- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] Chimera-users Digest, Vol 42, Issue 19
by Jonathan Hilmer 30 Oct '06

30 Oct '06

Although this does not relate to your question on licensing, is there any particular reason you're using such a complicated workflow? Chimera can be used to generate basic geometry (sphere/cylinder) from PDB files via povray, but so could any import system you have for the 3D modeling software. You would also lose the benefit of chemistry-centered structure for manipulation or selection: chains, residues, etc. I've been using Blender to handle complicated chemical models for a while now, and it wasn't that difficult to implement the import of various data types. With BioPython pdb files become trivial, and volumetric data sets are (very) difficult but possible. Jonathan > Hello- > > Do any of you have an idea of how much a single commercial license for Chimera would cost? > > I'm a 3D artist/animator/biology student that works at in the art dept. of a biotech company. I'm interested in the exporting .pdb files to .pov, then converting to .3ds to import to 3ds max. > > Thanks, > > Lydia Jablonski

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changing center of rotation
by Jonathan Hilmer 30 Oct '06

30 Oct '06

Although I haven't used EMAnimator, you can set the center of rotation within Chimera using the Set Pivot action: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/menu.html#actpivot There's also Tools/Movement/Rotation, and lastly, you can edit structures to insert artificial points at extreme high/low XYZ locations, which will in effect manually set the center used via the 'center of models' option. I wouldn't recommend the last option unless you have a good reason to do so, but it does work. Jonathan > Message: 1 > Date: Mon, 30 Oct 2006 11:52:42 -0800 (PST) > From: wendy ochoa <wencryo(a)yahoo.com> > Subject: [Chimera-users] rotating molecules for movies > To: chimera-users(a)cgl.ucsf.edu > Message-ID: <20061030195242.57847.qmail(a)web37306.mail.mud.yahoo.com> > Content-Type: text/plain; charset="us-ascii" > > Can anybody tell me how to use EMANIMATOR to make a movie of a molecule rotating. If I use the spin option, it uses the axis (0 1 0) but my molecule is not center at 0 0 0. Is there a way to fix the rotation center to the center of the molecule, or to the center of the view? > Thanks > > > >

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Re: [Chimera-users] viewing grid density
by Thomas Goddard 30 Oct '06

30 Oct '06

Bala reports that the problem was in an Amber input file. > From: "bala" <bala(a)igib.res.in> > To: "Thomas Goddard" <goddard(a)cgl.ucsf.edu> > Subject: RE: [Chimera-users] viewing grid density > Date: Fri, 27 Oct 2006 19:59:38 +0530 > > Hello Thomas and Elaine, > > Thank you for your information. I rechecked the amber input files and i = > found a mistake there in rms fitting the coordinates in my trajectory. > > regards, > Bala

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Re: [Chimera-users] rotating molecules for movies
by Thomas Goddard 30 Oct '06

30 Oct '06

Hi Wendy, Here are some Chimera commands that are useful for making movies with Movie Recorder: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/recorder/moviecomm… Here's a fancier Chimera movie script example. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/recorder/1gfl.com Here is the documentation for the Movie Recorder dialog and movie command: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/recorder/recorder.… http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html Tom

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rotating molecules for movies
by wendy ochoa 30 Oct '06

30 Oct '06

Can anybody tell me how to use EMANIMATOR to make a movie of a molecule rotating. If I use the spin option, it uses the axis (0 1 0) but my molecule is not center at 0 0 0. Is there a way to fix the rotation center to the center of the molecule, or to the center of the view? Thanks

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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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Re: [Chimera-users] Merge PDB Question
by Jonathan Hilmer 28 Sep '06

