- Chimera-users - RBVI Mailing Lists

Help, chimera keeps crashing on startup
by Ann Mullin 19 Oct '04

19 Oct '04

Hi, I run Chimera on MacOS 10.3 with X11. Today I started having problems with Chimera crashing on startup. I deleted the programs and downloaded them again. No help. I reinstalled X11. Again no help. Thanks for all help. Ann Mullin Research Scientist Cell and Molecular Biology Dept. Tulane University New Orleans, LA 70118-5698 504-865-6742 (Ph) 504-865-6785 (FAX) amullin(a)tulane.edu

2 1

by Dr .Julio Ortiz 13 Oct '04

13 Oct '04

Dear Srs: I am a new user of Chimera, and I really like it! I would like to know if some of the developers could include a new format for density maps amongs those that are readable in Chimera: EM format. That would increase its use in our group, because now we need convert our density maps to mrc each time that we want to use Chimera. With my actual skills in programming, to write a plugin will take me like a year, and I think that should be relative easy for someone with experience. As attachment I am sending a text file with a procedure wrote in matlab to read EM format files. The syntax should not be so different from python. I could also provide you with test data. Thank you very much for your help, Dr. Julio Ortiz -- Max-Planck Institut für Biochemie Abteilung Molekulare Strukturbiologie Am Klopferspitz 18 D-82152 Martinsried Germany Tel: +49 (89) 8578 2034 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

2 1

[Chimera-users] Re: streaks in Chimera image of virus electron density map
by Thomas Goddard 12 Oct '04

12 Oct '04

Hi Lu, The streaks on your Chimera density map display are very likely a driver bug specific to the Mac ATI Radeon 9600 Pro (RV350, 64 Mb). You don't see the streaks on a Mac with Radeon 9600 XT graphics (RV360, 128 Mb), and I don't see them with your data set on my Mac Radeon 9800 Pro (R350, 128 Mb). Setting the transparency to a non-zero value makes the streaks go away. When you use transparency Chimera does not use OpenGL display lists. This suggests that the graphics driver bug is related to display lists. OpenGL is an industry standard 3D graphics library that Chimera uses. We have had alot of graphics driver problems with Apple. We submit bug reports to them and sometimes visit them in Cupertino, but it is unlikely we could get this fixed since it appears to be limited to a graphics card they no longer sell. If the streaks do not bother you on-screen too much, a reasonable work-around might be to set transparency to 0.001 just when saving an image. This setting will substantially slow down rotation of the model so it is best to leave the transparency at 0 until you get the right orientation for image saving. Thanks for reporting the problem. Tom > Date: Tue, 12 Oct 2004 14:23:37 -0700 > From: Lu <lugan(a)scripps.edu> > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > Subject: Re: streaks in Chimera image of virus electron density map > > Hi Tom, > I see definitely see streaks in the Chimera display, and they appear to be > parallel to the one of the crystal lattices. They remain even if I rotate > the particle. When I loaded a .pdb with axis coordinates, they appear > parallel with the Y-axis. Another phenotype is that if I make the > transparency non-zero, the streaks go away. > The graphics card is an ATI Radeon 9600 Pro, 64mb. We don't notice this > problem on our other G5, which has an ATI RV360 chip with 128MB of RAM. So > there's a possibility that either our video card is bad, or that specific > ATI model has some issues. > I've attached an example map (which is a low resolution crystal structure > by the way) of our virus particle. It's dsn6/omap formatted. > I hope the problem is just isolated to our video card. > Thanks. > > -Lu > > On Tue, 12 Oct 2004, Thomas Goddard wrote: > > > Hi Lu, > > > > I took a look at the virus EM map image you sent to Eric Pettersen. > > I haven't seen this bug in Chimera. Do you see the streaks in the > > Chimera graphics window? Or do they only appear in the saved image? > > If they appear in the graphics window are they features that persist > > when the model is rotated? Also are the streaks parallel the data set > > x, y, or z axis? You could see this by displaying the outline box > > around the map with volume viewer / options / show outline box. > > > > I have the same Mac as you only my RV350 has 128 Mb. Do you happen > > to know what model graphics card you have, for example, mine is Radeon > > 9800 Pro? I don't think you can find this out from Mac OS -- you just > > have to know from when the machine was purchased. > > > > I suspect our latest Chimera snapshot release 2029 that just came > > out will exhibit the same problem. But it might be worth trying it. > > > > Can you reproduce the streaks with any small data set that I could > > get from you (by web, ftp, or email)? > > > > Hopefully we'll be able to figure this out quickly. > > > > Tom > >

