- Chimera-users - RBVI Mailing Lists

Movie - Display Spheres
by Jared Godar 20 Oct '06

20 Oct '06

Hello, I am trying to use the 'represent spheres' command to draw attention to specific residues in a model that is displayed as a ribbon. I would like to first show the ATP binding site of the molecule with magenta spheres, then show the three residuse which get phosphorolated. Currently, I am able to display one of these elements or the other as spheres, but not both at the same time. I've tried to use a single represent sphere command to specify all of the desired atoms, but can't seem to get the context right, represent sphere #0:426,431,432,ATP and represent sphere #0:426,431,432 & #0::ATP weren't working. Help on the syntax to simultaneously display the two commands listed below which are currently mutually exclusive would be appreciated. #SHOW ATP: color magenta #0::ATP; color magenta #0::mg; represent sphere #0::ATP #SHOW PO4 Residues show #0:426,431,432; color yellow #0:426; color orange red #0:431; color red #0:432; represent sphere #0:426,431,432 Thanks, Jared -- Jared A. Godar Graduate Student: Stewart Lab Vanderbilt University Medical Center Department of Molecular Physiology & Biophysics 708 Light Hall 2215 Garland Ave. Nashville, TN 37232-0615 Work: 615.322.7898 Fax: 615.322.7236 jared.godar(a)vanderbilt.edu

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Dock?
by S Joshua Swamidass 19 Oct '06

19 Oct '06

Hello, Are there any plans to develop a gui frontend for DOCK using chimera? Josh

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force fitting a protein into select volume in a EM reconstruction
by jayant_jacques 17 Oct '06

17 Oct '06

hi! Is it possible in chimera to choose a particular part of a EM envelope and a protein and fit them? AS the protein that I am trying to fit into the map finds a better fit else where in the EM envelope, after I painstakingly align it to the place where its supposed to be!!! 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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release candidate
by Eric Pettersen 17 Oct '06

17 Oct '06

We've made a release candidate (version 1.2303) available for download. It has many new features relative to the previous production release (1.2199). The features/improvements are listed here: http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2303.html Please let us know if you encounter any problems with the release candidate. If no major problems surface in the next few days, we will promote the candidate to production release status. Enjoy! Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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viewing
by jayant_jacques 17 Oct '06

17 Oct '06

Hi! I thank chimera users for answering and helping me in fitting my protein into EM Map. I have a small problem. When I rotate the protein, portions of the map and protein come into view and dissappear. I am not able to figure out how to turn off this feature in chimera! I would be grateful if told how to turn off this feature. 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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Re: [Chimera-users] About Chimera under Linux64
by Thomas Goddard 17 Oct '06

17 Oct '06

Hi Quentin, I suggest you use the 32-bit Linux Chimera version 1.2255. Or if you wait a few days a new 32-bit Linux Chimera version 1.2303 will be coming out. We do not regularly build a 64-bit Linux Chimera because we do not have a 64-bit Linux system in our lab. (I'll have to check on this -- maybe we have one now.) The only 64-bit version we routinely distribute is for the very obscure Tru64 operating system running on computers with Alpha processors. The current 64-bit Linux build (May 2005) is so old that it lacks many useful features for looking at EM maps. The reason we have not moved more quickly to support 64-bit distributions is because Chimera is strongly oriented towards interactive calculations -- that is calculations taking at most a few seconds. On gigabyte size data there is almost nothing that can be done in a few seconds. Still we understand that you may look at the data subsampled (using the volume dialog step size) and then want to create an image at full resolution (for example for a publication or talk) that may take many minutes to render and will need alot of memory -- not easily accomodated in a 32-bit address space. It is our plan to regularly distribute 64-bit Linux and Windows version in the future -- probably within a year. The main hold-up is that we do not have 64-bit machines setup in our lab yet. The usual method of working with large EM tomograms in Chimera is to focus on smaller regions of interest so that segmentation can be done interactively. Practical size chunks of data are 256^3. You can select these smaller regions in Chimera. For large pieces the graphics hardware is not able to render fast enough to allow smooth interactive rotation used in segmenting interactively. It is possible to display larger volumes and just display every other data plane along each axis. Tom > Date: Tue, 17 Oct 2006 14:11:12 +0200 > From: Quentin <derobill(a)mpi-cbg.de> > User-Agent: Thunderbird 1.5.0.7 (X11/20060922) > To: goddard(a)cgl.ucsf.edu > Subject: About Chimera under Linux64 > > Dear Mr. Goddard, > > I have been setting up the EM tomography in the Max-Planck Institute for > Molecular Cell Biology and Genetics Dresden (www.mpi-cbg.de Germany ) > since one year. We have a tecnai F30 dedicated for tomogram acquisition > and it runs after some efforts, with SerialEM/IMOD. I would like to > improve now the segmentation part of our work which is the bottleneck in > our fields. So I strive now to get a good set of software to segment and > visual our huge(600Mb to 6Gb) 3d electron density map (.mrc file format). > > Manfred Auer and Sergio Marco oriented me on your work, i.e. the volume > data display tools in Chimera. The first tests I did the last days, look > really promising. Your work is really helpful for the 3D Electron > Microscopy community. Thanks. > > I am just wondering why the compiled version for Linux64 of Chimera is > so old(May 17,2005). Is there some reason? Should I use a newer 32bit > version ? typically our dataset are 600Mb to 5Gb and we are running a > dual core Athlon 64 machine with soon 8Gb memory under Ubuntu64bit. > > Thanks for your attention, > > Best regards, > > Quentin de Robillard > > Pfottenhauerstr. 108 > 01307 Dresden > +49 351 210 20 61 >

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Re: [Chimera-users] fitting a protein inside an EM reconstruction
by Elaine Meng 12 Oct '06

12 Oct '06

Hi Jayant, Selecting something is not the same as making it movable. Selecting something makes Actions menu items apply to it. If you want to make different models movable/unmovable, use the "Active" checkboxes in the Model Panel (Favorites... Model Panel), or various "activate" functions in the right side of the Model Panel, or the small checkboxes under the Command Line (Favorites... Command Line). These activation methods determine which models can be moved with the mouse or with movement commands like "move" and "turn." As Tom said, however, the fitting tool requires atoms to be selected. Even if only a few atoms are selected, the fitting will move the entire model containing the atoms, but maximize the density values at the selected atoms. I hope this helps, Elaine On Oct 12, 2006, at 10:14 AM, jayant_jacques wrote: > > Hi! > I have been trying to fit a protein into an EM reconstruction. > > methodology > I display my protein of interest and EM map on the same window. > I select the protein and if I click fit. > > Problem > 1. Nothing happens!! If I move the protein the whole frame moves as a > whole. > 2. Also is it possible to click drag the protein into the envelope > and then give the fit command such that the program will take over the > fitting. As I have 3 proteins to fit into this EM Map. > > 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 > > <1963059423(a)Middle5.gif> ----- 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 12 Oct '06

12 Oct '06

Hi! I have been trying to fit a protein into an EM reconstruction. methodology I display my protein of interest and EM map on the same window. I select the protein and if I click fit. Problem 1. Nothing happens!! If I move the protein the whole frame moves as a whole. 2. Also is it possible to click drag the protein into the envelope and then give the fit command such that the program will take over the fitting. As I have 3 proteins to fit into this EM Map. 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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Fwd: single-sequence FASTA file does not open
by Lucas J. Thode 12 Oct '06

12 Oct '06

Oops, sorry about double-posting this, but I forgot to mention that I am not on the list, so remember to CC me. ----- Original Message ----- 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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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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