[ccp4bb] CCP4-6.4.0 Update 001

. 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

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

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

(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

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

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

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

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

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

); 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

[ccp4bb] CCP4-6.4.0 Update 006

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

[ccp4bb] CCP4-6.4.0 Update 007

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

Re: [ccp4bb] CCP4-6.4.0 Update 010

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

[ccp4bb] CCP4-6.4.0 Update 017

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

[ccp4bb] CCP4-6.4.0 Update 018

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

Re: [ccp4bb] copy FreeR - maintain resolution

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:

Re: [ccp4bb] P4132 vs. F23

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

[ccp4bb] CCP4 update 6.3.0 008

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

[ccp4bb] CCP4 6.3.0 update 011

to c...@stfc.ac.ukmailto:c...@stfc.ac.uk. Many thanks for using CCP4, Andrey Lebedev -- Scanned by iCritical.

[ccp4bb] CCP4 Update 014

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

[ccp4bb] CCP4 Update 017

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

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

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

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

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

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

Re: [ccp4bb] CCP4 Update 019

...@stfc.ac.ukmailto:c...@stfc.ac.uk Many thanks for using CCP4 Andrey Lebedev -- Scanned by iCritical.

Re: [ccp4bb] qtrview command line options

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

Re: [ccp4bb] CCP4 Update 019

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.

[ccp4bb] CCP4 Update 021

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

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

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

Re: [ccp4bb] Automatic LINK generation

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

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

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

Re: [ccp4bb] Ligand Protein Connection

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 (

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

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

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

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

[ccp4bb] CCP4-6.4.0 Update 020

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

Re: [ccp4bb] Latest BALBES database

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,

[ccp4bb] CCP4-6.5 Update 001

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

Re: [ccp4bb] distorted NRQ in JLigand 1.0.40

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

[ccp4bb] Morda updates moved

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

[ccp4bb] ccp4 7.0 update 044

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 *

Re: [ccp4bb] CCP4 series 7.0 update 045

, 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 > > > up

[ccp4bb] CCP4 series 7.0 update 045

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

[ccp4bb] ccp4-7.0 for windows

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

[ccp4bb] CCP4i2 on Windows: issue with update 52

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

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

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] Issue with CCP4 update 053

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

[ccp4bb] Fedora 29 breaks CCP4

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

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

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.

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

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;

[ccp4bb] CCP4 on MacOS Catalina

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.

Re: [ccp4bb] Twin law definition in REFMAC5

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