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Re: [scipion-users] Local Resolution estimation(MonoRes and DeepRes) and Local Deblur
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From: 范宏成 <187...@16...> - 2020-01-08 07:55:16
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Dear Jose, I got it. Thank you very much! Fan | | 范宏成 | | m18...@16... | 签名由网易邮箱大师定制 On 1/8/2020 15:34，Jose Maria Carazo<ca...@cn...> wrote： 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... | 签名由网易邮箱大师定制 On 1/7/2020 15:36，Pablo Conesa<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...> 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... | 签名由 网易邮箱大师 定制 On 1/2/2020 17:46，JOSE LUIS VILAS PRIETO<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 _______________________________________________ scipion-users mailing list sci...@li... https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - Madrid Scipion team _______________________________________________ scipion-users mailing list sci...@li... https://lists.sourceforge.net/lists/listinfo/scipion-users -- 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 |
