Hi Chun-Feng David,
in addition to Chimera vop zone and the methods suggested by Madhu,
you can also try the extraction of the geometrical asymmetric unit by
unit the SCIPION protocol xmipp3_extract_asymmetric_unit
(https://doi.org/10.1021/acs.jcim.9b01032). Four common icosahedral
symmetries are available.
Cheers,
MARTA
Quoting "Sevvana, Madhumati" <[log in to unmask]>:
> Hi,
> I use either of the two methods below.
>
> Method 1:
> You can use phenix.map_box
> Fit a model into the map using chimera (the map to model fit might
> not have to be accurate). Save the model with the map as a
> reference. Then use phenix.map_box to extract the map around the
> model.
>
> Method 2:
> You can use e2proc3d.py
>
> e2proc3d.py icosahedral-map.mrc asu.mrc --process mask.asymunit:au=1:sym=icos
> followed by
> e2proc3d.py icosahedral-map.mrc output.mrc --process
> mask.fromfile:filename=asu.mrc
>
> All the best.
> Madhu
>
> ---------------------------------------------------
> Madhumati Sevvana, Ph.D.
> Assistant Research Scientist
> Hockmeyer Hall of Structural Biology
> Purdue University, West Lafayette IN
>
>
> ________________________________
> From: Collaborative Computational Project in Electron
> cryo-Microscopy <[log in to unmask]> on behalf of Chun-Feng Hou
> <[log in to unmask]>
> Sent: Monday, September 21, 2020 18:47
> To: [log in to unmask] <[log in to unmask]>
> Subject: [ccpem] Please help. icosahedral asymmetric unit extraction
>
> Hi there,
>
> I have a 650 pixel box, 1.42 pixel/Angstrom icosahedral map that is
> about 1Gb. We would like to apply on some auto build programs but
> the size is limited to 300 Mb.
>
> My question is that is there a way to extract only the icosahedral
> asymmetric unit so I can cut down the size of the map? Or anyway to
> decrease the file size but not lose the density? I searched and
> there is one way that Chimera can apply an atomic model of from
> other source fit into the density and use volume viewer -> entry
> features/Atom box or /Zone to extract the map.
>
>
> Thank you!
>
>
> Chun-Feng David Hou, PhD
>
> Post-doctoral fellow,
> Dept. of Biochemistry & Mol. Biology
>
> Thomas Jefferson University
>
> JAH-4E, Lab 412; Office 411C
>
> 1020 Locust Street, 19107 Philadelphia PA
>
> Tel: 215-503-4015 (office)
>
>
>
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--
Marta Martinez Gonzalez
Biocomputing Unit (Lab B13)
National Center for Biotechnology-CSIC
Darwin, 3. Campus de la Universidad Autonoma de Madrid
28049 Madrid. Spain
Tel:+34 915854510 Fax:+34 913720112
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