Re: [scipion-users] Local Resolution estimation(MonoRes and DeepRes) and Local Deblur

[Pablo C. <pc...@cn...>]

Thanks Fan, Erney, just told me that deepres is not released in scipion 
2.0 but can be access in the devel "mode".

I guess any of he xmipp guys will be able to help you if you are willing 
to go that way.

On 5/1/20 16:25, 范宏成 wrote:
> Hi Pablo,
> I can see xmipp protocols in my scipion except for deepRes. Please see 
> attachment.
>
> Fan
>
>
>
>
>
> At 2020-01-05 23:04:56, pc...@cn... wrote:
>
>     Hi, can you check what is listed when you select the view "all" in
>     the top right drop-down. Can you see any Xmipp protocol?
>
>     El 2 ene. 2020 17:49, 范宏成 <187...@16...> escribió:
>
>         Dear Jose,
>         Regarding the DeepRes, I did't find in my scipion although I
>         usecrtl+F and search by writing the deepres.  I guess maybe my
>         scipion is not the developer version. So I tried to reinstall
>         my scipion (devel mode) and use plugin to install
>         xmipp(v3.19.04 source code).I found there existed deepRes in
>         my new install
>         scipion(scipion/software/em/xmipp/bin/xmipp_deepRes_resolution
>         and software/em/xmipp/bin/models/deepRes). However, I still
>         didn't search the deepRes in scipion gui. How to solve this
>         problem? Thank you!
>
>         Fan
>         	
>         范宏成
>         m18...@16...
>
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>         On 1/2/2020 17:46，JOSE LUIS VILAS PRIETO<jl...@cn...>
>         <mailto:jl...@cn...> wrote：
>
>             Dear Fan,
>
>             Thanks for getting in touch with us.
>
>             The input of localdeblur can be any local resolution map,
>             it means
>             that you can compute the local resolution with monores,
>             resmap,
>             blocres, o deepres. There is no one better than the other.
>
>             In the case of monores, as well as resmap, it is mandatory
>             that your
>             map contains noise, if it is noise free, use as I put  two
>             halves. It
>             should always be the best way of estimating the local
>             resolution.
>
>             Also, deepres is a good choice, because it overcomes the
>             noise
>             problem, and you can computer the local resolution map of
>             a noise-free
>             density map.
>
>             Deepres belongs to xmipp package and you should be able to
>             find it in
>             analisys tab in the left panel. Alternatively, you can do
>             crtl+F and
>             search by writing the name of the protocol, it means deepres.
>
>             Regarding with the micelle, you can create a mask and
>             apply it to remove it
>
>             Anything you need, please let us know
>
>             Kind regards
>
>             José Luis Vilas
>
>             Quoting 范宏成 <187...@16...>:
>
>                 Dear Colleagues,
>                 I have some questions about Local resolution
>                 estimation and Local
>                 Deblur.  Looking forward to your response . Thank you!
>                 1. MonoRes. Can MonoRes estimate the local resolution
>                 when I do
>                 focused refinement (masked refinement) using relion. I
>                 mean there
>                 maybe no region  to estimate the noise.  In this
>                 condition, I have
>                 to use the relion local resolution protocol to get the
>                 focused map
>                 local resolution.
>                 2. Local Deblur.  Can Local Deblur support the relion
>                 local
>                 resolution map or only support MonoRes,Resmap, Blocres?
>                 3. DeepRes. I recently read a paper about the DeepRes
>                 and find it
>                 very useful for my project.  I didn't find the DeepRes
>                 protocol in
>                 my scipion. My scipion version is v2.0(2019-04-23)
>                 Diocletian in
>                 Centos7 system(Binary version).  How can I use this
>                 protocol?
>                 4.DeepRes for membrane protein. In DeepRes paper, It
>                 said it is very
>                 important to mask out the micelle because DeepRes only
>                 trained with
>                 proteins.  If I don't mask out the micelle, What bad
>                 consequencies
>                 will happen? By the way, How to effectively and
>                 carefully  mask out
>                 the micellce? In my way, I deleted the micelle using
>                 particle
>                 substraction and run again auto-refinement in relion.
>                 In order not
>                 to delete the signal from the protein, I used to use
>                 the soft mask,
>                 So My membrante protein  had a small number of
>                 micelles around the
>                 TM domain. I'm afraid this residual micelle may cause bad
>                 consequencies when using DeepRes. Does someone have a
>                 better way to
>                 delete the micelle in membrane proteins?
>
>
>                 Fan Hongcheng
>
>
>                 | |
>                 范宏成
>                 |
>                 |
>                 m18...@16...
>                 |
>                 签名由网易邮箱大师定制
>
>
>
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-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*