Re: [ccp4bb] Twin law definition in REFMAC5

[Andrey Lebedev]

Dear Petr

Both questions, on twin law and R-factors, are mainly questions about 
definitions and standards.

From Online Dictionary of Crystallography: "The twin law is the SET of twin 
operations mapping two individuals of a twin." 

In your P 21 21 21 example with a=b, the set contains four operations:
2-fold rotations around [110] and [-110], and rotations around [001] by 90 and 
-90 degrees. These operations can be written as k,h,-l; -k,-h,-l; -k,h,l; 
k,-h,l. Four is because there are four operations in 222 point group. All four 
are equivalent twin operations for this particular twin. Any of them can be 
taken as a REPRESENTATIVE of the twin law, but it will be incorrect use of 
terminology to say that one of then IS a twin law.  It is valid to use any of 
them in calculations.

Again, the question about R-factors for data from twinned crystal is a question 
of definition. The standard definitions of R-cryst and R-free are NOT 
applicable to such data. (Let's leave alone the discussion on whether and when 
R-factors are useful statistics).

This is because the definitions of R-cryst and R-free use the notion of  
"observed" structure amplitudes. In case of non-twinned crystal, there is 
French-Wilson procedure (implemented in truncate program), which is a de-facto 
standard (good or bad - different story) for calculating "observed" structure 
amplitudes from "observed" intensities. To calculate the "observed" intensities 
from "twinned" intensities we need yet another standard, e.g. a standard 
de-twining procedure, which does not exist. Moreover, refinement programs do 
not use de-twinning, but, other way round, fit calculated "twinned" intensities 
to "observed" "twinned" intensities. This is robust. But when it goes to 
R-factors, there is range of options.

In Refmac, "twinned" refinement can be conducted against intensities or 
structure amplitudes, however calculated. The former is in theory more robust, 
but it uses definitions of R-factors that results in higher values, especially 
when there are many weak reflections.

For bureaucratic purposes, I may suggest the option of refinement against 
structure amplitudes (obtained e.g. using truncate). That will give lower 
R?factors. Alternatively, refinement against intensities can be followed by 
refmac job with zero cycles using structure amplitudes option.

Andrey

P.S. An important reminder from Garib: output mtz-file from refmac should not 
be used in subsequent refinements as input. It is only for map calculation and 
for internal use in model building pipelines. Please always use mtz-file form 
data reduction program (e.g. aimless) as input for refmac. This comment is 
especially relevant for "twin refinement".



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[ccp4bb] CCP4 on MacOS Catalina

[Andrey Lebedev]

Dear CCP4 Users

CCP4 Setup Manager and Update Manager are now functional on MacOS Catalina
in both user and administrative mode. The corrected version of Setup
Manager is now available from usual location, CCP4 Downloads
.

Technical details.
Previously both Setup and Update managers in admin mode were stalling at
the point when they launched external scripts. This was caused by
inconsistency between new elevation mechanism on Catalina and QProcess class
in Qt framework used in CCP4 Setup and Update Managers.

Best wishes
CCP4 core group



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[ccp4bb] CCP4-7.0 Update 70 including ARP/wARP-8.0 patch 1

[Andrey Lebedev]

Dear CCP4 Users

We would like to announce CCP4-7.0 update No 70 that includes the following.


*ARP/wARP: patch 1 for version  8.0*

Notes from Victor Lamzin, EMBL-Hamburg, Germany

News in ARP/wARP 8.0 patch 1:

Protein model building:
– Large structures up to 50,000 residues can now be handled; within this
limit the number of NCS-related copies can be up to 1000
– Both main-chain and side-chain building steps are now considerably faster
for large structures
– Output file names are customisable

Ligand building:
– Ligand validation using LigEnergy is added to all ligand-building
protocols

Webservice:
– Additional plots and a viewer are added

Other changes:
– Various bugs fixed in protein model building (both for MX and cryo-EM),
ligand building and webservice
– Example files have been updated


*CCP4i2: critical update*

The ccp4i2 interface will not work properly without update 70.

NB If you have already applied update 69 released last week and ccp4i2 does
not start, you will have to start CCP4 Update Manager from Terminal window
(see http://www.ccp4.ac.uk/updates/) or from ccp4i.


*Morda: update to v.28*

-

Tarballs and bundles for offline CCP4 Setup Manager consisting of
CCP4-7.0.070
and ARP/wARP 8.0 (patch 1) are available from CCP4 Downloads:
http://www.ccp4.ac.uk/download

Standalone version of ARP/wARP-8.0 can be downloaded from the ARP/wARP
homepage (www.arp-warp.org or www.embl-hamburg.de/ARP).

Please report any bugs to c...@stfc.ac.uk.

Many thanks for using CCP4 and ARP/wARP.

The CCP4 Core Team



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[ccp4bb] Fedora 29 breaks CCP4

[Andrey Lebedev]

Dear CCP4 users,

The recently released Fedora 29 breaks all the CCP4 graphical
components (interfaces and update manager).

This is because backward incompatibility of the fontconfig library and
possibly other libraries in Fedora 29.

The CCP4 core group working on this issue.

Meanwhile, please refrain from installing Fedora29 or upgrading
earlier Fedora version.

Regards,
Andrey



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[ccp4bb] ARP/wARP-8.0 + CCP4-7.0.065 joint release

[Andrey Lebedev]

Dear CCP4 Users

We would like to announce the joint release of ARP/wARP version 8.0
and CCP4-7.0.065.

ARP/wARP 8.0 provides a considerably improved performance for X-ray
crystallographic applications and it is now also capable of interpreting
cryo-EM maps at a resolution range 2.0-3.5 Å.

Installation and compatibility
-Checks for software installation have been enhanced
-32 and 64-bit platforms on OSX and Linux are supported
-ARP/wARP is fully compatible with the latest versions of CCP4 and Refmac

Protein chain tracing
-Protein chain tracing has been made faster and its memory handling
 has been improved
-DipCheck conformational space is introduced for the selection of
 the chain path
-NCS restraints are now default at resolution 1.5 Å or lower
-Loop closure can now be provided using a new module Loopy2018

Sequence docking and building
-Side chain guess and fit can now be accomplished using a new
 module SEQQY
-Handling of large structures has been enhanced and the maximum
 number of NCS copies increased to 60
-Both mono- and hetero-multimers can now be handled

DNA/RNA building
-Nucleotide chain tracing is enhanced with the addition of the
 second algorithm for phosphate detection
-Nucleotide chain tracing now proceeds in an iterative manner, as
 for protein tracing

Identification of crystallographic ligands
-Energy estimate for protein-ligand bound state is introduced
 during identification of crystallographic ligands

Solvent building
-Building of solvent structure exploits advanced features of Refmac
 including TLS and local NCS restraints.
-Solvent update can optionally be turned off providing a tool for
 model refinement with Refmac.

Building models into cryo-EM maps
-Protein and protein-nucleic acid models are built with a minimum user input
-Map over-sharpening is handled automatically
-Partial models can be completed by sequence-docking and loop building
-Models can be refined with a combined real- and reciprocal-space protocol
-A very fast secondary structure modelling option can be used separately.



An update No 65 for the CCP4-7.0 series automatically installs
ARP/wARP-8.0 on Mac OS X and Linux computers, where ARP/wARP-7.6 has
previously been installed as a part of CCP4 installation. (The
directory arp_warp_7.6 is _not_ removed , but CCP4 i1 and i2 are
switched to version 8.0). In addition, the update No 65 brings the
following changes.
* refmac5: correction to LINK records
* contact: increase MaxSelectedResidues
* dials: inclusion of mock module
* pointless: update to 1.11.6
* rabdam: update to 1.4.1
* crank2: fixes and improvements
* documentation: correction to freerflag documentation

In addition, tarballs and bundles for CCP4 Setup Manager consisting of
CCP4-7.0.065 and ARP/wARP 8.0 are available from CCP4 Downloads:
http://www.ccp4.ac.uk/download

Please report any bugs to c...@stfc.ac.uk.

Many thanks for using CCP4 and ARP/wARP.

The CCP4 Core Team



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[ccp4bb] Issues with update manager in ccp4 updates 52 and 53

[Andrey Lebedev]

Descriptions are now available online:
http://www.ccp4.ac.uk/updates/
If your update manager does not start, look at No 3 and 4 - they may
relate to your case.
Best wishes
Andrey

[ccp4bb] CCP4i2 on Windows: issue with update 52

[Andrey Lebedev]

Dear CCP4 Users,

The has been an issue with the CCP4 Update 52 released on 28 Feb 2018.