28 Sep '06

On the issue of using Chimera to write PDB files, would it be possible to change the format of the PDB output Chimera generates? I'm not too well-versed in the details of the pdb file format, but I ran into issues using Chimera-generated structures with a Blender plugin that used BioPython to handle parsing the files. Although I can't remember the details off the top of my head, it involved the use of multiple 'END' statements to separate models (in Chimera-generated files). It was easy enough to write a script to substitute 'MODEL', 'ENDMDL' pairs, but I'm sure it would be better implemented in whatever library handles the file IO in Chimera. Jonathan > Date: Thu, 28 Sep 2006 10:38:00 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Merge PDB Question > To: "Jared Godar" <jared.godar(a)vanderbilt.edu> > Cc: chimera-users(a)cgl.ucsf.edu > Message-ID: <4F99156D-A681-4EFB-AC6C-5A0C57D029E0(a)cgl.ucsf.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi Jared, > Currently you cannot bond different models, and the only way to > "merge" is to put the atoms in the same file before opening it. > There are actually other reasons your command wouldn't work: > > - seems to me that there is no model 1, only 1.1, 1.2, 1.3 and 1.4, > so the first part would specify zero atoms > - the ampersand & stands for intersection (logical AND, not english > and) and should be omitted, e.g. > command: bond #1.1:504.b@c #1.1:505.b@n > > What I've done in the past to handle similar cases (splicing stuff > from an NMR structure onto a Xray structure) is to first put the tail > (with a few extra residues to overlap with residues that are already > present) into a file by itself. Then I open that new file, so it > will be a new, separate model. I then match that model onto the > original model using atoms in the overlapping part. Then, write out > another PDB file of the tail relative to the untransformed original > model. Using text-editing, remove the part that overlaps since it > was just there for positioning purposes. FINALLY (text-editing > again) make another PDB file that combines the new tail with the > original protein. They may need to have the same chain ID as well. > Sorry this is such a long process. If you think you can hand- > position the tail sufficiently well you could skip the parts about > having the extra atoms, using them for matching, and deleting them. > > If you remove any intervening TER, the bond will already be there > when you open the new file. > > I hope this helps, > Elaine

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Re: [Chimera-users] [chimera-dev] chimera help
by Eric Pettersen 28 Sep '06

28 Sep '06

If you have a large number of PDBs then you might want to use Python, where you have access to loops and variables. Say you had the PDBs listed in a file, one per line, named "mypdbs". Then you might use a Python script like this: -------------------------------------- import chimera from chimera import runCommand f = open("mypdbs", "r") for line in f: pdbID = line.strip() runCommand("open " + pdbID) runCommand("scale 1.5; ~disp; ribbon; ribrepr smooth; rainbow") runCommand("copy file %s.png png supersample 5" % pdbID) runCommand("close all") -------------------------------------- Note that the "runCommand" function allows you to do things that you know the Chimera command for without knowing what the Python equivalent is. Assuming you name the script file with a ".py" ending so that Chimera can recognize it as Python, then you can run the script with any of the ways that Chimera opens files (File...Open dialog, "open" command, startup shell command argument). Also, Chimera needs the graphics window to be showing and not obscured by other windows in order to render the images. If you are doing a lot of images you may have to turn off your screen saver so that it doesn't hide the Chimera window. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu On Sep 28, 2006, at 9:14 AM, Elaine Meng wrote: > Hi Vishal, > Actually you can do this with a Chimera command script, as opposed > to programming in Python. A command script just contains the same > commands you would enter in the Command Line. I'm not sure of what > type of saving you had in mind, " but the "copy" command can be > used to save an image file, "save" to save a session, and "write" > to save a PDB file. > > This page links to all the command man pages, plus it discusses > command scripts (at the bottom): > http://www.cgl.ucsf.edu/chimera/1.2199/docs/UsersGuide/ > framecommand.html > > Just opening the command file will execute the commands. > Here are links to a couple of example command files: > http://www.cgl.ucsf.edu/chimera/1.2199/docs/UsersGuide/tutorials/ > setup.com > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/recorder/ > 1gfl.com > > And here is another, between the dashed lines: > ----------------------------------------------------------------- > open 1hxx > open 1pho > modelcolor coral #0 > modelcolor cornflower blue #1 > ~disp; rep bs; ribbon; ribrepr smooth > matchmaker #0 #1 > ----------------------------------------------------------------- > > I guess the main difficulty if you are saving images is how to get > a good view of the structures. Usually some rotation, scaling, etc. > is done interactively to make a better picture. > I hope this helps, > Elaine > > > On Sep 27, 2006, at 7:29 PM, Vishal Pua wrote: > >> Hi, I was wondering if there was a way to create a script, that >> would open pdb files, render them to look a certain way ex. wire >> or ribbon, then save, automatically? this would have to work for a >> number of pdb files? I have little programming experience, and >> wonder if there was an easy way to do this, thanks >> >> Vishal Pua >> _______________________________________________ >> Chimera-dev mailing list >> Chimera-dev(a)cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > > ----- > 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 > > > > > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev _______________________________________________ Chimera-dev mailing list Chimera-dev(a)cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev

