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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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