2011-09-30: Minor modifications
[SHIFTX2 v1.04 (Release 30 SEP 2011)]
* SHIFTX2 can be executed from any directory. For example,
$ python /user/home/shiftx2-v104/shiftx2.py -i input.pdb
* Increased the array size for the limitation of atom numbers
to support a PDB which has a lot of atoms, with insertion codes, for a residue.
* Fix the bug that cause an memory error in angle calculation module
2011-09-16: SHIFTX2 version 1.04 is released.
[What's New in SHIFTX2 v1.04]
Functional extensions:
* SHIFTX2 now supports multi-chain prediction as a single chain
(with the -u option)
* SHIFTX2 now accepts input file of any name and extension.
If the input file name is 'input.structure.file.pdb',
the output file name is 'input.structure.file.pdb.cs'.
Other minor modifications:
* File name changes:
- shiftx2_main.py is renamed to shiftx2.py and should be called as:
$ python shiftx2.py -i 1UBQ.pdb [options]
- SHIFTX+'s output file input.sxp is renamed to input.pdb.sxp.
(assuming the input file is 'input.pdb')
* Intermediate output files are now hidden by default. Use the '-e' or '--explicit'
option to reveal such intermediate result files as SHIFTX+ (input.pdb.sxp)
and SHIFTY+ output (input.pdb.shifty) files.
* Wildcard in Batch mode (-b option).
Batch mode has been updated to support wildcard of input file names.
For example,
$ python shiftx2.py -b 'A*.pdb'
(matches all file starts with A and ends with .pdb)
$ python shiftx2.py -b '/user/home/pdbdir/*'
(matches all files in folder /user/home/pdbidr/)
Please note the quotation mark is essential and cannot be omitted;
SHIFTX2 basically takes a regular expression for matching input file names.
* For CSV output format, column header is appended.
Bug fixes:
* Fixed the bug that causes Inconsistent residue numbers due to missing residues
in input file.
* Fixed the bug that causes reversing ordered insertion codes in input files.
Only the first insertion case will be calculated.
* Fixed a few bugs in the SHIFTY+ modules and updated reference database.
* Fixed the bug for warning messages in the java compiling process.
* Fixed the bug that causes errors in the selection of atoms with options
'ALL/BACKBONE/SIDECHAIN'
|
| 2011-05-06: SHIFTX2 version 1.03 is released. This version supports PDB files with NMR model ensembles. |
| 2011-03-25: SHIFTX2 version 1.02 is released. The homolog database is updated in this version. |
| 2011-01-21: SHIFTX2 version 1.01 is released. Side selection and batch processing mode is now available. |
| 2010-08-24: SHIFTX2 is released and available as both web servers and standalone versions |
|