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Merge PDB Question
by Jared Godar 28 Sep '06

28 Sep '06

I have an incomplete pdb crystal structure of a homohexameric protein containing six ~25AA tails. In the incomplete model, two of these six tails are complete (A and F) and the other four are truncated at various positions (B,C,D, and E). I have used the either the A or F complete tails as templates and generated appropriate length segments to compleate each of the truncated B-E tails by selecting the appropriate residues and saving the selected atoms as a new PDB. Currently, I have all six tails completed and saved as a single PDB. I would like to use the Bond command to covalently link the extended chains, but my single PDB is segregated into models 1.1, 1.2, 1.3, 1.4, and 1.5. When I use the Bond command as follows "bond #1: 504.b@c & #1.3:505.a@n", I get an error that only one atom is selected. Does Chimera consider #1 and #1.1 to be different models? If so, how can I merge these 5 models into one to allow me to create the bond? 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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Re: [Chimera-users] [chimera-dev] chimera help
by Elaine Meng 28 Sep '06

28 Sep '06

Hi Vishal, Actually you can do this with a Chimera command script, as opposed to programming in Python. A command script just contains the same commands you would enter in the Command Line. I'm not sure of what type of saving you had in mind, " but the "copy" command can be used to save an image file, "save" to save a session, and "write" to save a PDB file. This page links to all the command man pages, plus it discusses command scripts (at the bottom): http://www.cgl.ucsf.edu/chimera/1.2199/docs/UsersGuide/framecommand.html Just opening the command file will execute the commands. Here are links to a couple of example command files: http://www.cgl.ucsf.edu/chimera/1.2199/docs/UsersGuide/tutorials/ setup.com http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/recorder/ 1gfl.com And here is another, between the dashed lines: ----------------------------------------------------------------- open 1hxx open 1pho modelcolor coral #0 modelcolor cornflower blue #1 ~disp; rep bs; ribbon; ribrepr smooth matchmaker #0 #1 ----------------------------------------------------------------- I guess the main difficulty if you are saving images is how to get a good view of the structures. Usually some rotation, scaling, etc. is done interactively to make a better picture. I hope this helps, Elaine On Sep 27, 2006, at 7:29 PM, Vishal Pua wrote: > Hi, I was wondering if there was a way to create a script, that > would open pdb files, render them to look a certain way ex. wire or > ribbon, then save, automatically? this would have to work for a > number of pdb files? I have little programming experience, and > wonder if there was an easy way to do this, thanks > > Vishal Pua > _______________________________________________ > Chimera-dev mailing list > Chimera-dev(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev ----- 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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how to get nonbonded distance and torsion angle list
by Prem Prakash Pathak 28 Sep '06

28 Sep '06

Hi! I am using the chimera for the visualizing protien form *.pdb file. I wanted to get the nonbonded distance , *.upl file and angle constraint files. Would you please help me in solving the problem. PremPrakash