This will only affect I2-interface users on Windows with there CCP4
installation at version 7.0.052. (The version is shown at the very top
of the interface window). To apply new updates you will have to use
(only once) the old interface or to type "ccp4um" in CCP4-Console
window (the icon should be on your Desktop).

Apologies for any inconvenience caused and best wishes

Andrey

[ccp4bb] Issue with CCP4 update 053

[Andrey Lebedev]

Dear CCP4 users.

There has been an issue with the latest CCP4 Update 53, which affects
Mac OS X and Linux users if:
- the update was installed before Sunday 18th of March 22:30 GMT
- and CCP4 installation is password-protected.

Should these apply to you, the best way to deal with the faulty update
is as follows:

(1) Start  Update Manage from the command line using sudo or as root.

For example, If CCP4 environment is sourced, the following command will work

  sudo -E ccp4um

Otherwise you will have to specify full path to ccp4um. For example,
for most of Mac OS X users, the right command will be as follows

  sudo /Applications/ccp4-7.0/bin/ccp4um

(2) In the Update Manager window:

  "Next"; uncheck the check box next to 7.0.053; "Apply".

(3) After the above two steps your CCP4 installation will be back to
normal and you will be able to reapply update 53 and to apply all
subsequent updates in a usual way.

Apologies for any inconvenience caused and best wishes
Andrey

[ccp4bb] ccp4-7.0 for windows

[Andrey Lebedev]

Dear CCP4 users

A new ccp4-7.0 installer for Windows is now available:
http://www.ccp4.ac.uk/download/index.php#os=windows
- consolidates updates 1-50
- includes Coot and SHELX as optional components (do not forget to
register at SHELX web site).

Best wishes
Andrey

Re: [ccp4bb] CCP4 series 7.0 update 045

[Andrey Lebedev]

Dear CCP4 users

There were two mistakes in my previous e-mail announcing the update 7.0.045:
- an incorrect list of platforms for which the new version of shelxe
is provided and
- an out-of-date reference to SHELX web-site.

The correct statement is as follows:

shelxe (Mac OS X, Linux 64 bits, Windows 32 and 64 bits)
• update to 2017_1
• improved chain tracing at lower than 2A resolution
• further details at http://shelx.uni-goettingen.de/changes.php

Best wishes
Andrey

On 4 October 2017 at 22:16, Andrey Lebedev <andrey.lebe...@stfc.ac.uk> wrote:
> Dear All
>
>
> updates 045 has been release.  This contains
>
>
> shelxe (Mac, Linux 64 bit)
> • update to 2017_1
> • improved chain tracing at lower than 2A resolution
> • further details at http://shelx.uni-ac.gwdg.de/SHELX/changes.php
>
> coot (Mac, Linux)
> • correctsions to some typos
>
> molrep
> • fix for bug in map read
>
> sfcheck
> • removed bug in reading ccp4 map
>
> pointless
> • 1.11.4 increase number of images from Scalepack file
>
> lorestr
> • fixed CCP4i2 compatibility issue with -p2 file names
>
> ctruncate
> • bug fixes, protect 0 value diagonal elements in hessian
>
> hklfile
> • bug fixes
>
> acedrg
> • bug fixes
>
> ccp4i2
> • new nautilus interface
> • lorestr: fixed difference map import
> • crank2: fixes for specific space groups
> • arpwarp: added output xyz with dummy atoms removed
> • added task interface for morda-mp
>
> ccp4i
> • jsrview set as the default viewer for crank2
> • fixed termination of subprocesses
>
> morda-mp (Mac, Linux)
> • released python wrapper and i1 interface
>
> crank2
> • disabling ccp4i jsrview pop-up
> • prasa fine-tuning
> • fixes for specific space groups
> • fixed flip-mem variant of charge flipping
>
>
> All the best
>
> CCP4 Core team

[ccp4bb] CCP4 series 7.0 update 045

[Andrey Lebedev]

Dear All


updates 045 has been release.  This contains


shelxe (Mac, Linux 64 bit)
• update to 2017_1
• improved chain tracing at lower than 2A resolution
• further details at http://shelx.uni-ac.gwdg.de/SHELX/changes.php

coot (Mac, Linux)
• correctsions to some typos

molrep
• fix for bug in map read

sfcheck
• removed bug in reading ccp4 map

pointless
• 1.11.4 increase number of images from Scalepack file

lorestr
• fixed CCP4i2 compatibility issue with -p2 file names

ctruncate
• bug fixes, protect 0 value diagonal elements in hessian

hklfile
• bug fixes

acedrg
• bug fixes

ccp4i2
• new nautilus interface
• lorestr: fixed difference map import
• crank2: fixes for specific space groups
• arpwarp: added output xyz with dummy atoms removed
• added task interface for morda-mp

ccp4i
• jsrview set as the default viewer for crank2
• fixed termination of subprocesses

morda-mp (Mac, Linux)
• released python wrapper and i1 interface

crank2
• disabling ccp4i jsrview pop-up
• prasa fine-tuning
• fixes for specific space groups
• fixed flip-mem variant of charge flipping


All the best

CCP4 Core team

[ccp4bb] ccp4 7.0 update 044

[Andrey Lebedev]

Dear All,

update 044 is out. It contains the following changes

* arcimboldo
- lite: added coiled coil mode

* ccp4i
- fixed switching between hklin files with F and I

* ccp4-progs
- pdbcur: excluded insertion of TER into non-polymer chains

* crank2
- fixed enantiomorphic space group issue

* libg
- semi-automated search modes added

* lorestr
- CCP4i2 compatibility added

* mmdb2
- changes for pdbcur TER fix

* molrep
- SAPTF improvement

All the best

CCP4 core team

[ccp4bb] Morda updates moved

[Andrey Lebedev]

Dear All

Morda update bundles have been moved to a new location on October 5 2016. To 
continue using updates for Morda installed on or before that data, please 
replace the script MoRDa_DB/update_morda with its new version from here 
 and change permissions to 
executable. You will have to rename update_morda.txt to update_morda if you 
browser adds extension .txt to downloaded text file.

Download links as well as update and installation instructions are available 
from MoRDa homepage .

Alexey and Andrey

Re: [ccp4bb] distorted NRQ in JLigand 1.0.40

[Andrey Lebedev]

Dear Kevin

The bug in refmac which was causing this is fixed in ccp4-6.5.010.
So please apply the two last updates and try again. Does it work normally now?

Best regards
Andrey


On 26 May 2015, at 18:36, Kevin Jude wrote:

 Dear colleagues,
 I'm having an issue with a particular ligand in JLigand 1.0.40.  When I load 
 NRQ, the topology is correct but the bond lengths and angles are highly 
 distorted, making it uninterpretable to my eye.  A screenshot is viewable at 
 https://www.dropbox.com/s/44nmmc96899o3uo/NRQ.tiff?dl=0.
 
 If I make some edit to the molecule and then regularize it, everything looks 
 fine.  I have not found another ligand with similar behavior.  In an older 
 version (1.0.37), this does not happen.
 
 On the machine with JLigand 1.0.40 (aberrant behavior), I have:
 CCP4 software suite: library version 6.5.008
 CCP4 software suite: patch level 6.5.008
 Program: refmac5; version 5.8.0107
   --- LIBCHECK --- /Vers 5.2.02  ; 02.12.2014/
 dictionary version 5.44
 
 On the machine with JLigand 1.0.37 (normal behavior), I have:
 CCP4 software suite: library version 6.5.008
 CCP4 software suite: patch level 6.5.008
 Program: refmac5; version 5.8.0107
   --- LIBCHECK --- /Vers 5.2.00  ; 12.12.2011/
 dictionary version 5.44
 
 Best wishes
 Kevin Jude

[ccp4bb] CCP4-6.5 Update 001

[Andrey Lebedev]

Dear CCP4 Users

 
An update for the CCP4-6.5 series has just been released, consisting
of the following changes
 
• acedrg (linux and mac):
  – added ccp4i task interface
  – further improvements
 
• ample (linux and mac):
  – fixed executable path
 
• ccp4-base (linux and mac):
  – fixed setup script to unset unnecessary system variables
 
• ccp4-progs (all)
  – in pdbcur, added options to remove chain or TER record
 
• crank2 (all)
  – fixed interaction with pdbcur
 
• privateer (all)
  – minor changes for i2
 
• libccp4 (all)
  – fixed ccp4 versioning, which, in particular, affected privateer
 
• xia2 (linux and mac):
  – fixed -3d option
 
• documentation (all)
  – updated for pdbcur and privateer
 
 
Please report any bugs to c...@stfc.ac.uk.
 
Many thanks for using CCP4.

The CCP4 Core Team

Re: [ccp4bb] Latest BALBES database

[Andrey Lebedev]

Dear Michael

Indeed the Balbes database is three year old and there is no newer version 
elsewhere.
However, there is a good chance that updates will be resumed this year.

