[Blends-commit] r3550 - /projects/pan/trunk/debian-pan/tasks/mx

[picca at users.alioth.debian.org]

Author: picca
Date: Sun Aug  5 12:48:13 2012
New Revision: 3550

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3550
Log:
add more mx descriptions

Modified:
    projects/pan/trunk/debian-pan/tasks/mx

Modified: projects/pan/trunk/debian-pan/tasks/mx
URL: http://svn.debian.org/wsvn/blends/projects/pan/trunk/debian-pan/tasks/mx?rev=3550&op=diff
==============================================================================
--- projects/pan/trunk/debian-pan/tasks/mx (original)
+++ projects/pan/trunk/debian-pan/tasks/mx Sun Aug  5 12:48:13 2012
@@ -273,42 +273,107 @@
 Homepage: ?
 License: ?
 Pkg-Description: ?
-
-Suggests: cns_refine
-Homepage: ?
-License: ?
-Pkg-Description: ?
-Comment: ?
-
-Suggests: cns_solve
-Homepage: ?
-License: ?
-Pkg-Description: ?
-Comment: ?
+Remark: ESRF can you gives more information about this software
+
+Suggests: cns
+Homepage: http://cns.csb.yale.edu/v1.2/
+License: non-free
+Pkg-Description: Crystallography & NMR System (CNS) is the result of
+ an international collaborative effort among several research
+ groups. The program has been designed to provide a flexible
+ multi-level hierachical approach for the most commonly used
+ algorithms in macromolecular structure determination. Highlights
+ include heavy atom searching, experimental phasing (including MAD and
+ MIR), density modification, crystallographic refinement with maximum
+ likelihood targets, and NMR structure calculation using NOEs,
+ J-coupling, chemical shift, and dipolar coupling data.
 
 Suggests: crank
-Homepage: ?
-License: ?
-Pkg-Description: ?
-Comment: ?
+Homepage: http://www.ccp4.ac.uk/html/crank.html
+License: non-free
+Pkg-Description: Crank [1] is a program to automate macromolecular
+ structure determination for single or multiple-wavelength anomalous
+ diffraction (SAD/MAD) or single isomorphous replacement (SIRAS)
+ experiments. Crank interfaces with various crystallographic programs
+ and is designed to allow both the automation of the structure
+ determination process, but also allow the user to re-run and optmize
+ results, if necessary.
+ .
+ This version of Crank has interfaces to the programs CRUNCH2 [2] and
+ SHELXD [3] for substructure detection, BP3 [4], [5] for substructure
+ phasing, SOLOMON [6], DM [7], SHELXE [8], PIRATE [9] and RESOLVE [23]
+ for density modification and RESOLVE [24], BUCCANEER [25] and
+ ARP/wARP [10] for automated model building. ARP/wARP uses REFMAC [11]
+ for iterative refinement. Within REFMAC, either the likelihood
+ function restraining phases via Hendrickson-Lattman coefficients [12]
+ or a multivariate likelihood SAD function [13] is used. To calculate
+ FA values needed for substructure detection, crank interfaces with
+ the programs SHELXC [14] or AFRO [15]. For setting up and preparing
+ files, crank using programs from the CCP4 [16] suite, including
+ SFTOOLS [17] and TRUNCATE [18]. Also, crank uses the
+ Kantardjieff-Rupp algorithm [19] which performs a probabilistic
+ Matthew's coefficient [20] calculation for estimating the number of
+ monomers in the asymmetric unit. To visualize the results produced by
+ crank, an interface to COOT [26] is also available.
+ .
+ Crank can be run using its CCP4i [21] interface or via script using
+ the program GCX [22]. Crank's only dependency to produce a density
+ modified map is a licenced CCP4 version 5.99.x or later. If you would
+ like to use the SHELX [13] programs, ARP/wARP [10], RESOLVE [23],
+ [24] and/or BUCCANEER [25] within crank, you must have it installed
+ on your system with the appropriate licence. If these programs do not
+ appear in your path, they will not appear as options in the ccp4i
+ interface.
+Remark: You need a licenced version of CCP4 6.0 or higher installed to
+ use crank and if you wish to use the ARP/wARP, RESOLVE and/or
+ SHELX[C/D/E] software within crank, they also must be installed on
+ your system, and you must comply with the software's licence
+ agreement.
 
