Re: [ccp4bb] CCP4 7.1 released

2020-04-23 Thread David Waterman 
Not yet all. It is a significant project, but one that is very much
underway.
-- David


On Thu, 23 Apr 2020 at 18:55, David Schuller  wrote:

> Coincidentally, Python 2 had its final release just a few days ago. I
> trust python components of CCP4 are all now using Python 3.
>
> https://www.theregister.co.uk/2020/04/21/the_final_python_2_release/
>
> -
> ===
> All Things Serve the Beam
> ===
>David J. Schuller
>modern man in a post-modern world
>MacCHESS, Cornell University
>schul...@cornell.edu
>
> --
>
>
> On 2020-04-23 12:30, Eugene Krissinel wrote:
>
> Dear CCP4 Users,
>
> The CCP4 Core Group is very pleased to announce the release of the latest
> version of the CCP4 Software Suite. Version 7.1 (Skipton) is now available
> from the CCP4 download website . The
> release is available for all MS Windows, Linux and Mac OSX platforms.
> Is it really necessary to switch to CCP4 7.1 now?
>
> While CCP4 7.0 can be kept on your computers for as long as necessary and
> in parallel to CCP4 7.1 (Mac OSX and Linux only), we encourage all our
> users to switch over at first convenience because:
>
>1. the release brings new, updated and improved components that make
>structure solution with CCP4 yet more efficient and easy
>2. the update line for CCP4 7.0 is now discontinued
>3. support for CCP4 7.0, as well as for all earlier versions of CCP4,
>is no longer available
>
> CCP4 7.1 Release Highlights
>
> CCP4 Release 7.1 comes as a complete modernisation of version 7.0, which
> have seen the longest life time ever in CCP4 history, being released more
> than 4 years ago and complemented with 79 updates. However, changes in
> operating systems and advances in computer languages, accumulated over this
> significant time period, have made it necessary to introduce technical
> modifications, such as progressing to C++-11, that could not be carried out
> using the CCP4 update system.
> Main Updates and Improvements
>
> CCP4 7.1 represents the final state of 7.0 update series, complemented
> with newest versions of many important components, for example:
> COOT 0.9
>
> *The latest version of Interactive Model Building Software from Dr. Paul
> Emsley, MRC/LMB, Cambridge, with many improvements and new features.*
>
> Currently available only for Mac OSX and Linux users. The corresponding
> update for Windows systems will be issued as soon as feasible
> DIALS 2.1
>
> *Diffraction image processing software from Diamond Light Source Ltd.,
> CCP4 and the Lawrence Berkeley National Laboratory. DIALS now includes a
> scaling module and improved multi-crystal symmetry tools.*
> DUI 2019.12
>
> *A Graphical User Interface for DIALS programs.*
> XIA2 0.6.0
>
> *Automated diffraction image processing using an expert system.*
> PHASER 2.8.3
>
> *Maximum likelihood structure solution software from the group of Prof.
> Randy Read, Cambridge.*
> SHELX
>
> *SHELX Software from Prof. George Sheldrick, University of Goettingen,
> Germany (SHELXE is supported by Dr. Isabel Uson, Barcelona, Spain)*
> Buccaneer
>
> *BUCCANEER Software from Dr. Kevin Cowtan, University of York, UK, with
> important fixes and improvements*
>
> and many others. CCP4 continues to provide
> ARP/wARP 8.0
>
> *Automated Model Building Software from Dr. Victor Lamzin, EMBL Outstation
> in Hamburg, Germany* integrated with the CCP4 Core package.
>
> In CCP4 7.1, you will find considerably advanced and improved:
> CCP4i2
>
> *CCP4 Graphical Interface with many tasks and report pages revised and
> partly redesigned, numerous bugs fixed and overall stability enhanced.* In
> particular, CCP4i2 now contains the deposition module, which allows you to
> prepare files in mmCIF format, suitable for deposition to the PDB in a
> fairly automated manner.
> New Software
>
> In addition to numerous modifications, advances and updates, CCP4 7.1
> introduces a few brand new components:
> GEMMI
>
> *C++/Python application and library for handling coordinate and reflection
> data (from Marcin Wojdyr, Global Phasing Ltd., Cambridge, UK)*
>
> GEMMI is a highly efficient and sophisticated package for manipulating
> coordinate and reflection data in various formats (such as .pdb, .mmcif,
> .mtz). The package is very useful for developing MX-related applications in
> C++ and Python.
> MRparse
>
> *Assistant application for making and analysing search models for
> Molecular Replacement (from the group of Prof. Daniel Rigden, University of
> Liverpool, UK)*
>
> MRparse finds suitable structure homologs, aligns and represents them
> graphically for reference and more efficient MR ensembling. Available in
> CCP4i2 interface.
> CCP4 Cloud
>
> *A framework for distributed CCP4