Regards
Andrey


On 9 Sep 2014, at 16:26, Michael Weyand wrote:

 Dear all,
 
 may be my google-ing capabilites are to bad, but I can not find an
 update of the Balbes model database.
 The latest tar-file from the homepage is dated 12/2011, which is more or
 less the same to the CCP4 download.
 Is there any expert who is able to guide me to a more actual version?
 Not to say that I will then be able to solve the present MR problem, but ...
 
 Thanks in advance!
 
 Regards,
 Michael


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[ccp4bb] CCP4-6.4.0 Update 020

[Andrey Lebedev]

Dear CCP4 Users

An update for the CCP4-6.4.0 series has just been released, consisting
of the following changes

• crank:
  – bug fix in bp3
  – update to overcome OMP problem

• ctruncate:
  – update to 1.15.9

• aimless:
  – update to 0.3.7

• pointless:
  – update to 1.9.11
  – fix for inconsistency in number of reflections read from XDS_ASCII.hkl wrt 
XSCALE

• blend:
  – update to 0.5.3

• ample:
  – update to accommodate new MrBUMP
  – fix for results table
  – new interface options

• mrbump:
  – minor fix to the fasta search option

Note that auto-updates work only with CCP4 6.4.0 series, therefore
please upgrade if necessary.  The Update Manager is now included in the
package so you do not need to install it separately.  In addition, all
available updates will be installed automatically if you are using Setup
Manager for CCP4 installation.

Please report any bugs to c...@stfc.ac.ukmailto:c...@stfc.ac.uk.

Many thanks for using CCP4.

The CCP4 Core Team



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[ccp4bb] CCP4-6.4.0 Update 018

[Andrey Lebedev]

Dear CCP4 Users

An update for the CCP4-6.4.0 series has just been released, consisting
of the following changes

• refmac5 (all platforms):
  – Fixed restraints for M- and P-peptides
  – Fixed SAD scaling issue

• monomers (all):
  – Fixed description for M- and P-peptides and some other entries

• pointless (all):
  – Update to 1.9.10 fixing a long-standing bug in reindexing files with 
different (permuted) unit cells

• aimless (all):
  – Fix to explicit run definitioin

Note that auto-updates work only with CCP4 6.4.0 series, therefore
please upgrade if necessary.  The Update Manager is now included in the
package so you do not need to install it separately.  In addition, all
available updates will be installed automatically if you are using Setup
Manager for CCP4 installation.

Please report any bugs to c...@stfc.ac.ukmailto:c...@stfc.ac.uk.

Many thanks for using CCP4.

The CCP4 Core Team



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[ccp4bb] CCP4-6.4.0 Update 017

[Andrey Lebedev]

Dear CCP4 users,

An update for the CCP4-6.4.0 series has just been released, consisting
of the following changes:

* Phaser (all platforms): Bug fixes for version 2.5.6
* Ensembler (windows): Fixed mmdb binding

Note that auto-updates work only with CCP4 6.4.0 series, therefore
please upgrade if necessary. The Update Manager is now included in the
package so you do not need to install it separately. In addition, all
available updates will be installed automatically if you are using
Setup Manager for CCP4 installation.

Please report any bugs to c...@stfc.ac.ukmailto:c...@stfc.ac.uk.

Many thanks for using CCP4.

The CCP4 Core Team




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Re: [ccp4bb] CCP4-6.4.0 Update 010

[Andrey Lebedev]

Hi Boaz

It is 5.8.0069

And it prints the correct version for me on all platforms

Andrey

On 7 Mar 2014, at 13:13, Boaz Shaanan wrote:

Hi,

Is the refmac5  indeed 5.8.006? The current ccp4 version 5.8.0049.

 Boaz



Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bshaa...@bgu.ac.ilmailto:bshaa...@bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710





From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Charles Ballard 
[charles.ball...@stfc.ac.uk]
Sent: Friday, March 07, 2014 1:10 PM
To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] CCP4-6.4.0 Update 010

Dear CCP4 Users,

An update for the CCP4-6.4.0 series has just been released, consisting of the 
following changes

◆ ARP/wARP (Mac, Linux)
1. Fix in the use of free R flag in the ARP/wARP CCP4i interface for solvent 
building
2. Fix in the identification of non-crystallographic symmetry that in some 
cases led to zero target number of residues
3. Fix in recognition of secondary structural elements that in rare cases led 
to a 'bus error'
* Many thanks to Marcin Cymborowski, Carmelo Giacovazzo, Ulrich Gohlke and Vito 
Calderone for reporting these problem cases.

◆ imosflm (update to 7.1.0 for all platforms)
- Multi-lattice implementation
- Parallel processing of wedges

◆ feckless (0.0.2, all)
- Fixes several major bugs

◆ pointless (1.9.2, all)
- General update for multi-lattice

◆ ctruncate (1.13.13, all)
- Fixes negative eigenvalue exit during anisotropy analysis

◆ cnautilus (0.4, all)
- Some basic output markup and numbering of output sequences

◆ refmac5 (5.8.006, all)
- Fixes for ARP/wARP and forthcoming release of Crank2

Note that auto-updates work only with CCP4 6.4.0 series, therefore please 
upgrade if necessary.
The Update Manager is now included in the package so you do not need to install 
it separately.
In addition, all available updates will be installed automatically if you are 
using Setup Manager for CCP4 installation.

Please report any bugs to c...@stfc.ac.ukmailto:c...@stfc.ac.uk.

Many thanks for using CCP4.

the CCP4 core team.


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[ccp4bb] CCP4-6.4.0 Update 007

[Andrey Lebedev]

Dear CCP4 Users,

An update for the CCP4-6.4.0 series has just been released, consisting of the 
following changes:

  *   pointless
 *   fixed crash when using reference data with no alternative indexing
 *   with multiple files, include columns present in any file
 *   added crash message for running out of memory
 *   fixed bug in XML graphs for ccp4i2
 *   fixed (rare) crash if there are only 2 axial reflections
  *   aimless
 *   fixed NBINS option for multiple dataset
 *   added crash message for running out of memory
 *   fixed bug in XML graphs for ccp4i2
  *   ctruncate
 *   defensive codes added to estimation of twin fraction from L-test and 
Murray-Rust plot
 *   corrected typos
  *   molrep
 *   relaxed restrictions due to cell dimensions on integration radius in 
SRF
 *   corrected beta range for LRF from 90 to 180
 *   all occupancies in xyzout are now set to 1
 *   extinct harmonic coefficients set to zero in RF
  *   ccp4i
 *   molrep: corrected nmon and added np2, nml and score widgets
 *   crunch2 and bp3: corrections for new file layout

Note that auto-updates work only with CCP4 6.4.0 series, therefore please 
upgrade if necessary.
The Update Manager is now included in the package so you do not need to install 
it separately.
In addition, all available updates will be installed automatically if you are 
using Setup Manager for CCP4 installation.

Please report any bugs to c...@stfc.ac.ukmailto:c...@stfc.ac.uk.

Many thanks for using CCP4.

Andrey


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[ccp4bb] CCP4-6.4.0 Update 006

[Andrey Lebedev]

Dear CCP4 Users,

An update for the CCP4-6.4.0 series has just been released, consisting of the 
following changes:

  *   freerflag (all platforms)
 *   added option of assigning identical Free-R flag to twin-related 
reflections
  *   QtRView (Windows)
 *   fixed report page for Phaser
  *   MrBUMP (all)
 *   fix for SCOP search results error when chain is removed for zero length
 *   added option to disable ctruncate step
 *   fixed a minor bug in the ctruncate step
  *   ViewHKL (all)
 *   bring unmerged code in line with current Pointless and Aimless
 *   print phases in degrees not radians
 *   return filetype for non-MTZ files (for ccp4i2)
 *   cope with inverted column order in mtz-file
  *   ctruncate (all)
 *   fixed missing program name in output
  *   ccp4-core (Mac, Linux)
 *   added missing legacy program xplot84driver
  *   Examples (all)
 *   corrected data files toxd_old.mtz and aucn.sca
 *   technical changes to run-all script and regression tests
  *   ccp4-progs
 *   (all) minor fixes in domain2chain and vectors for strict compilers
 *   (Mac, Linux) minor fixes in sapi for strict compilers
 *   (all) technical changes to ccp4-python, imosflm and zanuda scripts
  *   GUI-2 (all)
 *   technical update adding cmtzjoin and cmtzsplit programs for ccp4i2

Note that auto-updates work only with CCP4 6.4.0 series, therefore please 
upgrade if necessary.
The Update Manager is now included in the package so you do not need to install 
it separately.
In addition, all available updates will be installed automatically if you are 
using Setup Manager for CCP4 installation.

