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Dear Kai,
I successfully installed CUDA and run Gautomatch and Gctf on a Centos Box. I then tried the same on my laptop under UBUNTU-14.04 that has an Nvidia Quadro 1000. However, despite not showing any error, the files created by Gautomatch are empty. Is this meant by your remark in the manual? The CUDA test program I tried worked correctly....
"Requirement:
--> CentOS/Redhat Linux x86_64 (might be problems on Ubuntu or SUSE)"
is this the problem you are referring to?
In any case, thanks for hints and for making these fantastic programs available!
best, Dieter
------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: [log in to unmask] ------------------------------------------------------------------------
Am 27.03.2016 um 12:54 schrieb Kai Zhang:
Dear all,
Many thanks for those who reported the issue of Gautomatch for picking rectangle K2 data.
Instead of clipping your micrograph before start Gautomatch,
you can now directly use such micrographs for Gautomatch auto-picking.
http://www.mrc-lmb.cam.ac.uk/kzhang/Gautomatch/Gautomatch_v0.53/
Other minor issues fixed:
1) --max_dist has been changed to --min_dist ;
2) changed the order of _rlnClassNumber #3 and _rlnAnglePsi #4 which was incorrect before.
Some useful features:
1) exclusive picking:
Specify the option --exclusive_picking and --excluded_suffix will allow to exclude user provided areas, example:
Gautomatch Micrograph/Falcon*.mrc --apixM 1.34 --diameter 400 --min_dist 240 --T template_all.mrcs --exclusive_picking --excluded_suffix _rubbish.star
this is helpful in the following case:
(a) Another cycle of auto-picking after 2D classification:
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.
(b) picking for partial structure:
Sometimes, you might have two/multiple domain complex, one is severely dominant and affect the picking of the other(the rest).
If you want to focused on another domain, it might be quite helpful to exclude 'good' particles from 2D classification.
(c) Strong orientation preference:
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.
(d) Detector defects:
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
Apart from '--exclusive_picking' and '--excluded_suffix', the '--global_excluded_box' option is helpful to solve these detector issue by providing a simple box file.
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
2) added output file *rejected.star files so that they could be directly loaded by Relion GUI for optimizing the parameters in challenging cases.
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.
Scripts that might be helpful:
http://www.mrc-lmb.cam.ac.uk/kzhang/useful_tools/
The purpose of each script is indicated by the name and the usage could be obtained by running it without any parameter.
A 500£ GPU + <1 hour learning, saving you tens of thousands of times invaluable time with much better results!
Many thanks,
Kai