Re: [ccp4bb] CCP4 7.1 released

2020-04-23 Thread David Schuller 
Coincidentally, Python 2 had its final release just a few days ago. I 
trust python components of CCP4 are all now using Python 3.


https://www.theregister.co.uk/2020/04/21/the_final_python_2_release/

-
===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu

--


On 2020-04-23 12:30, Eugene Krissinel wrote:



Dear CCP4 Users,

The CCP4 Core Group is very pleased to announce the release of the 
latest version of the CCP4 Software Suite. Version 7.1 (Skipton) is 
now available from the CCP4 download website 
. The release is available for all 
MS Windows, Linux and Mac OSX platforms.



Is it really necessary to switch to CCP4 7.1 now?

While CCP4 7.0 can be kept on your computers for as long as necessary 
and in parallel to CCP4 7.1 (Mac OSX and Linux only), we encourage all 
our users to switch over at first convenience because:


 1. the release brings new, updated and improved components that make
structure solution with CCP4 yet more efficient and easy
 2. the update line for CCP4 7.0 is now discontinued
 3. support for CCP4 7.0, as well as for all earlier versions of CCP4,
is no longer available


CCP4 7.1 Release Highlights

CCP4 Release 7.1 comes as a complete modernisation of version 7.0, 
which have seen the longest life time ever in CCP4 history, being 
released more than 4 years ago and complemented with 79 updates. 
However, changes in operating systems and advances in computer 
languages, accumulated over this significant time period, have made it 
necessary to introduce technical modifications, such as progressing to 
C++-11, that could not be carried out using the CCP4 update system.



  Main Updates and Improvements

CCP4 7.1 represents the final state of 7.0 update series, complemented 
with newest versions of many important components, for example:



COOT 0.9

/The latest version of Interactive Model Building Software from Dr. 
Paul Emsley, MRC/LMB, Cambridge, with many improvements and new features./


Currently available only for Mac OSX and Linux users. The 
corresponding update for Windows systems will be issued as soon as 
feasible



DIALS 2.1

/Diffraction image processing software from Diamond Light Source Ltd., 
CCP4 and the Lawrence Berkeley National Laboratory. DIALS now includes 
a scaling module and improved multi-crystal symmetry tools./



DUI 2019.12

/A Graphical User Interface for DIALS programs./


XIA2 0.6.0

/Automated diffraction image processing using an expert system./


PHASER 2.8.3

/Maximum likelihood structure solution software from the group of 
Prof. Randy Read, Cambridge./



SHELX

/SHELX Software from Prof. George Sheldrick, University of Goettingen, 
Germany (SHELXE is supported by Dr. Isabel Uson, Barcelona, Spain)/



Buccaneer

/BUCCANEER Software from Dr. Kevin Cowtan, University of York, UK, 
with important fixes and improvements/


and many others. CCP4 continues to provide


ARP/wARP 8.0

/Automated Model Building Software from Dr. Victor Lamzin, EMBL 
Outstation in Hamburg, Germany/ integrated with the CCP4 Core package.


In CCP4 7.1, you will find considerably advanced and improved:


CCP4i2

/CCP4 Graphical Interface with many tasks and report pages revised and 
partly redesigned, numerous bugs fixed and overall stability 
enhanced./ In particular, CCP4i2 now contains the deposition module, 
which allows you to prepare files in mmCIF format, suitable for 
deposition to the PDB in a fairly automated manner.



  New Software

In addition to numerous modifications, advances and updates, CCP4 7.1 
introduces a few brand new components:



GEMMI

/C++/Python application and library for handling coordinate and 
reflection data (from Marcin Wojdyr, Global Phasing Ltd., Cambridge, UK)/


GEMMI is a highly efficient and sophisticated package for manipulating 
coordinate and reflection data in various formats (such as .pdb, 
.mmcif, .mtz). The package is very useful for developing MX-related 
applications in C++ and Python.



MRparse

/Assistant application for making and analysing search models for 
Molecular Replacement (from the group of Prof. Daniel Rigden, 
University of Liverpool, UK)/


MRparse finds suitable structure homologs, aligns and represents them 
graphically for reference and more efficient MR ensembling. Available 
in CCP4i2 interface.



CCP4 Cloud

/A framework for distributed CCP4 Computation/

CCP4 Cloud represents a conceptually new approach to organising and 
maintaining crystallographic projects in CCP4 and running CCP4 tasks.

