[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.





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

[Eugene Krissinel]

Dear CCP4 Users,

CCP4 Core Team would like to apologise for temporary withdrawal of update 
6.4.0-002, announced earlier this week. The withdrawal is due to a technical 
fault in the update mechanism, which will be rectified soon. Currently, the 
update is put on hold and is not visible for client installations.

A few users reported problems with starting ccp4i immediately after 
installation of the update. Should you have experienced the same, please start 
ccp4um from terminal:

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

and uninstall update 6.4.0-002 by unchecking the corresponding box and pressing 
"Apply" (use 'sudo' *only* if your ccp4 is installed in write-protected area). 
After that, everything should be back normal.

Windows users, as well as those who are able to run ccp4i after 2nd update, 
need do nothing.

I would like to acknowledge prompt bug reports from responsible users on this 
occasion, which helped us to minimise the negative effect of the bug on all 
others. CCP4 as a project depends on the feedback from user community, and Core 
Team is grateful for all the help and feedback we receive.

Please refrain from update attempts until further announcement or until new 
updates are reported available by your ccp4i.

Many thanks,

Eugene Krissinel



Begin forwarded message:

From: Andrey Lebedev 
mailto:andrey.lebe...@stfc.ac.uk>>
Date: 6 November 2013 12:52:31 GMT
To: mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: [ccp4bb] Joint CCP4-6.4.0 and ARP/wARP-7.4 Update
Reply-To: mailto: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.org<http://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.



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

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Andrey,

since you mention the manual: is there a way to retrieve the manual
pages for the ccp4 programs? I often use 'man pointless' et al. to
check syntax etc and I miss the man pages in 6.4.0. Even the source
does not seem to contain them any more.

Best,
Tim

On 11/06/2013 01:52 PM, Andrey Lebedev wrote:
> 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.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
> 
> 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

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Comment: Using GnuPG with Icedove - http://www.enigmail.net/

iD8DBQFSeloAUxlJ7aRr7hoRAkmxAKCU6dqpZAjaUH0nWYnlsmAuaZ392QCeP74S
ir8+bKdHF+t2eaPUfCAolnU=
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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 /ccp4-6.4.0/bin/ccp4um
> where  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 :
>> 
>>> 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.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
> 


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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 /ccp4-6.4.0/bin/ccp4um
where  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 :
> 
>> 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.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]

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 :
> 
>> 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.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

[Joachim Reichelt]

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 :

> 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.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

[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.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


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