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single-sequence FASTA file does not open
by Lucas J. Thode 12 Oct '06

12 Oct '06

In Chimera beta 1 build 2199 on Windows XP Professional SP2, I cannot open a FASTA file that contains a single sequence. (The file in question is attached and looks to be a valid FASTA file according to the documentation I have read on the FASTA format.) What should I do about this issue? Error log: Opening F:\H Biotech Engineering\cftr.fasta Error reading F:\H Biotech Engineering\cftr.fasta: IOError: Only one sequence found in Aligned FASTA file 'F:\H Biotech Engineering\cftr.fasta'; check your alignment file for errors (see reply log for Python traceback info) Traceback (most recent call last): File "C:\Program Files\Chimera\share\__main__.py", line 59, in ? value = chimeraInit.init(sys.argv) File "C:\Program Files\Chimera\share\chimeraInit.py", line 308, in init tkgui.eventLoop() File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 2757, 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 1747, in __call__ return apply(self.func, args) File "C:\Program Files\Chimera\share\chimera\baseDialog.py", line 229, in <lambda> self.__buttonFuncName(txt))() File "C:\Program Files\Chimera\share\chimera\baseDialog.py", line 470, in OK self.Apply() File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 160, in Apply openPath(path, ftype) File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 258, in openPath mols = chimera.openModels.open(path, type=ftype) File "C:\Program Files\Chimera\share\chimera\__init__.py", line 1086, in open models = func(filename, *args, **kw) File "C:\Program Files\Chimera\share\MultAlignViewer\ChimeraExtension.py", line 33, in <lambda> lambda fn, e=emo, ft=fileType: e.open(fn, ft), File "C:\Program Files\Chimera\share\MultAlignViewer\ChimeraExtension.py", line 25, in open self.module('MAViewer').MAViewer(fileName, fileType) File "C:\Program Files\Chimera\share\MultAlignViewer\MAViewer.py", line 59, in __init__ seqs, fileAttrs, fileMarkups = self.readFile( File "C:\Program Files\Chimera\share\MultAlignViewer\MAViewer.py", line 761, in readFile seqs, fileAttrs, fileMarkups = parseFile(fileName, fileType) File "C:\Program Files\Chimera\share\MultAlignViewer\parse.py", line 100, in parseFile raise IOError("Only one sequence found in %s file" IOError: Only one sequence found in Aligned FASTA file 'F:\H Biotech Engineering\cftr.fasta'; check your alignment file for errors Done opening F:\H Biotech Engineering\cftr.fasta

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Vilualizing solvent distribution
by Atsutoshi Okabe 11 Oct '06

11 Oct '06

Dear all, I want to visualize solvent(water) distributions around one solute molecule. I do molecular dynamics calculation with Amber8 program. So I got the following ouput file using grid command of Ptraj module to analyze trajectories. This line is ignored 1 rdparm generated grid density 100 -49 50 100 -49 50 100 -49 50 30.000 30.000 30.000 90.000 90.000 90.000 ZYX -49 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 I think the output is in the format of a XPLOR formatted contour file and can visualize this output data within chimera soft ware. But I don't know how to treat this out put file in chimera . Can I use this file directory in chimera or have to do anything else before I use chimera? Thanks Atsutoshi

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Request: can model selection be added to the pull down selection menu?
by Boaz Shaanan 10 Oct '06

10 Oct '06

Hi, I wonder if you could consider adding the option of selecting models to the pull-down selection menu. Right now, only chains (and other things) can be selected but quite often, when reading different models with the same chain names, the only way to select specific chains from a model would be by using the command line where models can be specified. This works of course, but having the model-selection option in the pull-down menu might add flexibility. What do you think ? Regards, Boaz Boaz Shaanan, Ph.D. Associate Professor Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel‎

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Re: [Chimera-users] window size
by Viktor Hornak 06 Oct '06

06 Oct '06

Hi Elaine, this is exactly what I needed. Also, thanks for a pointer to experimental features page (it's nice!). One other vaguely related question I had was whether it's possible to find out what chimera commands correspond to actions picked from menus or panels (e.g. Actions->Atoms/Bonds->Hide; Camera -> orthographic from Viewing/Side View panel, etc.). My objective is to capture everything I do in a specific session in chimera command scripts, which have an advantage over saving the session in that 1) I see what I did directly in the script, 2) these scripts are much smaller than session files. Thanks for your help! -Viktor Elaine Meng wrote: > Hi Viktor, > From our experimental features page > > http://www.cgl.ucsf.edu/chimera/experimental/experimental.html > > you can download a "set magnification and window size" feature that > includes a "windowsize" command. > > A related feature (unfortunately broken in past releases, but will be > available in the next release) is the --geometry startup option. We > plan to make a release this month. The --geometry option is not quite > as straightforward as the windowsize command, because depending on the > system, the specified size might include some of the bars around the > graphics window. However, that just means you need to try it once, > use the "get pixels" button on the image-saving panel (File... Save > Image) to determine the actual graphics window dimensions, and at the > next startup use --geometry with the necessary additions or > subtractions to achieve the target size. That's what I've been doing. > > Startup options are described here: > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html > > However, if you are on a Windows system, it is not very convenient to > use startup options (one way is to make a separate Chimera shortcut > and modify its properties). If you are on Windows, getting the > "windowsize" command from the experimental features page may be the > way to go. > > I hope this helps, > Elaine > > On Oct 6, 2006, at 5:43 AM, Viktor Hornak wrote: > >> Dear All, >> >> I was wondering if there's chimera command that sets the size of chimera >> window. Basically I just want to have a well defined window size when I >> save pictures (or movies)... >> >> Thanks, >> -Viktor >> >> -- >> Viktor Hornak >> SUNY at Stony Brook >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > ----- > 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