[ccp4bb] CCP4 7.1 released

2020-04-23 Thread Eugene Krissinel 
Dear CCP4 Users,

The CCP4 Core Group is very pleased to announce the release of the latest
version of the CCP4 Software Suite. Version 7.1 (Skipton) is now available
from the CCP4 download website . The
release is available for all MS Windows, Linux and Mac OSX platforms.
Is it really necessary to switch to CCP4 7.1 now?

While CCP4 7.0 can be kept on your computers for as long as necessary and
in parallel to CCP4 7.1 (Mac OSX and Linux only), we encourage all our
users to switch over at first convenience because:

   1. the release brings new, updated and improved components that make
   structure solution with CCP4 yet more efficient and easy
   2. the update line for CCP4 7.0 is now discontinued
   3. support for CCP4 7.0, as well as for all earlier versions of CCP4, is
   no longer available

CCP4 7.1 Release Highlights

CCP4 Release 7.1 comes as a complete modernisation of version 7.0, which
have seen the longest life time ever in CCP4 history, being released more
than 4 years ago and complemented with 79 updates. However, changes in
operating systems and advances in computer languages, accumulated over this
significant time period, have made it necessary to introduce technical
modifications, such as progressing to C++-11, that could not be carried out
using the CCP4 update system.
Main Updates and Improvements

CCP4 7.1 represents the final state of 7.0 update series, complemented with
newest versions of many important components, for example:
COOT 0.9

*The latest version of Interactive Model Building Software from Dr. Paul
Emsley, MRC/LMB, Cambridge, with many improvements and new features.*

Currently available only for Mac OSX and Linux users. The corresponding
update for Windows systems will be issued as soon as feasible
DIALS 2.1

*Diffraction image processing software from Diamond Light Source Ltd., CCP4
and the Lawrence Berkeley National Laboratory. DIALS now includes a scaling
module and improved multi-crystal symmetry tools.*
DUI 2019.12

*A Graphical User Interface for DIALS programs.*
XIA2 0.6.0

*Automated diffraction image processing using an expert system.*
PHASER 2.8.3

*Maximum likelihood structure solution software from the group of Prof.
Randy Read, Cambridge.*
SHELX

*SHELX Software from Prof. George Sheldrick, University of Goettingen,
Germany (SHELXE is supported by Dr. Isabel Uson, Barcelona, Spain)*
Buccaneer

*BUCCANEER Software from Dr. Kevin Cowtan, University of York, UK, with
important fixes and improvements*

and many others. CCP4 continues to provide
ARP/wARP 8.0

*Automated Model Building Software from Dr. Victor Lamzin, EMBL Outstation
in Hamburg, Germany* integrated with the CCP4 Core package.

In CCP4 7.1, you will find considerably advanced and improved:
CCP4i2

*CCP4 Graphical Interface with many tasks and report pages revised and
partly redesigned, numerous bugs fixed and overall stability enhanced.* In
particular, CCP4i2 now contains the deposition module, which allows you to
prepare files in mmCIF format, suitable for deposition to the PDB in a
fairly automated manner.
New Software

In addition to numerous modifications, advances and updates, CCP4 7.1
introduces a few brand new components:
GEMMI

*C++/Python application and library for handling coordinate and reflection
data (from Marcin Wojdyr, Global Phasing Ltd., Cambridge, UK)*

GEMMI is a highly efficient and sophisticated package for manipulating
coordinate and reflection data in various formats (such as .pdb, .mmcif,
.mtz). The package is very useful for developing MX-related applications in
C++ and Python.
MRparse

*Assistant application for making and analysing search models for Molecular
Replacement (from the group of Prof. Daniel Rigden, University of
Liverpool, UK)*

MRparse finds suitable structure homologs, aligns and represents them
graphically for reference and more efficient MR ensembling. Available in
CCP4i2 interface.
CCP4 Cloud

*A framework for distributed CCP4 Computation*

CCP4 Cloud represents a conceptually new approach to organising and
maintaining crystallographic projects in CCP4 and running CCP4 tasks. With
this system, you can keep all your data and projects in the Cloud and
manage them using any modern browser running on a desktop PC, laptop,
tablet/ipad or even a smartphone, from any geographic location. In CCP4
Cloud, only the initial data need to be uploaded once; within a Project,
the data is passed from task to task behind the scenes, without exchange
with the client device. CCP4 Cloud represents Projects as branched trees,
making the structure solution pathway perfectly transparent and easily
reconcilable. All main stages of structure solution in MX: image
processing, phasing, model building, refinement, validation and PDB
deposition are presented in CCP4 Cloud as a collection of more than 75
tasks. Interactive tasks, such as Coot, are also available in CCP4 Cloud.
Using such tasks requires a local CCP4 7.1 setup, which contains the CCP4