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Dear all,<BR>
<BR>
Many thanks for those who reported the issue of Gautomatch for picking rectangle K2 data.<BR>
<BR>
Instead of clipping your micrograph before start Gautomatch,<BR>
you can now directly use such micrographs for Gautomatch auto-picking.<BR>
<A HREF="http://www.mrc-lmb.cam.ac.uk/kzhang/Gautomatch/Gautomatch_v0.53/">http://www.mrc-lmb.cam.ac.uk/kzhang/Gautomatch/Gautomatch_v0.53/</A><BR>
<BR>
Other minor issues fixed:<BR>
1) --max_dist has been changed to --min_dist ;<BR>
2) changed the order of _rlnClassNumber #3 and _rlnAnglePsi #4 which was incorrect before.<BR>
<BR>
<BR>
<B>Some useful features:</B><BR>
<B><FONT COLOR="#008000">1) exclusive picking:</FONT></B><BR>
Specify the option <B>--exclusive_picking</B> and <B><FONT COLOR="#000000">--excluded_suffix</FONT></B> will allow to exclude user provided areas, example:<BR>
<B><I><FONT COLOR="#808080">Gautomatch Micrograph/Falcon*.mrc --apixM 1.34 --diameter 400 --min_dist 240 --T template_all.mrcs --exclusive_picking --excluded_suffix _rubbish.star</FONT></I></B><BR>
<BR>
this is helpful in the following case:<BR>
<BR>
<B>(a) Another cycle of auto-picking after 2D classification:</B><BR>
In this case, usually you are pretty sure that some of the particles are completely rubbish, it will be much better to exclude them during picking. <BR>
<BR>
<B>(b) picking for partial structure:</B><BR>
Sometimes, you might have two/multiple domain complex, one is severely dominant and affect the picking of the other(the rest). <BR>
If you want to focused on another domain, it might be quite helpful to exclude 'good' particles from 2D classification.<BR>
<B>(c) Strong orientation preference:</B><BR>
If your templates were severely biased and mainly picked the preferred views, then it might be nice to exclude the preferred views and focused on rare views.<BR>
<B>(d) Detector defects:</B><BR>
Occasionally people might have a problem of detector defects, e.g. a black/white stripe, --exclusive_picking will help to get rid of these bad areas<BR>
Apart from <B>'--exclusive_picking' </B>and <B>'--excluded_suffix'</B>, the '<B>--global_excluded_box'</B> option is helpful to solve these detector issue by providing a simple box file.<BR>
<BR>
<B><I><FONT COLOR="#808080">Gautomatch Micrograph/K2_2016_02_06_1???.mrc --apixM 1.34 --diameter 400 --min_dist 240 --T template_all.mrcs --global_excluded_box K2_stripe_marked.box </FONT></I></B><BR>
<BR>
<BR>
2) added output file *rejected.star files so that they could be directly loaded by Relion GUI for optimizing the parameters in challenging cases. <BR>
<BR>
3) added --do_pre_filter, --pre_hp using a special mirror padding approach to get rid of the get rid of the severely gradient background. <BR>
<BR>
<BR>
Scripts that might be helpful:<BR>
<A HREF="http://www.mrc-lmb.cam.ac.uk/kzhang/useful_tools/">http://www.mrc-lmb.cam.ac.uk/kzhang/useful_tools/</A><BR>
The purpose of each script is indicated by the name and the usage could be obtained by running it without any parameter.<BR>
<BR>
<BR>
A 500£ GPU + <1 hour learning, saving you tens of thousands of times invaluable time with much better results! <BR>
<BR>
<BR>
Many thanks,<BR>
Kai<BR>
<BR>
<BR>
<BR>
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