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

[Jose M. C. <ca...@cn...>]

Just jumping into it, Orney the first author of this paper, will contact
you ASAP (he was coming back from being for Chritmast with his family in
Cuba)

We are extremely interested in all our methods to be widely used, and
clearly the situation as it is is far from perfect..... but Ernery will
contact you, and will also address the whole list with
a clear way to use his program. My apologises for the current situation

Wbw..JM

On Wed, Jan 8, 2020 at 3:02 AM 范宏成 <187...@16...> wrote:

> HI Pablo,
> I'd like to go that way. Thank you very much!
>
> 范宏成
> m18...@16...
>
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> On 1/7/2020 15:36，Pablo Conesa<pc...@cn...> <pc...@cn...>
> wrote：
>
> 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...> <187...@16...>
> escribió:
>
> Dear Jose,
> Regarding the DeepRes, I did't find in my scipion although I use crtl+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...>
> <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...> <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...
> |
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> --
> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
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-- 
Prof. Jose-Maria Carazo
Biocomputing Unit, Head, CNB-CSIC
Spanish National Center for Biotechnology
Darwin 3, Universidad Autonoma de Madrid
28049 Madrid, Spain


Cell: +34639197980