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"longbond" in scripts
by Eric Pettersen 26 Sep '06

26 Sep '06

We've made some improvements to the "longbond" command (breaks non- physical bonds that show missing structure segments) which are not backward compatible with the previous version. We are wondering if anyone makes any significant use of the longbond command in scripts. If you do, we would consider making a new command with the improved behavior and leaving the longbond command unchanged for backwards compatibility. So speak up if this affects you. --Eric Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Connolly surface and Triangulation
by Nihshanka Debroy 25 Sep '06

25 Sep '06

Hi, Not sure if this went the first time, so sending it again: ----------------------------------------------------------------------------------------------- I have been using Chimera to generate the Connolly surface for several different proteins and saving the surface information in X3D format. I was wondering what algorithms are used in the Connolly surface generation. Is it the same approach that Michael Connolly had come up with in his 1983 paper on Analytical Molecular Surface Calculation, or is it a variation of that algorithm? Also, when the surface information is saved by Chimera in X3D, it breaks the surface into triangular faces. I noticed that the coordinates of the points comprising the triangles are completely different from the atomic coordinates. I am interested in learning more about how the triangulation is created. If you could direct me to a link or paper that would help me better understand the algorithms involved in these two processes, that would be great! Thanks. Sincerely, Nihshanka

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chimera ubuntu/debian package?
by Javier Díez 25 Sep '06

25 Sep '06

Hy: Is there a chimera version for ubuntu or debian? I would like to add the url to my sources.list if it exits. Thank you any way. Javi

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Re: [Chimera-users] Map Oddities
by Thomas Goddard 22 Sep '06

22 Sep '06

Hi Albion, When you are running Chimera and it opens a Python code file with suffix .py and there is an older byte compiled version of the same file with suffix .pyc then Python automatically recompiles the .py file and you should see that the date on the .pyc file is updated. You never need to compile Python files by hand. Here are 3 ideas about how to make some programs that read MRC maps establish equivalent map positions. As I mentioned in my previous email some programs may fail with certain maps to associate the x,y,z axes with the correct data axes. And some may ignore all header info about positioning. So there are alot of different cases. I'm only going to make suggestions for the simple problems. One idea is to have Chimera print out the difference between the origin that a crystallography program would use versus the MRC 2000 origin. You could insert a little code in the Chimera mrc_format.py file to print this difference for MRC 2000 files. Specifically after the line self.data_origin = (v['xorigin'], v['yorigin'], v['zorigin']) add lines # Print difference between crystal and mrc 2000 origins ncs_nrs_nss = v['ncstart'], v['nrstart'], v['nsstart'] nxs, nys, nzs = ncs_nrs_nss[xa], ncs_nrs_nss[ya], ncs_nrs_nss[za] from VolumeData.griddata import scale_and_skew x0,y0,z0 = scale_and_skew((nxs,nys,nzs), self.data_step, self.cell_angles) print 'Origin difference ', self.name, '=', print x0 - v['xorigin'], y0 - v['yorigin'], z0 - v['zorigin'] The origin difference will be printed to the Chimera reply log and you can somehow apply it in other programs. A second idea is to try to modify the MRC 2000 map header so that the crystal origin is the same as the xorigin, yorigin, zorigin header values. This is generally not possible since the former uses integers while the latter uses float values. But if you don't care where the origin is as long as all programs agree, you might adjust xorigin, yorigin and zorigin to match the crystal origin. You would need some simple program to modify the map header. A third approach is to modify Chimera mrc_format.py so it never uses the MRC 2000 xorigin, yorigin, zorigin. If Chimera always uses the crystal origin that would probably more often agree with other software packages. I would recommend against this approach. You will later install a new version of Chimera without the modification and your fit PDB models will no longer align with their maps and you will probably forget why and scream. Tom > From: Albion Baucom <baucom(a)msg.ucsf.edu> > Subject: Re: [Chimera-users] Map Oddities > Date: Fri, 22 Sep 2006 17:12:51 -0700 > To: Thomas Goddard <goddard(a)cgl.ucsf.edu> > > Hi Tom, > Im going to take this off list since my inquiries get more specific > now, but you are welcome to post this back to list if you think it is > within the scope of the Chimera Users list. > > So, you were right. There is indeed a X, Y and Z origin field in the > map header. Thanks for pointing that out and giving me the code to > print those values to the reply log. > > A quick question regarding my modification to the mrc_format.py. I > don't know Python very well yet, and am wondering what happens when I > modified the source code. The modifications worked of course, but > Chimera did not recompile the code into a .pyc file. When are > the .pyc files accessed? > > OK, back to the original question :) > > So, offhand, could you suggest a fix for me so that other programs > that use the "other" origin can interpret the data the same as > Chimera? Naturally what is going to have to happen is I will have to > translate the PDB file a set distance based on the discrepancy > between the origin conventions. I would like to do this translation > as accurately as possible. > > What I noticed from an empirical re-docking of the PDB file into the > density in another program was it had to be moved approximately ~116A > in all 3 axes. This appears to be close to the following calculation > (for the x axis in this case) > > ( | xorg | - xlen) + (xlen/2) > > where xorg (-224) is the MRC2000 origin, and xlen (213.423) is the > xtal origin. In this case this comes out to be > > (224.000 - 213.423) + (xlen/2) = 117.289 > > Applying this to the model as a translation in all 3 axes looks > almost exactly like what I see in Chimera. > > Does this make any sense? This is all I could come up with that gave > an answer close to my empirical docking translation numbers. > > Thanks Tom. I really appreciate your help. > > Albion