Please report any bugs to c...@stfc.ac.ukmailto:c...@stfc.ac.uk.

Many thanks for using CCP4.

Andrey


-- 
Scanned by iCritical.

[ccp4bb] Joint CCP4-6.4.0 and ARP/wARP-7.4 Update

[Andrey Lebedev]

Dear CCP4 users

Two new updates for the CCP4 6.4.0 series have just been released.

NB. If  your CCP4 installation was damaged by previously released update No 2, 
please read NOTES at the end of this e-mail.

Update 6.4.0-003:
This is a technical update to repair the update mechanism. You will be prompted 
to restart CCP4I after its installation. Please do it!

Update 6.4.0-004:
This is a joint CCP4 and ARP/wARP update.

The following changes will be applied to the ARP/wARP installation:

• The use of non-crystallographic symmetry for protein chain tracing has been 
enabled (it was accidentally disabled in version 7.4).
• The `SAD refinement protocol' (Murshudov et al 2011) has undergone many fixes 
and now works well.
• The routine for ligand identification has been made faster and some small 
bugs have been fixed.
• A few bugs have been fixed in the ARP/wARP installer and shell-specific 
problems sometimes occurring on Linux should now be cured.
• The manual has been updated.

The following changes will be applied to the CCP4-6.4.0 installation:

• Update (all platforms): Bug fixes; increased maximum waiting time for 
background check in CCP4I
• Molrep (all platforms): New interface.
• MrBUMP (all): a new option of model re-building after SHELXE; a fix for 
phaser_sculptor dispatcher; improved option of running jobs on a cluster
• Xia2 (windows): update to release 0.3.6.3 (fixes ctruncate issue).
• Aimless (all): bug fixes.
• Pointless (all): bug fixes.
• ViewHKL (all): additional visual control to enhance weak reflections; bug 
fixes.
• QtRview: Now finds Coot executable automatically (mac); bug fixes
• Ctruncate: Bug fixes
• CCP4I: Fixed path to mmcif library enabling e.g. harvesting option of old 
truncate (mac); fixed task interfaces for bp3 and crunch2 (all); now can be 
installed and used on network drive (windows)


CCP4 Core Group apologises for the temporary disruption to the update system 
and thanks you for your patience.

Many thanks for using CCP4,

Andrey Lebedev


NOTES

If the update 6.4.0-002 has damaged your system and you can’t get ccp4i to 
work, please start ccp4um in manual mode:

[sudo] /path/to/ccp4-6.4.0/bin/ccp4um

and update your setup to 6.4.0-003. After that, re-start ccp4um manually again 
and install update 6.4.0-004, after which your system will be fully repaired.





-- 
Scanned by iCritical.

[ccp4bb] Joint CCP4-6.4.0 and ARP/wARP-7.4 Update

[Andrey Lebedev]

Dear CCP4 Users

An update for the CCP4-6.4.0 series has just been released. This is the first 
update for both CCP4 and ARP/wARP in tandem.

The ARP/wARP component of this update will be available to those Mac and Linux 
users who have previously installed both packages via the CCP4 Package manager 
or from the joint bundle downloaded from CCP4 web-site. A standalone ARP/wARP 
package including the current update can be downloaded from the EMBL-Hamburg 
site at www.arp-warp.orghttp://www.arp-warp.org/.

The following changes will be applied to the ARP/wARP installation:

• The use of non-crystallographic symmetry for protein chain tracing has been 
enabled (it was accidentally disabled in version 7.4).
• The `SAD refinement protocol' (Murshudov et al 2011) has undergone many fixes 
and now works well.
• The routine for ligand identification has been made faster and some small 
bugs have been fixed.
• A few bugs have been fixed in the ARP/wARP installer and shell-specific 
problems sometimes occurring on Linux should now be cured.
• The manual has been updated.

The following changes will be applied to the CCP4-6.4.0 installation:

• MrBUMP (all): a new option of model re-building after SHELXE; a fix for 
phaser_sculptor dispatcher.
• Xia2 (windows): update to release 0.3.6.3 (fixes ctruncate issue).
• aimless (all): bug fixes.
• pointless (all): bug fixes.
• ViewHKL (all): additional visual control to enhance weak reflections and bug 
fixes.
• truncate (Mac): Fixed harvesting option of old truncate.
• Molrep: New interface.
• Update (all): Increased maximum waiting time for background update check in 
ccp4i.

Andrey Lebedev


-- 
Scanned by iCritical.

Re: [ccp4bb] Joint CCP4-6.4.0 and ARP/wARP-7.4 Update

[Andrey Lebedev]

Hi Joachim

Thanks for reporting the problem

Please run 
sudo /software/ccp4-6.4.0/bin/ccp4um
and uninstall the last update for now.
There should be something wrong with your config files.
I'll trace what it could be and then contact you.

Regards

Andrey


On 6 Nov 2013, at 13:13, Joachim Reichelt wrote:

 Hi,
 
 I just installed the update using ccp4um.
 All I get now is:
 
 ccp4i
 Def file /software/ccp4-6.4.0/share/ccp4i/etc/unix/configure.def
 does not have correct file label configure
 Def file /software/ccp4-6.4.0/share/ccp4i/etc/preferences.def.dist
 does not have correct file label preferences
 Error in startup script: can't read array(MAPVIEWER_DEFAULT): no such 
 element in array
while executing
 set viewercmd $array(MAPVIEWER_DEFAULT)
(procedure set_default_mapviewer line 9)
invoked from within
 set_default_mapviewer $arrayname
(preferences arm line 2)
invoked from within
 switch -- $taskname {
directories {
  catch {update_defdir_menu $arrayname}
} configure {
  # We over-write the user TYPEDEF_LIST with...
(procedure InitialisePreferences line 113)
invoked from within
 InitialisePreferences preferences preferences
(file /software/ccp4-6.4.0/share/ccp4i/bin/ccp4i.tcl line 128)
invoked from within
 source [file join $env(CCP4I_TOP) bin ccp4i.tcl]
(file /software/ccp4-6.4.0/bin/ccp4i line 12)
 
 
 What went wrong?
 
 Am 06.11.2013 um 13:52 schrieb Andrey Lebedev andrey.lebe...@stfc.ac.uk:
 
 Dear CCP4 Users
 
 An update for the CCP4-6.4.0 series has just been released. This is the 
 first update for both CCP4 and ARP/wARP in tandem.
 
 The ARP/wARP component of this update will be available to those Mac and 
 Linux users who have previously installed both packages via the CCP4 Package 
 manager or from the joint bundle downloaded from CCP4 web-site. A standalone 
 ARP/wARP package including the current update can be downloaded from the 
 EMBL-Hamburg site at www.arp-warp.orghttp://www.arp-warp.org/.
 
 The following changes will be applied to the ARP/wARP installation:
 
 • The use of non-crystallographic symmetry for protein chain tracing has 
 been enabled (it was accidentally disabled in version 7.4).
 • The `SAD refinement protocol' (Murshudov et al 2011) has undergone many 
 fixes and now works well.
 • The routine for ligand identification has been made faster and some small 
 bugs have been fixed.
 • A few bugs have been fixed in the ARP/wARP installer and shell-specific 
 problems sometimes occurring on Linux should now be cured.
 • The manual has been updated.
 
 The following changes will be applied to the CCP4-6.4.0 installation:
 
 • MrBUMP (all): a new option of model re-building after SHELXE; a fix for 
 phaser_sculptor dispatcher.
 • Xia2 (windows): update to release 0.3.6.3 (fixes ctruncate issue).
 • aimless (all): bug fixes.
 • pointless (all): bug fixes.
 • ViewHKL (all): additional visual control to enhance weak reflections and 
 bug fixes.
 • truncate (Mac): Fixed harvesting option of old truncate.
 • Molrep: New interface.
 • Update (all): Increased maximum waiting time for background update check 
 in ccp4i.
 
 Andrey Lebedev
 
 
 --
 Scanned by iCritical.
 
 
 Mit freundlichen Grüßen
 
 Joachim Reichelt
 
 
 
 
 
 
 
 
 
 Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 
 Braunschweig | www.helmholtz-hzi.de
 Das HZI ist seit 2007 zertifiziertes Mitglied im audit berufundfamilie
 
 Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, 
 Bundesministerium für Bildung und Forschung
 Stellvertreter: Rüdiger Eichel, Abteilungsleiter Niedersächsisches 
 Ministerium für Wissenschaft und Kultur
 Geschäftsführung: Prof. Dr. Dirk Heinz; Dr. Michael Strätz
 Gesellschaft mit beschränkter Haftung (GmbH)
 Sitz der Gesellschaft: Braunschweig
 Handelsregister: Amtsgericht Braunschweig, HRB 477


-- 
Scanned by iCritical.

