ccp4/CHANGES - diff - 1.200.2.17

Return to CHANGES CVS log

Up to [CCP4] / ccp4

Diff for /ccp4/CHANGES between version 1.200 and 1.200.2.17

version 1.200, 2008/08/08 12:44:27

version 1.200.2.17, 2009/10/13 15:24:07

Line 1

-*- mode: indented-text; fill-column: 78;-*-

Summary of significant changes to CCP4 at version 6.1.3 ("No name")

---------------------------------------------------------------------------

* Building etc.:

* gnu compiler 4.4 compliant

* supports Snow Leopard

* Program changes:

* IPMOSFLM: updated to 7.0.5

* REFMAC: updated to 5.5.0106

* MOLREP: updated to 10.2.33

* SFCHECK: updated to 7.3.14

* CTRUNCATE: updated to 1.0.06

* Library changes:

* MMDB: update to 1.21

* Graphical User Interface:

* IMOSFLM: updated to 1.03

* Bugs fixed:

* Known issues:

* 3488: IMOSFLM: cannot launch batch jobs from interface

* 3630: SCALEPACK2MTZ: does not read symmetry from input file

* 3894: DBhandles not python 3.0 compliant

Summary of significant changes to CCP4 at version 6.1.2 ("Ingleborough")

---------------------------------------------------------------------------

* Building etc.:

* ccp4.setup-dist renamed ccp4.setup-csh

* ccp4i, crank, imosflm launchers copied to bin directory during

installation

* csh no longer used during installation, all steps use sh

* Program changes:

* POINTLESS: updated to 1.3.9

* SCALA: updated to 3.3.15

* REFMAC5: updated to 5.5.0098. PHOUT added for building of MR solutions

with BUCCANEER

* MOLREP: updated to 10.2.31

* SFCHECK: updated to 7.3.13

* SIGMAA: new version from Ian Tickle

* OASIS: minor update

* Graphical User Interface:

* CRUNCH2: new interface for experimental phasing program

* CRANK: update to 1.3

* database back end off by default

* Bugs fixed:

* 3596: IMOSFLM: requires project directory to exist, fails otherwise

* 3689: POINTLESS loop variable overflow

* 3690: REFMAC5 interface not backwardly compatible

* 3713: REFMAC5 interface amplitude based twin refinement

* 3722: CTRUNCATE in import scaled task

* 3790: MOLREP multi-copy search failure

* 3797: all_load shared library builds under newer linux ld

* 3816: TLSANL anisotropic Us

* various uninitialised variables caught

* Known issues:

* 3488: IMOSFLM: cannot launch batch jobs from interface

* 3630: SCALEPACK2MTZ: does not read symmetry from input file

* 3894: DBhandles not python 3.0 compliant

Summary of significant changes to CCP4 at version 6.1.1 ("The New Inn")

---------------------------------------------------------------------------

* Building etc.:

* intel 11: mostly supported

* Program changes:

* PDB_EXTRACT: updated to 3.004

* REFMAC5: updated to 5.5.0072

* POINTLESS: updated to 1.3.1

* MOLREP: updated to 10.2.23

* SFCHECK: updated to 7.3.10

* CHAINSAW: accepts fasta alignment files

* Library changes:

* MMDB: update to 1.19

* monomer dictionaries: various updates, including CYS-MPR

* Updated interfaces:

* REFMAC5: better integration of SAD refinement

* BP3: interface added

* TRUNCATE: CTRUNCATE options added

* DTREK2MTZ: CTRUNCATE now the default for intensity to SF conversion

* SCALEPACK2MTZ: CTRUNCATE now the default for intensity to SF conversion

* Bugs fixed:

* 3628: ccp4i import task

* 3592: SFTOOLS interface

* 3619: REFMAC5 interface ignoring external file

* 3655: CHAINSAW not deleting CISPEP records from PDB

* 3656: PISA writing to $CCP4/share/pisa directory

* 3558: CAD segv

* Known issues:

* 3488: IMOSFLM: cannot launch batch jobs from interface

* 3596: IMOSFLM: requires project directory to exist, fails otherwise

* 3630: SCALEPACK2MTZ: does not read symmetry from input file

Summary of significant changes to CCP4 at version 6.1 ("Holy Trinity Church")

---------------------------------------------------------------------------

Line 20

Line 125

area calculations - see the program documentation (Ian Tickle).

* CAVENV: program now uses symmetry mates of input molecule unless

SYMM OFF set. Gives protein and solvent volumes within map limits.