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Map Oddities
by Albion Baucom 22 Sep '06

22 Sep '06

Hi, I am trying to work out how maps are handled in various graphics programs so I can easily move between programs and expect to see the same thing in each session. Unfortunately at the moment that isn't working so well, and I would like to resolve this issue. Basically I have a situation where I have a PDB model and a CCP4 format EM density map in Chimera that are docked. When I open the exact same map and model in other programs such as O or Pymol, the map and the model are no longer in agreement. What I have noticed is that if I draw the unit cell for the map (P1 symmetry since this is an EM reconstruction), in Chimera, the model and map live in the center of the unit cell and are docked. If I draw the unit cell for O or Pymol, the map lives at the origin of the unit cell, at (0,0,0), which is in the corner, and model is outside of the unit cell offset by what appears to be some arbitrary translation (I have tried using half the unit cell dimensions as a translation, but that unfortunately gets me _very_ close to being correctly docked in the map, but off by some 10A). It appears Chimera is handling the map and model differently than the other packages and I am trying to get an idea of what happens when this map is loaded. I am including a listing of the map header from MAPMAN below. Thanks! Albion Grid = 96 96 96 Origin = -48 -48 -48 Extent = 96 96 96 Cell = 213.423 213.423 213.423 90.000 90.000 90.000 UVW = 1 2 3 Spcgrp = 1 Nr of points = 884736 Density min = -6.915E-01 Max = 2.397E+00 Average = 7.247E-11 Sigma = 2.290E-01 Variance = 5.243E-02 Mappage Prod= 8.257E+01 Plus = 57 Dyn. range = -6.903E-01 To = 2.398E+00 Cell vol. = 9.721E+06 Voxel vol. = 1.099E+01 Grid vol. = 9.721E+06 %Cell vol. = 100.00 Origin frac = -0.50000 -0.50000 -0.50000 Origin Cart = -106.712 -106.712 -106.712 Top frac = 0.48958 0.48958 0.48958 Top Cart = 104.488 104.488 104.488 Spacing = 2.223 2.223 2.223 Top = 47 47 47 Changes = F

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Movement Mouse Mode Extension
by Jared Godar 22 Sep '06