 Suggests: crystfel
-Homepage: ?
-License: ?
-Pkg-Description: ?
-Comment: ?
+Homepage: http://www.desy.de/~twhite/crystfel/
+License: GPLv3+
+Pkg-Description: CrystFEL is a suite of programs for processing
+ diffraction data acquired "serially" in a "snapshot" manner. That
+ means: a large number of individual diffraction patterns, each
+ corresponding to a random orientation of the crystal, with little or
+ no rotation or oscillation of the sample. This is exactly the
+ situation encountered when using the technique of Serial Femtosecond
+ Crystallography (SFX) with a free-electron laser source, which is the
+ application CrystFEL is primarily designed for.
+Remark: if you intent to package a software of this task, please
+ considere this one.
+Published-Authors: T. A. White, R. A. Kirian, A. V. Martin, A. Aquila, K. Nass, A. Barty and H. N. Chapman.
+Published-Title: "CrystFEL: a software suite for snapshot serial crystallography".
+Published-In: J. Appl. Cryst. 45, p335–341.
+Published-DOI: 10.1107/S0021889812002312
+Published-URL: http://www.desy.de/~twhite/crystfel/db5097-reprint.pdf
 
 Suggests: das
-Homepage: ?
-License: ?
-Pkg-Description: ?
-Comment: ?
-
-Suggests: dialboxlinuxdriverdialbox_to_remove
-Homepage: ?
-License: ?
-Pkg-Description: ?
-Comment: ?
+Homepage: http://www.biodas.org/wiki/Main_Page
+License: ?
+Pkg-Description: The Distributed Annotation System (DAS) defines a
+ communication protocol used to exchange annotations on genomic or
+ protein sequences. It is motivated by the idea that such annotations
+ should not be provided by single centralized databases, but should
+ instead be spread over multiple sites. Data distribution, performed
+ by DAS servers, is separated from visualization, which is done by DAS
+ clients. The advantages of this system are that control over the data
+ is retained by data providers, data is freed from the constraints of
+ specific organisations and the normal issues of release cycles, API
+ updates and data duplication are avoided.
+ .
+ DAS is a client-server system in which a single client integrates
+ information from multiple servers. It allows a single machine to
+ gather up sequence annotation information from multiple distant web
+ sites, collate the information, and display it to the user in a
+ single view. Little coordination is needed among the various
+ information providers.
+ .
+ DAS is heavily used in the genome bioinformatics community. Over the
+ last years we have also seen growing acceptance in the protein
+ sequence and structure communities.
+Remark: ESRF can you gives more information about this software
 
 Depends: dino
 
@@ -317,46 +382,143 @@
 License: ?
 Pkg-Description: ?
 Comment: ?
+Remark: ESRF can you gives more information about this software
 
 Suggests: domain-finder
-Homepage: ?
-License: ?
-Pkg-Description: ?
-Comment: ?
+Homepage: http://dirac.cnrs-orleans.fr/DomainFinder/
+License: GPLv3+
+Pkg-Description: DomainFinder is an interactive program for the
+ determination and characterization of dynamical domains in
+ proteins. Its key features are
+ .
+   * computational efficiency: even large proteins can be analyzed
+     using a desktop computer in a few minutes
+   * ease of use: a state-of-the-art graphical user interface
+   * export of results for visualization and further analysis (VRML,
+     PDB, and MMTK object format)
+ .
+ Dynamical domains are an important concept in the description of
+ protein dynamics. A dynamical domain is a region in a protein which
+ can move essentially like a rigid body relative to other
+ regions. Many, but not all, proteins have dynamical domains, and if
+ they do, the relative movements of the domains are usually related to
+ the function of the protein. The identification of dynamical domains
+ is therefore useful in understanding the function of the
+ protein. However, there are other situations in which the knowledge
+ of dynamical domains is helpful. In structure determination, it can
+ help to predict whether complexation with a ligand, crystal packing,
+ or other external influences can lead to important conformational
+ changes. In protein engineering, it can indicate whether a given
+ modification is likely to change the dynamical behavior of the
+ protein. In experimental observations of protein motion, it can
+ suggest regions of particular interest. In numerical simulations, it
+ can point out the slow motions whose correct sampling must be
+ verified.
+ .
+ DomainFinder is written in Python, a high-level object programming
+ language that is particularly well suited to the demands of
+ scientific computations. The speed-critical parts are implemented in
+ C. For common operations it makes use of the Molecular Modeling
+ Toolkit, a library of Python code for molecular modelling and
+ simulation applications. The results of a domain analysis can be
+ saved with all details in an MMTK data file, which permits all kinds
+ of further analysis.
 
