- Chimera-users - RBVI Mailing Lists

generating electrostatic potential map
by bala 27 Oct '06

27 Oct '06

Hello all, I want to generate the electrostatic potential map using Chimera. I tried through Delphi controler, however i am repeatedly getting an error as follows. I have successfully installed Delphi. Can someone suggest me what is wrong. __________DelPhi V. 4 Release 1.1 ______________ | | | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | many dielectric regions, multisalt ionic | | strength, different probe radii, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | | Recompiled on Linux and PC | | January 2002 -------- Walter Rocchia | |__________________ ___________________| DelPhi V. 4 program started on Fri Oct 27 2006 at 14:55:00 opening parameter file /tmp/tmpvpgS8V At least 30 nonlinear iterations atom radii read from file /usr/people/ojha/BALA/chim_amber.siz unknown header format in radius file: O5' A 1 1.7210 First it showed the same for H5 atom [which was the first atom in the siz/charge file], then i just tried by deleting the first line in the radius and charge file. Then the same error is coming for the second atom O5' in the file. Thanks in advance, Bala

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viewing grid density
by bala 26 Oct '06

26 Oct '06

Hello all, 1) I hve generated a solvent density map using Amber8 in XPLOR format. I am able to open the map in chimera. I hv also generated a refernce pdb file. Now i have to fix the reference structure of my molecule in the density map. I tried many options but i couldnt do that. Someone pls suggest me how i should do the same. 2) Also i am not clear with the meaning of the threshold levels given in the histogram. Although i could see the difference in the density map by sliding the vertical bar to various postions, i am getting what it can tell us exactly. Which is the most suitable threhold level etc. 3) Someone pls give me the link for the chimera mail list archive...i am unable to locate it. Bala

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To except box information in MD movie
by Atsutoshi Okabe 25 Oct '06

25 Oct '06

Hello, I viewed Amber format trajectory files ( topology/parameter file and trajectory file ) by MD movie. But I got the figure( attached file) I didn't intend. I think the reason is to read box information in the Amber trajectory file . How can I except the box information in MD movie window ?

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To color atoms
by Atsutoshi Okabe 24 Oct '06

24 Oct '06

Hi, I visualized one ligand molecule (a kind of sugar) written by PDB format within chimera. But all atoms have non color(attached file ) I want to color these atoms (i.e. the oxygen has red .) Could you please teach me how to color atoms?

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1.2304 production
by Eric Pettersen 23 Oct '06

23 Oct '06

We haven't received any major bug reports for the release candidate, so we have promoted it to a production release (1.2304) which includes a few quite minor bug fixes and some documentation improvements relative to the release candidate. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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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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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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Slicing a 3d model
by Thomas Goddard 04 Oct '06

04 Oct '06

Hi Pu Qian, Use clip planes to cut a model in half in Chimera. There are two types of clip planes. The front and back clip planes are always parallel to the screen. The per-model clip planes can be oriented at any angle. Both can clip away the back as well as the front. The following web page describes how to use both for EM density maps. http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#slab Clipping works on all types of data in Chimera including atomic models of proteins. For EM data it helps to have Chimera cover the holes left when a contour surface is clipped. This is described here. http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#capping Also you can color according to density on the sliced surface. http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#colorc… All of these URLs come from the Chimera guide to volume display http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html and you may find other useful features for viewing your EM map there. The following page shows examples of clipping, capping and coloring including a movie of a slab moving through an EM map of a virus particle. http://www.cgl.ucsf.edu/chimera/experimental/viper_em/viper_em.html Chimera reads many density map file formats (CCP4, MRC, SPIDER, O, XPLOR, Purdue image format, ...) http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume I do not know if IMAGIC5 uses any of these formats or has its own. Chimera does not read any specific IMAGIC5 format. Tom > From: P Qian <P.Qian(a)sheffield.ac.uk> > Date: October 4, 2006 1:43:50 PM PDT > Subject: Sheffield Qian, how to make cut 3d model > > > > 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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