22 Sep '06

I have installed the Movement Mouse Mode Extension, but I get the following error whenever I try to select anything other than the 'Normal' movement mode on the drop-down menu. ImportError: cannot import name functionCallables (see reply log for Python traceback info) Any insight on how I can get this feature to work for me? Thanks, Jared (Log info below) 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\CGLtk\Hybrid.py", line 170, in <lambda> set_variable_cb = lambda v=self.variable, n=name: v.set(n) File "C:\Program Files\Chimera\share\CGLtk\Hybrid.py", line 780, in set self.tk_variable.set(value) File "C:\Program Files\Chimera\bin\lib\lib-tk\Tkinter.py", line 191, in set return self._tk.globalsetvar(self._name, value) 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\CGLtk\Hybrid.py", line 832, in cb callback() File "C:\Program Files\Chimera\share\CGLtk\Hybrid.py", line 800, in tk_variable_changed_cb cb() File "C:\Program Files\Chimera\share\MoveSelection\gui.py", line 64, in mode_changed_cb move.set_mouse_mode(mmap[self.mode.get()]) File "C:\Program Files\Chimera\share\MoveSelection\move.py", line 569, in set_mouse_mode m = mover(create = True) File "C:\Program Files\Chimera\share\MoveSelection\move.py", line 598, in mover the_mover = Selection_Mover() File "C:\Program Files\Chimera\share\MoveSelection\move.py", line 36, in __init__ self.original_move_callbacks = self.wrap_mouse_modes() File "C:\Program Files\Chimera\share\MoveSelection\move.py", line 42, in wrap_mouse_modes from chimera.mousemodes import addFunction, functionCallables ImportError: cannot import name functionCallables -- Jared A. Godar Graduate Student: Stewart Lab Vanderbilt University Medical Center Molecular Physiology & Biophysics Dept. Light Hall 708 Work: 615.322.7898 Fax: 615.322.7236

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Connolly surface and Triangulation
by Nihshanka Debroy 21 Sep '06

21 Sep '06

Hi, I have been using Chimera to generate the Connolly surface for several different proteins and saving the surface information in X3D format. I was wondering what algorithms are used in the Connolly surface generation. Is it the same approach that Michael Connolly had come up with in his 1983 paper on Analytical Molecular Surface Calculation, or is it a variation of his algorithm? Also, when the surface information is saved by Chimera, it breaks the surface into triangular faces. I noticed that the coordinates of the points comprising the triangles are completely different from the atomic coordinates. I am interested in learning more about how Chimera creates the triangulation. If you could direct me to a link or paper that would help me better understand the algorithms involved in these two processes, that would be great! Thanks, Nihshanka

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AMBER netCDF trajectory
by Mingfeng Yang 20 Sep '06

20 Sep '06

Dear Chimera developers, The latest release of AMBER supports netCDF format trajectory. Is there any plan for Chimera to support AMBER's new format? Best, Mingfeng

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Chimera secondary-school use
by Thomas Goddard 19 Sep '06