 Suggests: dps2ar
-Homepage: ?
-License: ?
-Pkg-Description: ?
-Comment: ?
+Homepage: http://www.embl-hamburg.de/Auto-Rickshaw/DPS2AR/
+License: ?
+Pkg-Description: The EMBL-Hamburg automated crystal structure
+ determination platform is a system which contains several distinct
+ decision-makers which utilize a number of macromolecular
+ crystallographic software programs to produce a software pipeline for
+ automated and efficient crystal structure determination. A large
+ number of possible structure solution paths are encoded in the system
+ and the optimal path is selected by the decision-makers as the
+ structure solution evolves. The processes have been optimised for
+ speed so that the pipeline can be used effectively for validating the
+ X-ray experiment at a synchrotron beamline. Currently, the platform
+ offers SAD, SIRAS, 2W-MAD, 3W-MAD or 4W-MAD phase determination,
+ molecular replacement (MR) and MRSAD phasing. Recently it has been
+ extended to include RIP and MRRIP phasing.
+ .
+ Auto-Rickshaw comes in two flavours : a Beamline Version and an
+ Advanced Version. Both versions use a similar GUI for input, but the
+ Advanced Version requires the sequence information for the protein
+ target in order to build the side chains.
+ .
+ The “Beamline Version” is explicitly designed for use in validation
+ of the X-ray experiment at the synchrotron beamline as soon as the
+ data have been collected and processed.  Once the X-ray experiment is
+ validated, the “Advanced Version” can be used for a more complete
+ model building if the resolution of the data permits. The “Advanced
+ Version” of the platform uses ARP/wARP, beta-version of SHELXE,
+ RESOLVE and BUCCANEER
+ .
+ The Auto-Rickshaw platform has been installed on a 64-processors
+ Linux cluster and is remotely accessible to academic users via a
+ web-server . It allows to evaluate the success of their X-ray
+ diffraction experiments in the shortest possible time. This helps to
+ ensure an efficient use of the beam time available. The platform is
+ undergoing continuous development. This includes the improvement of
+ the platform's decision makers, the incorporation of new
+ functionalities as well as continuous software upgrades. An
+ emulation of the Auto-Rickshaw job submission.
+ .
+ Auto-Rickshaw server is freely accessible to users at academic
+ institution upon online registration .
 
 Suggests: dviewer
 Homepage: ?
 License: ?
 Pkg-Description: ?
-Comment: ?
+Remark: ESRF can you gives more information about this software
 
 Suggests: dyndom3d
-Homepage: ?
-License: ?
-Pkg-Description: ?
-Comment: ?
+Homepage: http://fizz.cmp.uea.ac.uk/dyndom/3D/
+License: non-free
+Pkg-Description: DynDom3D is a new program for the analysis of domain
+ movements in large, multi-chain, biomolecular complexes. The program
+ is applicable to any molecule for which two atomic structures are
+ available that represent a conformational change indicating a
+ possible domain movement. Unlike the original DynDom (DynDom1D) the
+ method is blind to atomic bonding and atom type and can therefore be
+ applied to biomolecular complexes containing different constituent
+ molecules such as protein, RNA or DNA. At the heart of the method is
+ the use of blocks located at grid points spanning the whole
+ molecule. The rotation vector for the rotation of atoms from each
+ block between the two conformations is calculated. Treating
+ components of these vectors as coordinates means that each block is
+ associated with a point in a “rotation space” and that blocks with
+ atoms that rotate together, perhaps as part of the same rigid domain,
+ will have co-located points. Thus a domain can be identified from the
+ clustering of points from blocks within it. Domain pairs are accepted
+ for analysis of their relative movements in terms of screw axes based
+ upon a set of reasonable criteria. The results provide a depiction of
+ the conformational change within each molecule that is easily
+ understood, giving a perspective that is expected to lead to new
+ insights. It has basically five parameters: a minimum domain size (in
+ number of atoms), a ratio of interdomain displacement to intradomain
+ displacement, a grid length, a block factor, and a block occupancy
+ percentage.
 
 Suggests: edna
-Homepage: ?
-License: ?
-Pkg-Description: ?
-Comment: ?
-
-Suggests: edna2html
-Homepage: ?
-License: ?
-Pkg-Description: ?
-Comment: ?
+Homepage: http://wiki.edna-site.org/index.php/Main_Page
+License: ?
+Pkg-Description: EDNA is a framework for developing plugin-based
+ applications especially for online data analysis in the X-ray
+ experiments field. This article describes the features provided by
+ the EDNA framework to ease the development of extensible scientific
+ applications. This framework includes a plugins class hierarchy,
+ configuration and application facilities, a mechanism to generate
+ data classes and a testing framework. These utilities allow rapid
+ development and integration in which robustness and quality play a
+ fundamental role. A first prototype, designed for macromolecular
+ crystallography experiments and tested at several synchrotrons, is
+ presented.
 
 Suggests: elves
-Homepage: ?
-License: ?
+Homepage: http://ucxray.berkeley.edu/~jamesh/elves/
+License: non-free
 Pkg-Description: ?
 Comment: ?