Discussion List Archives

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

[SA_Scat] New MEMPROT release

  • To: "sa_scat@iucr.org" <sa_scat@iucr.org>
  • Subject: [SA_Scat] New MEMPROT release
  • From: PEREZ Javier <javier.perez@synchrotron-soleil.fr>
  • Date: Thu, 6 Apr 2017 08:21:15 +0000
  • Accept-Language: fr-FR, en-US
  • DKIM-Filter: OpenDKIM Filter v2.10.3 brouette.synchrotron-soleil.fr E1ACF70006C
  • DKIM-Filter: OpenDKIM Filter v2.10.3 brouette.synchrotron-soleil.fr 53AEE700079
  • DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed;d=synchrotron-soleil.fr; s=email; t=1491466877;bh=RG/gEPPvvbqaEPFgS00HlRQb3/xPP5EYckz+8ffl7TE=;h=From:To:Subject:Date:From;b=IJUa+5+12+cI3tlPBsKeMgbELo7pRB1xQVhnGdVwfjcpvIXQQn8+ts3pa93NJr32lCehb/ABgaWik8zDO13Kx0vQ6OMBBRXNne7r0dR6WwDbtf/nWVILz5ztTq9RgXrO0AGsu2SNe04ePlNPc7o2RHBks4rgqz/5eQtu3dxxuLU=
  • DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed;d=synchrotron-soleil.fr; s=email; t=1491466876;bh=RG/gEPPvvbqaEPFgS00HlRQb3/xPP5EYckz+8ffl7TE=;h=From:To:Subject:Date:From;b=AKTGRVC7ivz4JisZVi8ipwK1RhYqN4HAW9Doe4L2Y/t7g0qgrkjpo+ywm232YCZt/fQqYwNmFUtJmvwfC+Jis9DpsKDT4KVLvOsq4kqG04lF2uT5H54NK8m3yAYA3FUpWATbh3f0hTVgGQjxFKDUlC65VFGoBaMsi7vMyRYE9O8=
Dear all,Please find recent news from our MEMPROT program.Have a nice day !Javier
MEMPROT is an application meant to build a space-filling model of a detergent corona around a transmembrane protein, based on SAXS data fitting.
Welcome to Memprot Release 2! In the new version, we are happy to present:
1. New features:
1.1. Crysol 3 support.While Crysol 3 is *much* slower than Crysol 2, our initial tests suggest that it is significantly better for many proteins, especially transmembrane transporters and other proteins with big, long channels.Choose the version of Crysol you want to use with Memprot with one simple switch!
1.2. Adaptive Shape Algorithms.Two independent algorithms were implemented that make the surface of the detergent corona follow/mimic the surface of the transmembrane part of the protein. This enables attempts to model the corona around the proteins whose cross-section deviates significantly from an ellipsoid. Again the choice between different algorithms can be easily controlled by one simple variable
1.3. Various code optimisations.Memprot 2 is faster and the speed of the calculations is now limited by Crysol (especially when using Crysol 3). You can see it by yourself - a set of rudimentary timers was implemented.
1.4. Rudimentary Manual.We started working on documentation of Memprot so that all information about it can be found in a single, easily available place. In this iteration we laid the fundaments.
2. Bugfixes:
2.1. The option to limit the data by the qmin variable was not working properly in previous releases. It should now work correctly.2.2. Output format in Crysol 2 changed slightly recently. Memprot has been adapted accordingly.
3. *Tentative* plans for future:
3.1. Steepest Descent minimization: save time by going straight to (hopefully global) minimum of Chi^2 space3.2. Parallelization: save time by calculating many models at the same time on your local HPC cluster3.3. Support for programs alternative to Crysol: Check if your model gives consistently good fits across different programs.3.4. Improvements to Memprot Manual:
MEMPROT can be found on (also brand new) Soleil Website:French:https://www.synchrotron-soleil.fr/fr/lignes-de-lumiere/swingEnglish:https://www.synchrotron-soleil.fr/en/beamlines/swing
Memprot is a young program! We will *VERY MUCH* appreciate any questions, comments, suggestions and bug reports! Please write to us:Javier PĆ©rez: javier.perez@synchrotron-soleil.fr<mailto:javier.perez@synchrotron-soleil.fr>Maciej Baranowski: maciej.baranowski@synchrotron-soleil.fr<mailto:maciej.baranowski@synchrotron-soleil.fr>

Javier PĆ©rezGroup leader - Beamline SWINGSynchrotron SOLEILSaint-Aubin - BP 4891192 Gif sur Yvette CedexFranceTel : +33 (0)1 69 35 96 19 (office)        +33 (0)1 69 35 97 53 (beamline)javier.perez@synchrotron-soleil.fr<mailto:javier.perez@synchrotron-soleil.fr>http://www.synchrotron-soleil.fr/portal/page/portal/Recherche/LignesLumiere/SWING_______________________________________________sa_scat mailing listsa_scat@iucr.orghttp://mailman.iucr.org/cgi-bin/mailman/listinfo/sa_scat

Reply to: [list | sender only]
International Union of Crystallography

Scientific Union Member of the International Science Council (admitted 1947). Member of CODATA, the ISC Committee on Data. Partner with UNESCO, the United Nations Educational, Scientific and Cultural Organization in the International Year of Crystallography 2014.

International Science Council Scientific Freedom Policy

The IUCr observes the basic policy of non-discrimination and affirms the right and freedom of scientists to associate in international scientific activity without regard to such factors as ethnic origin, religion, citizenship, language, political stance, gender, sex or age, in accordance with the Statutes of the International Council for Science.