Re: [ccp4bb] Joint CCP4-6.4.0 and ARP/wARP-7.4 Update

[Andrey Lebedev]

Dear all

If you had a problem similar to that Joachim and Ingo had (see below), please 
run
sudo path/ccp4-6.4.0/bin/ccp4um
where path is the full path to your ccp4-6.4.0 installation,
and uninstall the last update.

Then you can launch ccp4i and install it again as usual.

Thanks!

Andrey

On 6 Nov 2013, at 13:13, Joachim Reichelt wrote:

 Hi,
 
 I just installed the update using ccp4um.
 All I get now is:
 
 ccp4i
 Def file /software/ccp4-6.4.0/share/ccp4i/etc/unix/configure.def
 does not have correct file label configure
 Def file /software/ccp4-6.4.0/share/ccp4i/etc/preferences.def.dist
 does not have correct file label preferences
 Error in startup script: can't read array(MAPVIEWER_DEFAULT): no such 
 element in array
while executing
 set viewercmd $array(MAPVIEWER_DEFAULT)
(procedure set_default_mapviewer line 9)
invoked from within
 set_default_mapviewer $arrayname
(preferences arm line 2)
invoked from within
 switch -- $taskname {
directories {
  catch {update_defdir_menu $arrayname}
} configure {
  # We over-write the user TYPEDEF_LIST with...
(procedure InitialisePreferences line 113)
invoked from within
 InitialisePreferences preferences preferences
(file /software/ccp4-6.4.0/share/ccp4i/bin/ccp4i.tcl line 128)
invoked from within
 source [file join $env(CCP4I_TOP) bin ccp4i.tcl]
(file /software/ccp4-6.4.0/bin/ccp4i line 12)
 
 
 What went wrong?
 
 Am 06.11.2013 um 13:52 schrieb Andrey Lebedev andrey.lebe...@stfc.ac.uk:
 
 Dear CCP4 Users
 
 An update for the CCP4-6.4.0 series has just been released. This is the 
 first update for both CCP4 and ARP/wARP in tandem.
 
 The ARP/wARP component of this update will be available to those Mac and 
 Linux users who have previously installed both packages via the CCP4 Package 
 manager or from the joint bundle downloaded from CCP4 web-site. A standalone 
 ARP/wARP package including the current update can be downloaded from the 
 EMBL-Hamburg site at www.arp-warp.orghttp://www.arp-warp.org/.
 
 The following changes will be applied to the ARP/wARP installation:
 
 • The use of non-crystallographic symmetry for protein chain tracing has 
 been enabled (it was accidentally disabled in version 7.4).
 • The `SAD refinement protocol' (Murshudov et al 2011) has undergone many 
 fixes and now works well.
 • The routine for ligand identification has been made faster and some small 
 bugs have been fixed.
 • A few bugs have been fixed in the ARP/wARP installer and shell-specific 
 problems sometimes occurring on Linux should now be cured.
 • The manual has been updated.
 
 The following changes will be applied to the CCP4-6.4.0 installation:
 
 • MrBUMP (all): a new option of model re-building after SHELXE; a fix for 
 phaser_sculptor dispatcher.
 • Xia2 (windows): update to release 0.3.6.3 (fixes ctruncate issue).
 • aimless (all): bug fixes.
 • pointless (all): bug fixes.
 • ViewHKL (all): additional visual control to enhance weak reflections and 
 bug fixes.
 • truncate (Mac): Fixed harvesting option of old truncate.
 • Molrep: New interface.
 • Update (all): Increased maximum waiting time for background update check 
 in ccp4i.
 
 Andrey Lebedev
 
 
 --
 Scanned by iCritical.
 
 
 Mit freundlichen Grüßen
 
 Joachim Reichelt
 
 
 
 
 
 
 
 
 
 Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 
 Braunschweig | www.helmholtz-hzi.de
 Das HZI ist seit 2007 zertifiziertes Mitglied im audit berufundfamilie
 
 Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, 
 Bundesministerium für Bildung und Forschung
 Stellvertreter: Rüdiger Eichel, Abteilungsleiter Niedersächsisches 
 Ministerium für Wissenschaft und Kultur
 Geschäftsführung: Prof. Dr. Dirk Heinz; Dr. Michael Strätz
 Gesellschaft mit beschränkter Haftung (GmbH)
 Sitz der Gesellschaft: Braunschweig
 Handelsregister: Amtsgericht Braunschweig, HRB 477


-- 
Scanned by iCritical.

Re: [ccp4bb] Joint CCP4-6.4.0 and ARP/wARP-7.4 Update

[Andrey Lebedev]

Dear all

A comment to my last e-mail

If your ccp4 installation is not write-protected,
do not use sudo, just run
ccp4um

Regards

Andrey

On 6 Nov 2013, at 14:49, Lebedev, Andrey (STFC,RAL,SC) wrote:

 
 Dear all
 
 If you had a problem similar to that Joachim and Ingo had (see below), please 
 run
 sudo path/ccp4-6.4.0/bin/ccp4um
 where path is the full path to your ccp4-6.4.0 installation,
 and uninstall the last update.
 
 Then you can launch ccp4i and install it again as usual.
 
 Thanks!
 
 Andrey
 
 On 6 Nov 2013, at 13:13, Joachim Reichelt wrote:
 
 Hi,
 
 I just installed the update using ccp4um.
 All I get now is:
 
 ccp4i
 Def file /software/ccp4-6.4.0/share/ccp4i/etc/unix/configure.def
 does not have correct file label configure
 Def file /software/ccp4-6.4.0/share/ccp4i/etc/preferences.def.dist
 does not have correct file label preferences
 Error in startup script: can't read array(MAPVIEWER_DEFAULT): no such 
 element in array
   while executing
 set viewercmd $array(MAPVIEWER_DEFAULT)
   (procedure set_default_mapviewer line 9)
   invoked from within
 set_default_mapviewer $arrayname
   (preferences arm line 2)
   invoked from within
 switch -- $taskname {
   directories {
 catch {update_defdir_menu $arrayname}
   } configure {
 # We over-write the user TYPEDEF_LIST with...
   (procedure InitialisePreferences line 113)
   invoked from within
 InitialisePreferences preferences preferences
   (file /software/ccp4-6.4.0/share/ccp4i/bin/ccp4i.tcl line 128)
   invoked from within
 source [file join $env(CCP4I_TOP) bin ccp4i.tcl]
   (file /software/ccp4-6.4.0/bin/ccp4i line 12)
 
 
 What went wrong?
 
 Am 06.11.2013 um 13:52 schrieb Andrey Lebedev andrey.lebe...@stfc.ac.uk:
 
 Dear CCP4 Users
 
 An update for the CCP4-6.4.0 series has just been released. This is the 
 first update for both CCP4 and ARP/wARP in tandem.
 
 The ARP/wARP component of this update will be available to those Mac and 
 Linux users who have previously installed both packages via the CCP4 
 Package manager or from the joint bundle downloaded from CCP4 web-site. A 
 standalone ARP/wARP package including the current update can be downloaded 
 from the EMBL-Hamburg site at www.arp-warp.orghttp://www.arp-warp.org/.
 
 The following changes will be applied to the ARP/wARP installation:
 
 • The use of non-crystallographic symmetry for protein chain tracing has 
 been enabled (it was accidentally disabled in version 7.4).
 • The `SAD refinement protocol' (Murshudov et al 2011) has undergone many 
 fixes and now works well.
 • The routine for ligand identification has been made faster and some small 
 bugs have been fixed.
 • A few bugs have been fixed in the ARP/wARP installer and shell-specific 
 problems sometimes occurring on Linux should now be cured.
 • The manual has been updated.
 
 The following changes will be applied to the CCP4-6.4.0 installation:
 
 • MrBUMP (all): a new option of model re-building after SHELXE; a fix for 
 phaser_sculptor dispatcher.
 • Xia2 (windows): update to release 0.3.6.3 (fixes ctruncate issue).
 • aimless (all): bug fixes.
 • pointless (all): bug fixes.
 • ViewHKL (all): additional visual control to enhance weak reflections and 
 bug fixes.
 • truncate (Mac): Fixed harvesting option of old truncate.
 • Molrep: New interface.
 • Update (all): Increased maximum waiting time for background update check 
 in ccp4i.
 
 Andrey Lebedev
 
 
 --
 Scanned by iCritical.
 