1 0

Re: [Chimera-users] display vectors
by Eric Pettersen 11 Oct '04

11 Oct '04

On Oct 11, 2004, at 6:50 AM, Mingfeng Yang wrote: > I want to show motions of some atoms. Is it possible to draw vectors > origin from each atoms in Chimera? Specifically, I like to draw an > arrow, originning from each atom, with direction and length to > describe the motion. The answer is yes, though the process is a little involved. Can I ask you in what context you are doing this? Is it related to an MD trajectory? Perhaps in future releases we could make this easier if we know specifically what you want to do and what data you are working from. Anyway, there are two methods I can suggest: VRML and pseudobonds. You can show exactly what you want with VRML, but it may be more effort. Pseudobonds may be easier, but you can’t have arrowheads. For VRML, you just compose a VRML file using a cylinder and cone for each arrow. The cone is the “arrowhead” and you have the cylinder go from the atom to the base of the cone, and have the cone point in the right direction. If you don’t know how to use VRML, this page has a spec and examples: http://www.web3d.org/x3d/specifications/vrml/ISO_IEC_14772-All/ index.html For pseudobonds, you would make up a fake molecule where the “atoms” are at the ends of the vectors you want to show. If you make a PDB file, start it with a TER card and use HETATM records for each atom, with a different residue number for each. This will ensure that Chimera won’t connect any of the atoms in the fake molecule. You can then use the PBReader tool (in the Utilities category) to read in the pseudobonds to display (including colors and optional labels). You can use the pseudobond panel (under inspectors) to control if the pseudobonds are wires or sticks, if they are dashed [wire only], and so forth. Let me know if you need any more help getting started with this. Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

1 0

[Chimera-users] streaks in Chimera image of virus electron density map
by Lu 11 Oct '04

11 Oct '04

Hello, I've been using Chimera to generate beautiful images of entire virus particle from an O-style map file. However, most of the images that I capture have a few black streaks in the image. The streaks appear as thin, parallel lines, like someone dragged a pen across a painting before it dried. Does anyone know how I can remove these streaks without having to resort to Photoshop? I can provide sample images too. Thanks in advance! -Lu Gan

3 2

Problems in Windows XP
by Jutta J Roth 28 Sep '04

28 Sep '04

To whom it may concern: We have been trying to run chimera in Windows XP and unfortunately are not able to do so. The program runs great on the Mac machines though. The only problem obvious for us is, that the collaboratoryHub shortcut does not show up. We can start the program, but when we try to open a file the sequence window starts flickering and the structure does not load. We really like the program a lot and would like to cite it in a paper we are currently working on, but in order to do that we need to get it to work on the PCs. Therefore every advice would be highly appreciated. Thanks! Sincerely, Jutta Roth ''''''''''''''''''''''''''''''''''''''''''''''' Jutta Johanna Roth Department of Ecology and Evolutionary Biology Yale University 165 Prospect Street New Haven, CT 06511 Tel.: 203.432.9741 (w) 203.776.2364 (h) Fax: 203.432.3870

2 1

display of single letter AA code?
by Mark Daniels 28 Sep '04

28 Sep '04

Hello Chimera administrator(s)- I was wondering if there is any way fior Chimera to display amino acid residue names in single-letter format, rather than the three-letter format one gets when selecting Actions-->Label-->residue-->name ? I have looked over all the documentation I can but have not found anything to answer this question. Thanks in advance- Mark Mark J Daniels Department of Cell Biology The Scripps Research Institute La Jolla, CA 92037

