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Hi Chiara, There several parameters you might try to improve for a specific dataset. --local_radius 1024.00 default value seems a bit too big, though more stable. For micrographs with better SNR, try to reduce this weighting radius. --local_overlap 0.50 larger value, say 0.8, is always better, but the speed is slower. --local_boxsize 512 300-800 all seem to work OK in most cases, but do try to see which works best. --write_local_ctf specify it for diagnosis, not necessary for batch processing. P.S. Note the current local power spectra weighting scheme and local CTF refinement strategy implemented in GCTF was >4 years old. Though I believe it works well in most cases, there is always some room to make it better and things have been slightly improved in many aspects in the newer versions. I will release it at some point when I settle down in US. Best wishes Kai > Hi Chiara, > You don't have to convert your particle into .box format. Simply specify _autopick.star for the --boxsuffix. I would first link all the micrographs > into the folder that contains the particle coordinates that you have picked in RELION. In my case, it is the folder Autopick/job010/micrographs > . > Here is an example command line: > Gctf-v1.06_sm_20_cu8.0_x86_64 *.mrc --do_local_refine --boxsuffix _autopick.star --apix 1 --kV 300 --Cs 2.7 > Hope it answers your question. > Best, > Chen > ________________________________ > From: Collaborative Computational Project in Electron cryo-Microscopy <[log in to unmask]> on behalf of Chiara Rapisarda > <[log in to unmask]> > Sent: Monday, July 9, 2018 1:05:57 PM > To: [log in to unmask] > Subject: [ccpem] tilted collect ctf estimation in relion > Hello, > I have just collected a series of 40 deg tilted micrographs and I would like to do a per particle CTF estimation in RELION 2.1 (as I used to do on > EMAN2). I couldn’t find a thread where the topic was discussed. Is it even > possible, and if not, are there any other options ? Would it work by command line? > I found this command: Gctf-v0.50_sm_30_cu5.0_x86_64 > Micrographs/Falcon*.mrc --do_EPA --apix 1.07 --do_local_refine --boxsuffix > .box > I have autopicked particles on relion, would I be able to use this command > if I convert my particles into a .box format? > Thank you for any help, > Chiara > Chiara Rapisarda > Post doc > Université de Bordeaux, CNRS, INSERM > [log in to unmask] > Tel. +33 (5) 4000 3617 > Institut européen de chimie et biologie > 2, rue Robert Escarpit > 33607 Pessac, France > www.iecb.u-bordeaux.fr > ________________________________ > 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 ######################################################################## To unsubscribe from the CCPEM list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1