 
 Mit freundlichen Grüßen
 
 Joachim Reichelt
 
 
 
 
 
 
 
 
 
 Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 
 Braunschweig | www.helmholtz-hzi.de
 Das HZI ist seit 2007 zertifiziertes Mitglied im audit berufundfamilie
 
 Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, 
 Bundesministerium für Bildung und Forschung
 Stellvertreter: Rüdiger Eichel, Abteilungsleiter Niedersächsisches 
 Ministerium für Wissenschaft und Kultur
 Geschäftsführung: Prof. Dr. Dirk Heinz; Dr. Michael Strätz
 Gesellschaft mit beschränkter Haftung (GmbH)
 Sitz der Gesellschaft: Braunschweig
 Handelsregister: Amtsgericht Braunschweig, HRB 477
 


-- 
Scanned by iCritical.

[ccp4bb] CCP4-6.4.0 Update 001

[Andrey Lebedev]

Dear CCP4 Users,

An update for the new CCP4-6.4.0 series has just been released, consisting of 
the following changes:

• Qt libraries (Mac, Linux): critical fixes for some Mac OSX setups and for KDE 
desktops
• TclTk libraries (Linux): recompiled to be made functional on CentOS4
• TclTk libraries (Windows): fixes that make fresh ccp4 installation work 
without rebooting
• Coot (Mac): fixed keyboard shortcuts
• Coot (Linux): now runs from command lines without sourcing ccp4
• MrBUMP (all): fixed MAFFT option
• AMPLE (Mac, Linux): added subtask for membrane proteins; bug fixes for Mac
• Xia2 (Mac, Linux): update to Xia2 release 0.3.6.3 (fixes ctruncate issue)
• QtRView (all): fixes that allow display of large summaries, e.g. from aimless
• iMosflm (Linux): fixed critical issue on 32 bit Linuxes

Note that auto-updates work only with CCP4 6.4.0 series, therefore upgrade if 
necessary. 
Update Manager is now included in the package so you do not need to install it 
separately.
In addition, all available updates will be installed automatically if you are 
using Setup Manager for CCP4 installation.

Please report any bugs to c...@stfc.ac.uk

Many thanks for using CCP4

Andrey Lebedev


-- 
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Re: [ccp4bb] mtz for zanuda - which symmetry?

[Andrey Lebedev]

Input pdb and mtz should form a valid input for refmac, hence the same cell and 
sym and merged mtz.

On 26 Apr 2013, at 09:17, Frank von Delft frank.vonde...@sgc.ox.ac.uk wrote:

 Hi -
 
 For Zanuda, the mtz input it wants:  what spacegroup are the data meant to be 
 merged to?  The highest possible, potentially twinned? Or the lowest possible?
 
 I've looked reasonably hard (10min on the manuals and The Google), and the 
 answer did not leap out at me at all.  Even though it seems a rather crucial 
 question - or is it not, in which case, why not, what am I missing?
 
 phx
--
Scanned by iCritical.

[ccp4bb] CCP4 Update 021

[Andrey Lebedev]

Dear CCP4 Users

A CCP4 update has just been released, consisting of the following changes.

* QtRView: corrected Prosmart result page; enabled incorporation of web-links 
into citation section

If you do not currently receive updates, consider re-installing your
CCP4 setup using the latest binary packages, which now have the CCP4 Update 
Manager (ccp4um) integrated.

Note that auto-updates will work correctly only with CCP4 release 6.3.0, 
therefore upgrade if necessary. Please report any bugs to 
c...@stfc.ac.ukmailto:c...@stfc.ac.uk

Many thanks for using CCP4

Andrey Lebedev


-- 
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Re: [ccp4bb] CCP4 Update 019

[Andrey Lebedev]

Dear CCP4 Users

A CCP4 update has just been released, consisting of the following changes.

* Update Manager (ccp4um), QtRView: Technical update in preparation for the 
next release
* Gesamt, Superpose: Corrections to the previous update (Now print 
superposition matrices also in fractional coordinates);
   better presentation in QtRView result viewer
* Refmac, ProSmart: Results of superposition analysis and external restraints 
are now accessible through QtRView report

If you do not currently receive updates, consider re-installing your
CCP4 setup using the latest binary packages, which now have the CCP4 Update 
Manager (ccp4um) integrated.

Note that auto-updates will work correctly only with CCP4 release 6.3.0, 
therefore upgrade if necessary. Please report any bugs to 
c...@stfc.ac.ukmailto:c...@stfc.ac.uk

Many thanks for using CCP4

Andrey Lebedev




-- 
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Re: [ccp4bb] qtrview command line options

[Andrey Lebedev]

After ccp4 update No 19, Log–files can be opened with qtrview from the command 
line:

logview name.log

This also works for log-files generated with quick scale and quick symmetry 
from imosflm.

If ccp4 database entries do not exist, input and output files will not be shown 
in the viewer
(except for quick scale and quick symmetry files).

Regards

Andrey



On 11 Mar 2013, at 20:06, Lebedev, Andrey (STFC,RAL,SC) wrote:

 
 Hi Ed
 
 Thank you for the suggestion.
 We are looking into this and hopefully will provide a solution soon.
 
 Regards
 
 Andrey
 
 
 On 11 Mar 2013, at 14:26, Ed Pozharski wrote:
 
 Is there some way of opening a log file (specifically, the
 pointandscale.log that imosflm bridge to scala generates) with qtrview
 from command line?
 
 I tried, of course, this
 
 qtrview pointandscale.log
 
 but it opens empty, no log-file. I tried qtrview -h and qtrview --help
 and man qtrview but there is seemingly no documentation.
 
 I found the source code (yes, I can google) and can deduce that
 available options at startup are 
 
 --log-file
 --report-xml
 --report-xrt
 --inp-file
 
 The only thing that works is 
 
 qrtview --log-file pointandscale.log
 
 but that only shows me the log-file itself, i.e. no graphs etc.  I
 understand that the program was designed primarily for ccp4 gui and I
 know loggraph (and it works).
 
 By the way, checkout instructions for the qtrview repository at
 
 https://fg.oisin.rc-harwell.ac.uk/projects/qtrview/
 
 don't work throwing this error
 
 bzr: ERROR: Connection error: curl connection error (server certificate
 verification failed. CAfile: /etc/ssl/certs/ca-certificates.crt CRLfile:
 none)
 on https://fg.oisin.rc-harwell.ac.uk/anonscm/bzr/qtrview/.bzr/smart 
 
 Cheers,
 
 Ed.
 
 -- 
 Hurry up before we all come back to our senses!
  Julian, King of Lemurs
 


-- 
Scanned by iCritical.

Re: [ccp4bb] CCP4 Update 019

[Andrey Lebedev]

Dear CCP4 Users

A CCP4 update has just been released, consisting of the following changes.

* Aimless: Task interface fixed in part of input customisation section
* Molrep: Improvements to scoring system and bug fixes
* Logview: Command-prompt routine for viewing individual log files with QtRView
Simply call it with path to the log file as the only parameter
* QtRView: Cosmetic improvements and changes for Logview
* Gesamt: Now prints superposition matrices also in fractional coordinates
* Superpose: Now prints superposition matrices also in fractional coordinates

If you do not currently receive updates, consider re-installing your
CCP4 setup using the latest binary packages, which now have the CCP4 Update 
Manager (ccp4um) integrated.

Note that auto-updates will work correctly only with CCP4 release 6.3.0, 
therefore upgrade if necessary. Please report any bugs to 
c...@stfc.ac.ukmailto:c...@stfc.ac.uk

Many thanks for using CCP4

Andrey Lebedev


-- 
Scanned by iCritical.

Re: [ccp4bb] qtrview command line options

[Andrey Lebedev]

Hi Ed

Thank you for the suggestion.
We are looking into this and hopefully will provide a solution soon.

Regards

Andrey


On 11 Mar 2013, at 14:26, Ed Pozharski wrote:

 Is there some way of opening a log file (specifically, the
 pointandscale.log that imosflm bridge to scala generates) with qtrview
 from command line?
 
 I tried, of course, this
 
 qtrview pointandscale.log
 
 but it opens empty, no log-file. I tried qtrview -h and qtrview --help
 and man qtrview but there is seemingly no documentation.
 
 I found the source code (yes, I can google) and can deduce that
 available options at startup are 
 
 --log-file
 --report-xml
 --report-xrt
 --inp-file
 
 The only thing that works is 
 
 qrtview --log-file pointandscale.log
 
 but that only shows me the log-file itself, i.e. no graphs etc.  I
 understand that the program was designed primarily for ccp4 gui and I
 know loggraph (and it works).
 
 By the way, checkout instructions for the qtrview repository at
 
 https://fg.oisin.rc-harwell.ac.uk/projects/qtrview/
 
 don't work throwing this error
 
 bzr: ERROR: Connection error: curl connection error (server certificate
 verification failed. CAfile: /etc/ssl/certs/ca-certificates.crt CRLfile:
 none)
 on https://fg.oisin.rc-harwell.ac.uk/anonscm/bzr/qtrview/.bzr/smart 
 
 Cheers,
 
 Ed.
 
