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Thank you very much! Best, Yangqi Sent from Mail for Windows 10 From: Ambroise Desfosses Sent: Tuesday, May 14, 2019 5:40 AM To: Yangqi Gu; [log in to unmask] Subject: Re: [ccpem] Convert relion helical coordinates to eman box file Dear Yangqi, I attach csh script (relion_star_to_eman_helix_coordinates.csh) doing this conversion from a particle.star file, and optionally creating eman2's database for easy visualisation in e2helixboxer.py The particle.star file can come from autopicking, or manually picked filaments (so, you would need to extract the segments). I also attach two child scripts required. Running relion_star_to_eman_helix_coordinates.csh without arguments will give you the list of required arguments. Relion stores the coordinates of center of the box corresponding to the segments. Eman stores the upper left corner of segments (or extremities), and therefore x and y coordinates have to be modified by x-boxsize/2 and y-boxsize/2 (boxsize is defined in eman .box format in 3rd and 4th column). You can certainly write a simpler script doing only this conversion from your manually picked coordinates. Please note that some optional arguments in the scripts are not yet "implemented". Good luck Ambroise On 5/13/19 10:35 PM, Yangqi Gu wrote: > Hi all, > I have manually picked relion helical particles by picking the start and end coordinates and I want to convert to the eman2 coordinates (I just need the tube start-end coordinates, rather than particle coordinates). I am wondering if there is a quick way to do it? If there is no implemented convention, I am wondering if EMAN use the same convention as relion when recording the helical coordinates? In that case,I can write a bash script to do. The reason I asked, because I noticed the same image displayed using e2display.py vs relion_display, they seems rotating 180 between each other. > Best, > Yangqi > > ######################################################################## > > To unsubscribe from the CCPEM list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1 ######################################################################## To unsubscribe from the CCPEM list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1