19 Sep '06

Follow up on "[Chimera-users] first time use of chimera". ------------------ From: "Rich Kaufman" <richkaufmanpv(a)hotmail.com> To: goddard(a)cgl.ucsf.edu Subject: Chimera, afterthought Date: Tue, 19 Sep 2006 11:38:26 -0500 Dear Tom, Just to mention a few more details, I am trying to use electron density maps we generated in the lab using a Spider processing of cryo-EM photos .I will be downloading PDB's from the RCSB to dock with these. After properly hand docking the PDB, I will then load the density map and the hand-aligned PDB into a Normal Mode Flexible Fitting package ( NMFF ) for fine-tuning of the fit, to give a higher resolution picture of the electron density map. I've been working on this project for about three months. I had never heard of any of these things prior to that. It's been an amazing learning curve for me....quite interesting. Sincerely, Rich Kaufman, ( background....mainly physics; teacher of high school chemistry and physics ) P.S. One goal of this project is to enable me to use these techniques at the secondary education level. I don't know if that's doable....suggestions welcomed. --------------------- Date: Tue, 19 Sep 2006 10:00:38 -0700 (PDT) From: Thomas Goddard <goddard(a)cgl.ucsf.edu> To: richkaufmanpv(a)hotmail.com Subject: Re: Chimera, afterthought Hi Rich, Oh! I sent my previous email before I read this one about what you are actually doing. You're doing some fancy stuff. If you hand-align a PDB model in the SPIDER map you can then do a local position optimization within Chimera using menu entry Tools / Volume Data / Fit Models in Maps This moves the model using a rigid rotation and translation to maximize the map values at selected atom positions. Here's a page describing how to use it: http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#fitmod… The bottom of the following tutorial also gives step by step instructions for placing a PDB model in a map: http://www.cgl.ucsf.edu/Outreach/Workshops/UCSF-Fall-2005/07-VolumeData/tut… In fact, most of the tutorials on the following page do this kind of fitting: http://www.cgl.ucsf.edu/chimera/tutorials/tutorials.html The normal mode fitting you will do is fancier, allowing the model to deform to fit into the map. The following page explains alot of the Chimera features for working with density maps. http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html The myosin animation on the following web page shows fitting a model into a map: http://www.cgl.ucsf.edu/chimera/animations/animations.html Finally, here are some databases that show some cryo-EM maps of viruses and other systems. http://viperdb.scripps.edu/tnumlist.php?N=all http://www.ebi.ac.uk/msd-srv/emsearch/AccEMServ?criterion=Retrieve+All&valu… I'm sure this is more than you wanted to know! Tom

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visualizing a confocal image stack
by William Beaver 19 Sep '06

19 Sep '06

Hello. I have a stack of intensity images (8bit) taken from confocal microscopy of dapi expression in Drosophila that I'd like to visualize. I cannot figure out the format that the volume viewer requires to view the data; more specifically, none of the formats in 'registered file types' are familiar to me and I've been unable to find anything about them to sort out which format I should convert to. I have read the image sequences into matlab (3d matrix) and can write output to just about anything from there if I know the format. Does anyone have an idea for what the best/easiest/only format I should use? A pointer to a spec on the format if it's not something trivial (like matlab 'save stack.txt varname -ascii') would be appreciated. If it makes a difference, at some point soon I'd like to visualize more channels that just dapi (dll, for example) simultaneously. Thanks in advance. I really do appreciate it! -William ------------ William Beaver wbeaver(a)cs.ucsd.edu

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Re: [Chimera-users] Movie Question: EM Densities about robbon structures
by Thomas Goddard 18 Sep '06

18 Sep '06

Hi Jared, If you use Chimera commands that specify how many frames to rotate, shift, scale, fade over, ... then it does not matter how fast or slow your machine is. Each frame is recorded only after it is drawn, and none will be skipped. Only when you move a model by hand with the mouse will it matter how fast the machine is. Here are some problems with smooth transitions I have observed. Fading out a PDB model in stick mode produced all kinds of weird flickering of the bonds. This I believe is a bug in Chimera transparency of bonds and I plan on submitting a bug report for that. Smoothly changing the contour level does not produce a very smooth change in surface appearance. Little spots pop up or disappear at discrete contour levels. This is because the contouring algorithm (marching cubes) changes the surface triangulation in discrete ways when the contour level passes through a grid point data value. I don't know of any remedy although using surface smoothing (volume dialog under surface and mesh options) may help. Let me know what problems you encounter. I am interested in improving the Chimera movie capabilities. Tom > Date: Mon, 18 Sep 2006 13:11:39 -0500 > From: "Jared Godar" <jared.godar(a)vanderbilt.edu> > Sender: jared.godar(a)gmail.com > To: "Thomas Goddard" <goddard(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Movie Question: EM Densities about robbon structures > > I did, thank you much... I have successfully installed the additional > extensions and am attempting to incorporate them into a .CMD script for my > movie. So far that is going fairly smoothly, with the exception of frames > involving fading in/out of structures are taking significantly longer than > others resulting in a jumpy movie. I'm going to attempt to try it on a > fastest machine and see if that helps. > > The independent rotation is working, the fade in/out of specific models is > good, and I'm going to try the contour transition next. > > Thanks again, > > Jared

