March 2009 - Chimera-users - RBVI Mailing Lists

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 `~: `~: `~: `~: `~: `~: `~: `~: `~:

2 1

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 -----------------------------------------------

2 1

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

2 1

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.

4 3

(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 -----------------------------------------------

3 3

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

2 1

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

3 3

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/ >> >

1 0

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

2 1

matchmaker output
by Elaine Meng 04 Mar '09

04 Mar '09

> I want to simplify the question I asked yesterday. Is there any way to > store the output of Match Maker, specifically the RMSD values for > every > residue and the list of residues in the alignment regions in an > external file from command line? Hello, I just wanted to bring up a related issue: the sequence alignment you get from MatchMaker is not a fully structure-based alignment. If the sequences are fairly easy to align, this is not an issue, but when sequence identity is low, you may want to generate a structure-based sequence alignment with Match->Align after superimposing the structures with MatchMaker. More explanation... by default, MatchMaker: (1) generates a pairwise sequence alignment using standard methods. Some structure information is used at this step because the alignment score includes both residue type (alanine, arginine, ...) and secondary structure (helix, strand ...). (2) uses the sequence alignment to fit the structures. At first all columns are used, but iterating the fit discards the columns where the structures match poorly in space. If there are sections of the alignment that are wrong, the iteration process tends to exclude them from fitting, resulting in a good-looking superposition. Therefore, a successful and correct superposition (as determined by eye) does not mean all the parts of the sequence alignment are right. If the sequences are similar enough that you don't think errors in the MatchMaker sequence alignment are an issue, saving the residue pairing and RMSD header (which for pairwise is simply the CA-CA distance) directly from that alignment is fine. If you are getting into the twilight zone of sequence similarity, I suggest running Match->Align on the superposition, then proceeding with that second sequence alignment instead. Another advantage of Match->Align is that it can make a single sequence alignment of >2 superimposed structures. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchalign/matchal… > <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchma… > Best, 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

1 0

Chimera-users March 2009