<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Sergej,<div class=""><br class=""></div><div class="">for storing the new location and orientation of a map you could resample it in Chimera. I don’t know if it is the only option to do it (in Chimera), but if you move a first map and align it to a second map that has not been moved (as in moved separately from other models; if all models are active this doesn’t qualify as movement here) you can type</div><div class=""><br class=""></div><div class="">vop resample #[moved map] ongrid #[map that has not been moved] update true</div><div class=""><br class=""></div><div class="">into the Chimera command line</div><div class=""><br class=""></div><div class="">A new third map will open (copy of the first one) which will have a resampled coordinate system and will be at the same place as the second map when you re-open it. This way you don’t have to move the models every time you open them. </div><div class=""><br class=""></div><div class="">Cheers,</div><div class=""><br class=""></div><div class="">Michael</div><div class=""><br class=""></div><div class="">------------------------------------------------------------<br class=""> <br class=""> Michael Saur, Dr. rer. nat. <br class=""> <br class=""> Max Planck Institute for Molecular Physiology <br class=""> Otto-Hahn-Straße 11<br class=""> Room B2.25 <br class=""> 44227 Dortmund<br class=""><br class=""> Phone: +49 231 - 133 2312 <br class=""> E-mail: <a href="mailto:michael.saur@mpi-dortmund.mpg" class="">michael.saur@mpi-dortmund.mpg</a>.de <br class=""><br class="">------------------------------------------------------------</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div><blockquote type="cite" class=""><div class="">On 29. 07. 2015, at 15:05, Sergej Masich <<a href="mailto:Sergej.Masich@ki.se" class="">Sergej.Masich@ki.se</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">Dear colleagues, <br class=""><br class="">I am looking for a program(s) that would allow me to align manually two density maps. We have reconstructed several particles that may have a common origin and we are trying to trace common features in these particles. We have software that presumably may help us but it requires pre-aligned densities.<br class=""><br class="">I checked Chimera that allows storing rotational and translational parameters for individual maps in Python scripts for saved session. However, I cannot find any definition of these parameters. Moreover, I have not found any routine in Chimera to apply these parameters to reorient tomographic maps.<br class=""><br class="">Can you advise a program/set of programs that would allow me to (1) align two tomographic maps under visual control; (2) store corresponding rotational and translational parameters; and (3) use these parameters to obtain aligned densities?<br class=""><br class="">Any advice is appreciated. Thank you in advance.<br class=""><br class="">Sergej Masich<br class="">=============================<br class="">Dr. Sergej Masich<br class="">Dept. of Cell and Molecular Biology<br class="">Karolinska Institutet<br class="">Box 285<br class="">171 77 Stockholm, Sweden<br class="">tel: (+)46 - 8 - 524 873 61<br class="">mobile: (+)46 - 736 - 833 693<br class="">e-mail: <a href="mailto:Sergej.Masich@ki.se" class="">Sergej.Masich@ki.se</a><br class=""><br class="">_______________________________________________<br class="">3dem mailing list<br class=""><a href="mailto:3dem@ncmir.ucsd.edu" class="">3dem@ncmir.ucsd.edu</a><br class="">https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem<br class=""></div></blockquote></div><br class=""></body></html>