 -- 
 Hurry up before we all come back to our senses!
   Julian, King of Lemurs


-- 
Scanned by iCritical.

Re: [ccp4bb] [Err] Re: [ccp4bb] statistical or systematic? bias or noise?

[Andrey Lebedev]

I've just have the same thing.
I'll write to Jin Kwang and remove him from the bb-list if he will not respond 
by tomorrow evening

Andrey

On 11 Mar 2013, at 19:27, Ed Pozharski wrote:

 By the way, am I the only one who gets this thing with every post?  If
 anyone can ask Jin Kwang (liebe...@korea.ac.kr) to either clean up his
 mailbox or unsubscribe, that would be truly appreciated.  Delete button
 is easy and fun to use, but this has been going on for quite some time.
 
 
 
 On Tue, 2013-03-12 at 04:16 +0900, spam_mas...@korea.ac.kr wrote:
 ransmit Report:
 
 liebe...@korea.ac.kr ߼; 5 õ Ͽ4ϴ.
 ( / : 554 Transaction failed. 402 Local User Inbox Full
 (liebe...@korea.ac.kr) 4,61440,370609(163.152.6.98))
 
  / 
 User unknown   :; ڰ x =
 Socket connect fail: 
 DATA write fail: ޼ ۽ 
 DATA reponse fail  : κ ޼ 
 
 
 -- 
 Bullseye!  Excellent shot, Maurice.
  Julian, King of Lemurs.

Re: [ccp4bb] [Err] Re: [ccp4bb] statistical or systematic? bias or noise?

[Andrey Lebedev]

It should stop. I'll see after sending this message.

On 11 Mar 2013, at 19:27, Ed Pozharski wrote:

 By the way, am I the only one who gets this thing with every post?  If
 anyone can ask Jin Kwang (liebe...@korea.ac.kr) to either clean up his
 mailbox or unsubscribe, that would be truly appreciated.  Delete button
 is easy and fun to use, but this has been going on for quite some time.
 
 
 
 On Tue, 2013-03-12 at 04:16 +0900, spam_mas...@korea.ac.kr wrote:
 ransmit Report:
 
 liebe...@korea.ac.kr ߼; 5 õ Ͽ4ϴ.
 ( / : 554 Transaction failed. 402 Local User Inbox Full
 (liebe...@korea.ac.kr) 4,61440,370609(163.152.6.98))
 
  / 
 User unknown   :; ڰ x =
 Socket connect fail: 
 DATA write fail: ޼ ۽ 
 DATA reponse fail  : κ ޼ 
 
 
 -- 
 Bullseye!  Excellent shot, Maurice.
  Julian, King of Lemurs.

[ccp4bb] CCP4 Update 017

[Andrey Lebedev]

Dear CCP4 Users

A CCP4 update has just been released, consisting of the following changes.

* Geomcalc: io bug fixing in residue numbering
* Pisa: fixes for handling back slashes on windows
* Aimless: fixes in Define Run section of the aimless task interface
* Ample/MrBUMP: now runs shelxd_mp in mp mode

If you do not currently receive updates, consider re-installing your
CCP4 setup using the latest binary packages, which now have the CCP4 Update 
Manager (ccp4um) integrated.

Note that auto-updates will work correctly only with CCP4 release 6.3.0, 
therefore upgrade if necessary. Please report any bugs to 
c...@stfc.ac.ukmailto:c...@stfc.ac.uk

Many thanks for using CCP4

Andrey Lebedev


-- 
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[ccp4bb] CCP4 Update 014

[Andrey Lebedev]

Dear CCP4 Users

A CCP4 update has just been released, consisting of the following changes.

All systems:

 *   Ctruncate: Introduced DNA/RNA reference curve; uses flat prior on request, 
or when have tNCS or twinning
 *   Othercell: Various bug fixes
 *   PISA, QtPISA: Stability fixes and generation of Remark 350 in no-complex 
situations
 *   PDBCur: Finish gracefully, rather than terminate, when atom selection is 
empty
 *   PDB_Merge: Various bug fixes
 *   Xia2: Correction to Ctruncate wrapper

Linux and Mac only: *)

 *   Aimless: Various bug fixes
 *   Pointless: Correction for XDS input
 *   Scala: Corrected output for CC(1/2)

 *)  Corresponding changes for Windows have been already included in update No 
13

Windows only:

 *   Phaser.ensembler: Corrected path to syminfo.lib


If you do not currently receive updates, consider re-installing your CCP4 setup 
using the latest binary packages, which now have CCP4 Update manager (ccp4um) 
integrated.

Note that auto-updates will work correctly only with CCP4 release 6.3.0, 
therefore upgrade if necessary. Please report any bugs to 
c...@stfc.ac.ukmailto:c...@stfc.ac.uk


Many thanks for using CCP4.

Andrey Lebedev


-- 
Scanned by iCritical.

[ccp4bb] CCP4 6.3.0 update 011

[Andrey Lebedev]

Dear CCP4 Users,

A CCP4 update has just been released, consisting of the following changes:

* Aimless: Improvements to the CCP4i interface to Aimless
* MrBUMP: Some changes to the output for compatibility with QtRView
* Xia2: Updated to version 0.3.5.0
* Areaimol: Fix for already allocated array problem
* CCP4 update: Modifications required for integration in the next CCP4 Release

Specific changes for Windows platforms include:

* Sortmtz: Fixes making big data sets treatable
* CCP4 update: Fixes related to system security

The easiest way to obtain the update is to install the CCP4 update client, if 
you have not done so already. Details on how to install the CCP4 Update Manager 
are available from:

http://www.ccp4.ac.uk/download/update_manual.html

Note that auto-updates will work correctly only with CCP4 release 6.3.0, 
therefore upgrade if necessary. Please report any bugs to 
c...@stfc.ac.ukmailto:c...@stfc.ac.uk.

Many thanks for using CCP4,

Andrey Lebedev


-- 
Scanned by iCritical.

[ccp4bb] CCP4 update 6.3.0 008

[Andrey Lebedev]

Dear CCP4 Users,

A CCP4 update has just been released, consisting of the following changes:

*  Arp/Warp: fixes problem with overwriting modules.def file by other 
updates; enables Arp/Warp tasks in ccp4i (OS X and Linux)
*  Phaser: added DLL files missing in the previous update (Windows)
*  Pointless: fixed option Choose solution ... by Space group name for 
non-standard settings, e.g. P21 2 21 (all platforms)
*  Zanuda: fixed problem with MSE atoms defined as HETATM in pdb-files (all 
platforms)

The easiest way to obtain the update is to install the CCP4 update 
clienthttp://www.ccp4.ac.uk/download/update_manual.html, if you have not done 
so already. Note that autoupdates will work correctly only with CCP4 release 
6.3.0, therefore upgrade if necessary. Report bugs to 
c...@stfc.ac.ukmailto:c...@stfc.ac.uk.

Many thanks for using CCP4,

Andrey Lebedev


-- 
Scanned by iCritical.

Re: [ccp4bb] P4132 vs. F23

[Andrey Lebedev]

Hi Mike.

I would be more careful about incorrect space group. Yes, sometimes 
auto-indexing gives strange results.
However, in your case two sets of crystals differ by two factors, diffraction 
quality and space group.
Therefore it seems more likely that you have two crystal forms.
Could you please send me log-files from pointless or ctruncate? Then I would be 
able to say something more definite.

Regards

Andrey

On 28 May 2012, at 08:46, Mike John wrote:

Hi, All,

we got many datasets from crystals of our protein. when the crystal has high 
quality, it will be indexed as F23 (correct space group). While diffracting 
poorer, it will be indexed as incorrect space group  P4132. The crystals are 
twined. My question is:
Given twinning, why the correct space group F23 will be indexed as an incorrect 
space group P4132 for most of our crystals (most crystals has poorer quality)? 
Theoretical analysis of twin operator and symmetry operator to connect F23 and 
P4132 would be highly appreciated. Thanks

Mike

Re: [ccp4bb] copy FreeR - maintain resolution

[Andrey Lebedev]

Hi Tim

I did not try it myself but it seems to be what you need:
- import free-R flag from higher-resolution mtz as usual
- remove reflections with missing FP:
sftools (READ .mtz; SELECT ONLY COLUMN FP PRESENT; WRITE yyy.mtz)

Andrey


On 12 Apr 2012, at 10:00, Tim Gruene wrote:

 -BEGIN PGP SIGNED MESSAGE-
 Hash: SHA1
 
 Dear all,
 
 I would like to copy the freeR-flags from B.mtz to A.mtz. B.mtz has
 higher resolution.
 
