Dear everybody, Is there a way in Chimera to save density maps when I rotate them with the modified angles? In practice, I use the 'fit map in map' to align two maps in respect to each other and I would like to save them for further analysis with different softwares. Therefore I would like to conserve their position (shift and rotation). Thanks in advance, Gabor -- Gabor Papai IGBMC Department of Structural Biology and Genomics 1, rue Laurent Fries, BP 10142 67404 Illkirch, France phone +33-3-90244796 Fax +33-3-88653201 E-mail: papai@igbmc.u-strasbg.fr
Hi Gabor, This question was recently discussed on the Chimera mailing list: http://www.cgl.ucsf.edu/pipermail/chimera-users/2006-July/000877.html Currently Chimera cannot write out a rotated map. That would require resampling the map (degrading resolution) because none of the common map formats support specifying a rotation for the grid of data values. A number of people have requested the ability to write out rotated maps even if it requires resampling and it will be added at some point, I'd estimate within 6 months. It is possible to get from Chimera the rotation matrix for a map but that is probably not usable in other software. It would be helpful to know what other software you want to use the rotated map in. If you use the other software for plane by plane display with planes aligned to the data axes then resampling would be the only option. Tom
Hi Tom, I am currently exploring sample heterogeneity using tomographic approach on single particles. Because of the tomography I have a missing cone in the angular information, so my structures are distorted in the Z direction. To obtain a reasonable structure I have to average the similar structures and I want to do it in IMAGIC. My thought is to average the projections of several structures in the same direction and rebuild the model. Therefore I need to align the different starting density maps in rotation and translation also. Since this feature is not working very well in IMAGIC I would like to use Chimera, but I need the transformation values (angles and shifts) after the fitting, to apply it on the density maps. It would also help me a lot if you tell me how I can obtain these informations! Thanks in advance! Bye, Gabor -- Gabor Papai IGBMC Department of Structural Biology and Genomics 1, rue Laurent Fries, BP 10142 67404 Illkirch, France phone +33-3-90244796 Fax +33-3-88653201 E-mail: papai@igbmc.u-strasbg.fr
Hi Gabor, Thanks for the details about what you are doing. The Fit Map in Map tool I gave you reports the 3 by 3 rotation matrix and the translation vector to fit one map in another in the Chimera Reply Log which is displayed with menu entry Favorites / Reply Log. Here is an example of the output: Fit map microtubule.mrc <1> in map microtubule.mrc using 11355 points correlation = 0.999, overlap = 3.167e+08 steps = 68, shift = 7.29, angle = 5.69 degrees Transformation of microtubule.mrc <1> (#1) in microtubule.mrc (#0): 0.99999980 -0.00061658 0.00010850 -0.06294723 0.00061658 0.99999981 -0.00002551 -0.03578213 -0.00010849 0.00002558 0.99999999 81.17044268 In this example I just fit a microtubule map to itself shifted along its length. The rotation matrix is the first 3 columns and you see it is approximately the identity matrix. The shift is the last column, 81 angstroms along the z-axis. The third line that reports "shift" and "angle" just indicate how big a move was made from the hand-placed position to the optimal fit -- not the relative orientations of the maps. I don't know if this matrix is usable in IMAGIC. I could easily add the same information in expressed as rotation axis vector and rotation angle. Euler angles is a bit trickier since there are many alternate conventions. By the way, I changed the way correlation is calculated to use the conventional meaning. It is described in the Chimera manual. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.htm... The code I gave you gave higher correlation values using a different definition. The code optimizes overlap, not correlation, so the actual fitting has not changed. I also added an option to only use the data within the contour surface for fitting. The new code is on the web and should work with Chimera 1.2309 https://www.cgl.ucsf.edu/cgi-bin/chimera-get.py?file=experimental/fitmapinma... Michael Schmid at Baylor College of Medicine gave an interesting talk on aligning tomograms of carboxysomes in a way that accounts for the missing wedge. I think this paper reports the results (I have not read it). Schmid MF, Paredes AM, Khant HA, Soyer F, Aldrich HC, Chiu W, Shively JM. Structure of Halothiobacillus neapolitanus Carboxysomes by Cryo-electron Tomography. J Mol Biol. 2006 Dec 1;364(3):526-35. Epub 2006 Sep 14. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=Ab... I leave today for a workshop in Germany and return Sunday. So I will not be able to offer more help until Monday. Tom
participants (2)
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Gabor Papai -
Thomas Goddard