* CRANK: updated to version 1.20. Greatly enhanced (Raj Pannu)

* CRANK: updated to version 1.2.0. Greatly enhanced (Raj Pannu)

* IMOSFLM: update imosflm to 0.6.1

* IMOSFLM: update imosflm to 1.0.0

* LOGGRAPH: is now able to give a basic view of the XMGR-style

normplot and correlplot output from SCALA, for systems where xmgr(ace)

is unavailable.

* MOLREP: updated to version 10.2.6.

* MOLREP: updated to version 10.2.12.

* MOSFLM: updated to version 7.0.4.

* OASIS: updated to OASIS-2006.

* PDBCUR: new option to delete ANISOU records.

Line 33

Line 138

* PDBSET: estimated molecular weight based on the sequence of residues

is automatically calculated when the SEQUENCE keyword is specified.

* PHASER: updated to 2.1.4. This version covers MR, SAD and combined MR and SAD.

* REFMAC5: updated to version 5.5.0044. This adds twinned and anomalous

* REFMAC5: updated to version 5.5.0066. This adds twinned and anomalous

refinement (Garib Murshudov, Raj Pannu, Pavol Skubak).

* SCALA: updated to version 3.3.6

* SCALA: updated to version 3.3.9

* SFCHECK: updated to version 7.3.1.

* SFCHECK: updated to version 7.3.7.

* Library changes:

* Addition of a new library "Diffraction Image" which also comes with 4 small

* Addition of a new "Diffraction Image" library which also comes with 4 small

jiffies installed in bin - diffdump, printpeaks, automask diff2jpeg.

jiffies installed in bin - diffdump, printpeaks, automask and diff2jpeg.

* Monomer dictionary updated to 4.13

* New programs:

Line 49

Line 154

* BAUBLES/SMARTIE: new program for re-rendering CCP4 log files with

HTML markup (Peter Briggs & Kevin Cowtan).

* BALBES: automated molecular replacement (Fei Long, Garib Murshudov,

Alexei Vaguin).

Alexei Vagin).

* cBUCCANEER: statistical model building, optimised for experimental

phasing. (Kevin Cowtan)

* CRUNCH2: direct mothod experimental phasing as part of CRANK (Jan

Line 58

Line 163

checking data quality (Norman Stein).

* DBCCP4I: new database server for CCP4i, which includes a graphical

viewer for CCP4i projects plus other tools. (Wanjuan Yang & Peter Briggs)

* IMOSFLM: imported imosflm 0.5.3

* IMOSFLM: imported imosflm 1.0.0

* MrBUMP: Automated molecular replacement, search model retrieval and

search model preparation for molecular replacement.

* MTZ2CIF: new program for generating mmCIF reflection files suitable

for deposition, intended to replace OUTPUT CIF option of MTZ2VARIOUS.

See program documentation for more information. (Peter Briggs)

* PARROT: automatic density modification and phase improvement (Kevin Cowtan)

* PISA: the standalone version of the Protein Interfaces, Surfaces and

Assemblies server. (Eugene Krissinel) -- optional

* POINTLESS: Laue and Patterson group determination, v1.2.21. (Phil Evans)

* POINTLESS: Laue and Patterson group determination, v1.2.23. (Phil Evans)

-- optional

* R500: new program for correcting REMARK 500 lines in PDB files.

* RAPPER: conformer modelling through sampling residue rotameric states.

Line 113

Line 219

* MOSFLM-in-batch: now recognises keywords SYNCHROTRON POLARISATION,

DISPERSION and DIVERGENCE (used for data collected at a synchrotron)

and POSTREFinement keywords WIDTH, MOSADD and MOSSMOOTH.

* PARROT: new interface for the PARROT program.

* PISA webservice: the EBI Protein Interfaces Surfaces and Assemblies

webservice can be launched from the "Structure Analysis" and "Program

List" modules

Line 165

Line 272

XDLMAPMAN, XDLDATAMAN, IPDISP (replaced by idiffdisp)

* Examples:

* phaser_EP.exam: new example for Phaser 2.1.1, using a sulfur-SAD

* phaser_EP.exam: new example for Phaser 2.1.4, using a sulfur-SAD

dataset for bovine cubic insulin.

* pointless.exam: new examples for pointless

* rampage.exam: new example for rampage mode of rapper

* refmac_sad: new example for refmac SAD target function

* acorn: new example running from 1 Zn atom (Deuterolysin)

Summary of significant changes to CCP4 at version 6.0

-----------------------------------------------------------

Legend:

Removed from v.1.200
changed lines
	Added in v.1.200.2.17

ccp4@ccp4.ac.uk