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fitting a protein inside an EM reconstruction
by jayant_jacques 06 Oct '06

06 Oct '06

hi! I am having a small problem in fitting crystal structures into the EM reconstruction. Problem definition When I open the protein that I am trying to fit into the EM map along side the EM map, the Em Map shrinks. The EM map which is the super set, which holds 3 proteins appears shrunk with respect to the protein that I am trying to fit inside the EM Map and the crystal structure How am I to overcome this hurdle? thanks Jayant Jayasundar Jayant James Postdoc, Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology(VCAPP), Washington state university, Pullman 99164-6520, USA. http://www.chick.com/reading/tracts/0001/0001_01.asp Phone office:335-5937, Cell:1-509-432-5790

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window size
by Viktor Hornak 06 Oct '06

06 Oct '06

Dear All, I was wondering if there's chimera command that sets the size of chimera window. Basically I just want to have a well defined window size when I save pictures (or movies)... Thanks, -Viktor -- Viktor Hornak SUNY at Stony Brook

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OpenGL error in GfxInfo::initialize 'out of memory'
by Dmitry Osolodkin 05 Oct '06

05 Oct '06

Hello all, I have a very small but annoying problem. I had two versions of libGL.so.1, so I have renamed the version in /usr/X11R6/lib/. Now I can run Chimera, but it works rather slow and says OpenGL error in GfxInfo::initialize 'out of memory'. I use Mandriva Linux 2006 and FireGL drivers by ATI. Could anone help me? Thanks. Dmitry Osolodkin

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Re: [Chimera-users] Chimera-users Digest, Vol 42, Issue 2
by Jonathan Hilmer 05 Oct '06

05 Oct '06

Pu Qian, Although resources-intensive, I find it useful to have multiple, identical, overlapping copies of the same density set. It allows complex 'removal' of sections in the final image by the combination of multiple clipping planes. For example, the three planes with definitions of [1,0,0], [0,1,0], and [0,0,1] all with an origin at the center of your data will cut away 1/8 of a spherical region, if you have three copies of the density loaded. This also makes it easy to animate the cutout. The alternative is to use the volume eraser (http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/volerase…) which works, but I've found it less useful for movies. When working with large data sets and this method, use cropped density sets to minimize unnecessary resource usage. Jonathan > > To whom it may concern, > > > > I'm a new user of Chimera. It is a very good software! > > > > Here, I would like to ask you a few questions? To show inside of > > protein > > (3d model),I need to cut it into half (sometime, maybe only part, > > for example, > > 1/4 etc.). Just like an apple, if I want to show its core, I need > > to cut the > > apple into two parts from its middle. Does Chimera has such > > function? (I think > > it has.) My 3d data comes from electron microscopy single particle > > analysis > > using IMAGIC5. Dose Chimera accept 3d data from IMAGIC5? If so, > > which type of > > 3d data I should produce for Chimera? It would be a great > > appreciated if you > > could reply me in your convenience. Hope it will not bother you too > > much. > > > > Sincerely yours, > > > > > > Pu Qian > > > > Dr. Pu Qian > > Department of Molecular Biology > > The University of Sheffield > > Firth Court, Western Bank > > Sheffield, S10 2TN > > UK

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Spider to Brix
by Batsal Devkota 05 Oct '06

05 Oct '06

Hi, When I convert spider file to brix and load both of them in Chimera, they do not superimpose on top of each other. I adjusted the origin to be 0,0,0 for both the maps and still the maps seem to be rotated with respect to one another. any insight?? Thank you, Batsal. -------------------------------------------------- Batsal Devkota Graduate Student, School of Biology GeorgiaInstitute ofTechnology Atlanta, GA 30332-0400

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volumetric filling
by jayant_jacques 04 Oct '06

04 Oct '06

hi! I am striving to perform voluertric filling of a crystal structure into an EM reconstruction. I have down loaded and complited the Linux_64 bit version. I first load my crystal structure and then the EM reconstruction on the same screen and set the EM reconstruction as DATa. I am not able to figure out where the FIT buttons is located in the pop up menus!!! I would be very grateful if you could help me sort out this issue! Thanks Jayant NB I am using the online manual to help me in this endeavour http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmodels/fitmodel… Jayasundar Jayant James Postdoc, Department of Veterinary and Comparative Anatomy, Pharmacology and Physiology(VCAPP), Washington state university, Pullman 99164-6520, USA. http://www.chick.com/reading/tracts/0001/0001_01.asp Phone office:335-5937, Cell:1-509-432-5790

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