 As far as I can tell the ccp4 utilities for doing so extend the
 resolution from A to match the resolution of B which results in mtzdmp
 displaying the wrong resolution of the data which I find very annoying.
 
 Is there a tool or switch to freerflag which only tags those
 reflections which are actually present in A?
 
 I am aware of the 'resolution' keyword in most of those programs but
 this is not what I want, because it might still alter the reflection list.
 
 Cheers,
 Tim
 
 - -- 
 - --
 Dr Tim Gruene
 Institut fuer anorganische Chemie
 Tammannstr. 4
 D-37077 Goettingen
 
 GPG Key ID = A46BEE1A
 
 -BEGIN PGP SIGNATURE-
 Version: GnuPG v1.4.12 (GNU/Linux)
 Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
 
 iD8DBQFPhpmzUxlJ7aRr7hoRAqxFAKCtWQyPxjoh/YeNQOU/vPnwJDdTcQCeJp5R
 krRZlS1cYIwlUOOfqKH2pvw=
 =FJYt
 -END PGP SIGNATURE-

Re: [ccp4bb] How to make covalent bond in COOT

[Andrey Lebedev]

On 7 Dec 2011, at 10:08, Paul Emsley wrote:

 On 07/12/11 09:47, Tim Gruene wrote:
 
 if you want coot to refine the bond length, you have to rename the
 residue to some name coot does not yet understand and create a cif-file
 which includes the restraints of the residue, the ligand, and the bond
 between the two.
 
 JLigand is the way to do this.
 
 (the interface to JLigand will be in Coot 0.7).
 
 Paul

It will be also possible to launch JLigand from CCP4 GUI starting from 
ccp4.6.3.0.

Currently JLigand and tutorials can be downloaded from here:
http://www.ysbl.york.ac.uk/mxstat/JLigand/index.html
or from here:
ftp://ftp.ccp4.ac.uk/JLigand/index.html
  
Andrey

Re: [ccp4bb] ccp4 on Win7 'clipper::Message_fatal'

[Andrey Lebedev]

Yes, you are right, both -hklin and -mtzin are valid option keys.

I have reproduced your error message.
The problem is in the command line option -colout yap-ii-77-73.

Now I must check what happens on Linux.
Meanwhile a quick fix for you: use no more than 10 characters in the box
Modifier to append to column labels.

Does this recipe work for you?

Andrey

On 6 Dec 2011, at 14:51, Yuri wrote:

 The thing is, I did not run any command myself. I was using the GUI. So the 
 command was written for me.
 Thats why I thought it was really odd that this may be a wrong command.
 Obviuosly the GUI for RedHat works.
 
 Best,
 
 
 On Tue, 6 Dec 2011 13:14:36 +, andrey.lebe...@stfc.ac.uk wrote:
 Hi Yuri
 
 Perhaps you have used incorrect command line keys.
 
 I have installed ccp4 using Marcins script on my Windows 7 Virtual Box.
 Then I used ccp4i to run ctruncate with my test case.
 Run  Run  View Com File showed the following command:
 ctruncate -mtzin
 C:/Users/andrey/Desktop/HemH_tutorial/test_scala1.mtz -mtzout
 C:/Ccp4Temp/HemH_4_1_mtz.tmp -colin /*/*/\[IMEAN,SIGIMEAN\]
 -colano /*/*/\[I(+),SIGI(+),I(-),SIGI(-)\]
 
 This is different from yours (-mtzin, not -hklin):
 ctruncate -hklin C:/Ccp4Temp/oye1_77-73_3_1_mtz.tmp -hklout 
 C:/Ccp4Temp/oye1_77-73_3_3_mtz.tmp -colin /*/*/\[IMEAN,SIGIMEAN\] 
 -colano /*/*/\[I(+),SIGI(+),I(-),SIGI(-)\] -colout yap-ii-77-73 -nres 400
 
 
 
 Please try using ccp4i or try -mtzin instead of -hklin.
 Does it work?
 
 Andrey
 
 On 6 Dec 2011, at 01:24, Yuri Pompeu wrote:
 
 Dear Developers,
 I was trying to get ccp4 up and running on a Windows7 pc, and even though 
 the installation proceeds smoothly,
 I cant get any task to finish succesfully.
 Below is what the log file has to say about it.
 I saw someone having trouble with the windows install as well. I have the 
 installation packaged posted by Marcin installed.
 Thanks for any help
 
 * Information from CCP4Interface script
 ***
 The program run with command: ctruncate -hklin 
 C:/Ccp4Temp/oye1_77-73_3_1_mtz.tmp -hklout 
 C:/Ccp4Temp/oye1_77-73_3_3_mtz.tmp -colin /*/*/\[IMEAN,SIGIMEAN\] 
 -colano /*/*/\[I(+),SIGI(+),I(-),SIGI(-)\] -colout yap-ii-77-73 -nres 400
 has failed with error message
 CCP4MTZfile - internal error
 
 This application has requested the Runtime to terminate it in an unusual 
 way.
 Please contact the application's support team for more information.
 terminate called after throwing an instance of 'clipper::Message_fatal'
 ***
 
 
 #CCP4I TERMINATION STATUS 0 CCP4MTZfile - internal error  This application 
 has requested the Runtime to terminate it in an unusual way. Please contact 
 the application's support team for more information. terminate called after 
 throwing an instance of 'clipper::Message_fatal'
 #CCP4I TERMINATION TIME 05 Dec 2011  20:19:00
 #CCP4I MESSAGE Task failed
 
 -- 
 Yuri Pompeu

Re: [ccp4bb] Ligand Protein Connection

[Andrey Lebedev]

Hi Sam

Except for torsion angles, here is a good tutorial for you (the second one)

http://www.ysbl.york.ac.uk/mxstat/JLigand/

Andrey

On 29 Sep 2011, at 22:12, Sam Arnosti wrote:

 Hi every one
 
 I have a problem with docking my ligand into the electron density map and 
 make the connections ( bonds ) with the protein.
 
 It is a Lysine residue that makes a Schiff Base with a long chain aldehyde.
 
 I do not know how to make the bonds and control the torsion angles of the 
 ligand.
 
 I am using the CCP4 and Coot program for refining.
 
 Thanks
 
 Sam

Re: [ccp4bb] **Possible spam**[ccp4bb] Superpose, SSM

[Andrey Lebedev]

Hi Matthias

Thank you for your report.
This is a genuine bug, lsqkab puts \015\015\012 in the end of line instead of 
\015\012
We will try to fix it.

Andrey

On 26 Sep 2011, at 20:42, Matthias Zebisch wrote:

 Dear CCP4 users,
 
 I am using the ccp4i version 6.2.0 under windows 7. I've come across a 
 problem with superpose.
 The outputfile appears to have additional line feeds (see picture) which, 
 however are not seen in the windows notepad.
 The structure can also be opened in coot and pymol. However, it is not 
 possible to use it within CCP4, eg. for a subsequent superposition.
 
 Is this problem known to anybody and is there a simple workaround available? 
 I need to compare hell of a lot of relative domain orientations...
 
 I did not have this problem on a second computer with ccp4 6.1.2. When I 
 updated to 6.2.0, the situation was as described above.
 
 Any help will be highly appreciated,
 
 Thanks, Matthias
 superpose.png

Re: [ccp4bb] Automatic LINK generation

[Andrey Lebedev]

Dear Hailiang

There are several protein-sugar and sugar-sugar link defined in the standard 
refmac library.

You may try running refmac with the default options with the input pdb file in 
which
- sugar residues included,
- no LINK record are specified.

If all required links are in the refmac's library, the refinement will work,
and the output PDB will contain the LINK records, e.g.
...
LINKC1   NAG A1539ND2  ASN A 341NAG-ASN
LINK NAG A1539 NAG A1540BETA1-4
MODRES  NAG A 1539  NAG-b-D RENAME
MODRES  NAG A 1540  NAG-b-D RENAME
...

In the log file you will see:
...
  WARNING : link: NAG--NAG is without link_id
link will be created with covalent bond only. Bond= 1.430
...
  WARNING : link:NAG-ASN  is found dist = 1.427 ideal_dist= 1.439
ch:AA   res: 341  ASN  at:ND2 .-Aj   res:1539  NAG  at:C1  
.

  WARNING : link:BETA1-4  is found dist = 1.430 ideal_dist= 1.439
ch:Aj   res:1539  NAG  at:O4  .-Ak   res:1540  NAG  at:C1  
.
...
The last two warnings actually mean that everything is fine.
Ignore the first warning, as it is overridden by the third one.

All the best
Andrey