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first time use of chimera
by Rich Kaufman 18 Sep '06

18 Sep '06

9/18 To whom it may concern: I would like an abbreviated guide to loading a pdb and an electron density map into chimera for comparison and hand docking. I have only worked with visualization software for a few months and still, frequently, can't do what I want with it. Chimera was suggested as the easiest or perhaps only software to do what I need to do. Currently, I only have only got VMD downloaded, but can install chimera if its worthwhile. Sincerely, Rich Kaufman, U.KS. biochem. dept, Kansas City, Ks.

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Movie Question
by Jared Godar 15 Sep '06

15 Sep '06

Hello there, I have a few technical questions about a movie I am trying to make with chimera. I have PDB files for three predicted structural elements of a larger protein whose structure my lab is resolving through cryo EM. I've converted these PDB files to MRC's of the desired resolution we are trying to obtain with the reconstruction. In an effort to produce animation which highlights structural elements of these three subdomains, I have encountered a couple difficulties translation the movie I envision through Chimera. I would like to start with the three subunits spaced across the X axis and rotating about the central y axis of each subunit. Then, one at a time, have a single unit grow and translate to the center, then while the other two subunits fade away, then return to it's original position. I've been able to script this type of motion for each of the individual subunits, but I hit a problem when I try to incorporate all three. - Is there a way to have multiple proteins roll about their own respective y axis instead of orbiting about the central y axis of the scene? - Is there a way to selectively show / hide (fade over specified number of frames) PDB's or MRC's like you can show / hide / fade text? Thank you in advance for your help. -Jared -- Jared A. Godar Graduate Student: Stewart Lab Vanderbilt University Medical Center Molecular Physiology & Biophysics Dept. Light Hall 708 Work: 615.322.7898 Fax: 615.322.7236

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Movie Question: EM Densities about robbon structures
by Jared Godar 15 Sep '06

15 Sep '06

Hello there, I have a few technical questions about a movie I am trying to make with chimera. I have PDB files for three predicted structural elements of a larger protein whose structure my lab is resolving through cryo EM. I've converted these PDB files to MRC's of the desired resolution we are trying to obtain with the reconstruction. In an effort to produce animation which highlights structural elements of these three subdomains, I have encountered a couple difficulties translation the movie I envision through Chimera. I would like to start with the three subunits spaced across the X axis and rotating about the central y axis of each subunit. Then, one at a time, have a single unit grow and translate to the center, then while the other two subunits fade away, then return to it's original position. I've been able to script this type of motion for each of the individual subunits, but I hit a problem when I try to incorporate all three. - Is there a way to have multiple proteins roll about their own respective y axis instead of orbiting about the central y axis of the scene? - Is there a way to selectively show / hide (fade over specified number of frames) PDB's or MRC's like you can show / hide / fade text? Thank you in advance for your help. -Jared -- Jared A. Godar Graduate Student: Stewart Lab Vanderbilt University Medical Center Molecular Physiology & Biophysics Dept. Light Hall 708 Work: 615.322.7898 Fax: 615.322.7236

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Dual monitor display
by John Hatten Jr. 15 Sep '06

15 Sep '06

Hi all. I'm a bit of a chimera newbie. I've been using DOCK for a while, and chimera has turned into a natural choice for combing through the results. I've noticed that chimera quits when I try to run it in dual display with XP. I get an error message that there is a driver conflict. Is there a way to fix this? I would love to have my display window on one screen and the tool windows on the other. Thanks for the wonderful software, its a great tool. Sincerely, John Hatten jahatten(a)duke.edu

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