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That's likely the cause of the problem. --angpix shuld fix it. S > Hi, > > > You need --angpix, I mean the old pixel size. > > > relion_image_handler --i run1_class001.mrc --o > run1_class001_image_handler.mrc --rescale_angpix 1.06 --new_box 304 > *--angpix *2.12 > > > Hugo > > > On 06/10/16 15:08, Elena Zehr wrote: >> Hi Sjors and everyone, >> >> Thank you very much for your feedback. >> >> I put no for "map on gray scale" and changed pixel size >> >> I think maybe my map is not scaled correctly. I use the following >> command: >> >> relion_image_handler --i map_2x.mrc --new_box (old box size *2) >> --rescale_angpix (old pixel size /2) --o map_1X.mrc >> >> Is this the right command to scale the map or I also need something >> else. >> >> Thank you so much again! >> Elena > > -- > Hugo Muñoz Hernández, PhD student > > Centro de Investigaciones Biológicas CIB-CSIC > Consejo Superior de Investigaciones Científicas > C/ Ramiro de Maeztu, 9 > 28040 Madrid (Spain) > > http://www.cib.csic.es/es/grupo.php?idgrupo=47 > > Tel: +34 91 8373112 ext 4436, Lab.B-47 > > -- Sjors Scheres MRC Laboratory of Molecular Biology Francis Crick Avenue, Cambridge Biomedical Campus Cambridge CB2 0QH, U.K. tel: +44 (0)1223 267061 http://www2.mrc-lmb.cam.ac.uk/groups/scheres