model was highlighted, and then set it to show surface. When I select the regions which are not showing up, and try to surface model them individually, it does not work either. Is there any solution, or some reason why this would happen? The tracts are between 2 and 5 amino acids long. Attached is an image (jpg) of the problem I'm describing. Thanks for your help in advance, Leiah Luoma

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Importing Midas within non-Chimera python installation
by Drew Bryant 05 Mar '09

05 Mar '09

Hello, As part of a larger python-based project I'm working on, I need to do automated image generation with Chimera. How can the Midas module (no need for any gui components) be imported into a non-chimera installation of python? I think this is a little more complicated than just setting the PYTHONPATH to point at the chimera files, because of the compiled shared objects. For example, my attempt at importing Midas (after adding CHIMERA/share to the PYTHON PATH) raises: /home/dbryant/CHIMERA/share/Midas/__init__.py in <module>() /home/dbryant/CHIMERA/share/chimera/__init__.py in <module>() <type 'exceptions.ImportError'>: libgfxinfo.so: cannot open shared object file: No such file or directory Currently I'm using a non-gui daily build of Chimera for 64-bit Linux and calling the chimera binary via the shell (which works), but I need to be able to pass parameters to the script being run at the command line. Thanks, Drew Bryant

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Re: [Chimera-users] Chimera failed abnormally; the exit code was 3.
by Greg Couch 05 Mar '09

05 Mar '09

Another chimera bug fixed by updating the graphics driver! FYI, this is frequently true on any platform, but especially true for laptops, Windows Vista, and Linux with software OpenGL (the mesa package). - Greg On Thu, 5 Mar 2009, Andy LiWang wrote: > Dear Greg, > Many thanks for your help. Even though I am running Vista, I used your > hyperlink to find the following site for Vista: > http://support.dell.com/support/downloads/driverslist.aspx?os=WLH&osl=EN&ca… > = > > After downloading updates from the site above for Chipset (Intel Driver for > Mobile Chipset) and Video (nVidia driver for Quadro FX 360M), Chimera works > on my Dell Precision M4300 Vista laptop! > > My best regards, > Andy > --- > > On Wed, Mar 4, 2009 at 1:34 PM, Greg Couch <gregc(a)cgl.ucsf.edu> wrote: > >> On Wed, 4 Mar 2009, Andy LiWang wrote: >> >> Dear Sir/Madam, I just installed Chimera on my Dell Precision M4300 laptop >>> equipped with a NVIDIA Quadro FX 360M graphics card. I downloaded >>> chimera-1.3.2577-win32.exe< >>> https://www.cgl.ucsf.edu/cgi-bin/chimera-get.py?file=win32/chimera-1.3.2577…> >>> from your website and it auto-installed when I double clicked it. >>> >>> However, when I started up Chimera it aborted with the following two error >>> windows: >>> Microsoft Visual C++ Runtime Library >>> Runtime error! >>> Program: C:\Program Files\Chimera\bin\pythonw.exe >>> abnormal program termination >>> >>> Chimera Launcher Error >>> Chimera failed abnormally; the exit code was 3. >>> Use the --debug command line option for the full error message >>> >>> I look forward to your suggestions. >>> >>> Sincerely yours, >>> Andy LiWang >>> >> >> In the Windows version of chimera you can use the "Chimera - Debug" menu >> entry to get the debug output (press the Start button on the taskbar, go to >> All Programs, the UCSF Chimera, then Chimera - Debug). Then copy and paste >> the debug text into an email to me. >> >> Because there are frequently graphics/video driver problems with laptops, >> I'd also recommend updating your graphics/video driver to the latest >> version from Dell. The last one for Windows XP is version 175.75 from >> 7/3/2008, < >> http://support.dell.com/support/downloads/download.aspx?c=us&l=en&s=gen&rel… >>> . >> >> Greg Couch >> UCSF Computer Graphics Lab >> http://www.cgl.ucsf.edu/chimera/ >> >

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Chimera failed abnormally; the exit code was 3.
by Andy LiWang 04 Mar '09

04 Mar '09

Dear Sir/Madam, I just installed Chimera on my Dell Precision M4300 laptop equipped with a NVIDIA Quadro FX 360M graphics card. I downloaded chimera-1.3.2577-win32.exe<https://www.cgl.ucsf.edu/cgi-bin/chimera-get.py?file=win32/chimera-1.3.2577…> from your website and it auto-installed when I double clicked it. However, when I started up Chimera it aborted with the following two error windows: Microsoft Visual C++ Runtime Library Runtime error! Program: C:\Program Files\Chimera\bin\pythonw.exe abnormal program termination Chimera Launcher Error Chimera failed abnormally; the exit code was 3. Use the --debug command line option for the full error message I look forward to your suggestions. Sincerely yours, Andy LiWang --- Associate Professor School of Natural Sciences UC Merced Atwater, CA 95301 Tel: (209) 228-4617 Fax: (209) 724-4356

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