Hi Pietro!
As for free and open-source (GPLv3 license) refinement software, I am
developing Vagabond.
https://vagabond.hginn.co.uk
It is based on refining bond torsion angles in an ensemble of related
structures which also captures flexibility (no B factors!). There are no
restraints, only constraints. This allows a significant side-step of the
parametrisation problem and reduces the level of overfitting in the map
(which is more widespread than I first realised).
It is in the middle of development, very young and therefore not as
polished or refined as other (atomistic) refinement software, and is
currently best used as an intermediate tool, when you have confusing and
muddy electron density, to create a less overfitting-biased map to build
into and then continue with your favourite other refinement software.
git clone https://www.github.com/helenginn/vagabond.git
Typing this into a command line will demonstrate how open source it is!
Helen
---
On Thursday, 7 May 2020 09:34:13 PDT Roversi, Pietro (Dr.) wrote:
Dear all,
we are in the editorial stages of a manuscript that I submitted to
Wellcome Open Research for publication.
The journal/editor ask us to list fully Open Source alternatives to the
pieces of software we used, for example for data processing and
refinement.
What refinement programs are fully Open Source?
Thanks!
Pietro
Pietro Roversi
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