2 1

Request info
by Negi, Surendra S. 22 Sep '04

22 Sep '04

Hi, How can i save some region of an EM data in Chimera. I can corp the region of my interest in EM map using chimera but I am unable to save the data in mrc format. How can i save this region of EM data in mrc file. Thanks for your help. Best, surnedra

2 1

Fwd: [Chimera-users] Chimera, Python, WindowsXP or AMD64 conflict?
by David Piper 17 Sep '04

17 Sep '04

Unfortunately, there is not a suitable graphics driver update for the ATI Radeon card for the notebook I am using. David

1 0

Just fixed Re: [Chimera-users] WinXP SP1 python error on File -> Open
by Pattanayek, Sabuj 17 Sep '04

17 Sep '04

Hi, I just tried this and it fixed the problem: Delete these directories: C:\Documents and Settings\All Users\Application Data\chimera C:\Documents and Settings\sabuj\Application Data\chimera (whatever your username may be) Then uninstall and reinstall chimera and file->open works again. Thanks, ...Sabuj Quoting "Pattanayek, Sabuj" <sabuj.pattanayek(a)vanderbilt.edu>: > Hi, > > I'm getting a strange error when I start chimera and do file->open. This is > the > reply log: > > ValueError: list.index(x): x not in list > (see reply log for Python traceback info) > Traceback (most recent call last): > File "C:\Program Files\Chimera\share\__main__.py", line 56, in ? > value = chimeraInit.init(sys.argv) > File "C:\Program Files\Chimera\share\chimeraInit.py", line 301, in init > tkgui.eventLoop() > File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 2891, in > eventLoop > app.mainloop() > File "C:\Program Files\Chimera\bin\lib\lib-tk\Tkinter.py", line 965, in > mainloop > self.tk.mainloop(n) > File "C:\Program > Files\Chimera\bin\lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line 1751, > in > __call__ > _reporterror(self.func, args) > File "C:\Program > Files\Chimera\bin\lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line 1814, > in > _reporterror > displayerror(msg) > File "C:\Program > Files\Chimera\bin\lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line 1377, > in > displayerror > _errorReportFile.write(text + '\n') > File "C:\Program > Files\Chimera\bin\lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line 1747, > in > __call__ > return apply(self.func, args) > File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 272, in > _importModel > clientSticky='ew') > File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 178, in > __init__ > OpenModeless.__init__(self, **kw) > File "C:\Program Files\Chimera\share\OpenSave\__init__.py", line 185, in > __init__ > ModelessBase.__init__(self, **self.dialogKw) > File "C:\Program Files\Chimera\share\chimera\baseDialog.py", line 378, in > __init__ > BaseDialog.__init__(self, master, *args, **kw) > File "C:\Program Files\Chimera\share\chimera\baseDialog.py", line 220, in > __init__ > self.fillInUI(self.__top) > File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 181, in > fillInUI > OpenModeless.fillInUI(self, parent) > File "C:\Program Files\Chimera\share\OpenSave\__init__.py", line 92, in > fillInUI > self.millerBrowser = MillerBrowser(parent, **self.millerKw) > File "C:\Program Files\Chimera\share\OpenSave\miller.py", line 184, in > __init__ > self.makeMainColumn(initialdir, firstTime=1) > File "C:\Program Files\Chimera\share\OpenSave\miller.py", line 509, in > makeMainColumn > titleMode=None, firstTime=firstTime) > File "C:\Program Files\Chimera\share\OpenSave\miller.py", line 823, in > __init__ > index = normItems.index( > ValueError: list.index(x): x not in list > > I have also posted the screenshot here > http://linegli.mc.vanderbilt.edu/~sabuj/chimeraOpenError.jpg > > Also if I do "c:\Program Files\Chimera\bin\chimera.exe" file.pdb from the > command line, then do file -> open, it works again. I've tried running it > with > and without precompiling modules after installation, but get the same > result. > > I've downloaded the binary installation several times, done uninstall, then > install, but I'm still getting the same error. I have not been able to > re-create > the error on another winxp sp1 machine. > > Any help would be appreciated, > Thanks, > Sabuj Pattanayek > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

2 1